diff --git a/build.yaml b/build.yaml index cf1938b499d..96f7f551b64 100644 --- a/build.yaml +++ b/build.yaml @@ -735,7 +735,7 @@ steps: # This was likely from running mill in server mode; mill main exits before # the jar has finished being written. time retry make shadowJar - if [ ! -f out/assembly.dest/out.jar ]; then + if [ ! -f out/hail/assembly.dest/out.jar ]; then echo 'no out.jar found after mill assembly returned. going to sleep' sleep 5 fi @@ -774,7 +774,7 @@ steps: # See `build_hail_jar_and_wheel` time retry make shadowJar - if [ ! -f out/assembly.dest/out.jar ]; then + if [ ! -f out/hail/assembly.dest/out.jar ]; then echo 'no out.jar found after mill assembly returned. going to sleep' sleep 5 fi @@ -807,7 +807,7 @@ steps: # See `build_hail_jar_and_wheel` time retry make shadowTestJar - if [ ! -f out/test/assembly.dest/out.jar ]; then + if [ ! -f out/hail/test/assembly.dest/out.jar ]; then echo 'no out.jar found after mill assembly returned. going to sleep' sleep 5 fi @@ -832,7 +832,7 @@ steps: cd /io/repo/hail time tar czf test.tar.gz -C python test pytest.ini - time tar czf resources.tar.gz -C src/test resources + time tar czf resources.tar.gz -C hail/test resources time tar czf data.tar.gz -C python/hail/docs data time TESTNG_SPLITS=5 python3 generate_splits.py time tar czf splits.tar.gz testng-splits-*.xml @@ -867,7 +867,7 @@ steps: # See `build_hail_jar_and_wheel` time retry make shadowJar - if [ ! -f out/assembly.dest/out.jar ]; then + if [ ! -f out/hail/assembly.dest/out.jar ]; then echo 'no out.jar found after mill assembly returned. going to sleep' sleep 5 fi @@ -965,7 +965,7 @@ steps: export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json python3 -m hailtop.aiotools.copy 'null' '[ - {"from": "src/test/resources", + {"from": "hail/test/resources", "to": "{{ global.test_storage_uri }}/{{ token }}/test/resources"}, {"from": "python/hail/docs/data", "to": "{{ global.test_storage_uri }}/{{ token }}/doctest/data"} @@ -976,8 +976,8 @@ steps: valueFrom: default_ns.name mountPath: /test-gsa-key inputs: - - from: /repo/hail/src/test/resources - to: /io/repo/hail/src/test/resources + - from: /repo/hail/hail/test/resources + to: /io/repo/hail/hail/test/resources - from: /repo/hail/python/hail/docs/data to: /io/repo/hail/python/hail/docs/data dependsOn: @@ -996,15 +996,15 @@ steps: script: | set -ex cd /io - mkdir -p src/test - tar xzf resources.tar.gz -C src/test + mkdir -p hail/test + tar xzf resources.tar.gz -C hail/test tar xzf splits.tar.gz export HAIL_TEST_SKIP_R=1 java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-$HAIL_RUN_IMAGE_SPLIT_INDEX.xml inputs: - from: /resources.tar.gz to: /io/resources.tar.gz - - from: /derived/debug/hail/out/test/assembly.dest/out.jar + - from: /derived/debug/hail/out/hail/test/assembly.dest/out.jar to: /io/hail-test.jar - from: /splits.tar.gz to: /io/splits.tar.gz @@ -2444,7 +2444,7 @@ steps: valueFrom: default_ns.name mountPath: /batch-gsa-key inputs: - - from: /derived/release/hail/out/assembly.dest/out.jar + - from: /derived/release/hail/out/hail/assembly.dest/out.jar to: /io/hail.jar - from: /git_version to: /io/git_version @@ -3387,7 +3387,7 @@ steps: # #14452 - must build wheel with release `hailtop/hailctl/deploy.yaml` # use `-o` to prevent `mill` from rebuilding the "SHADOW_JAR" make upload-artifacts HAIL_RELEASE_MODE=1 DEPLOY_REMOTE=origin \ - -o out/assembly.dest/out.jar + -o out/hail/assembly.dest/out.jar echo Setting arguments and invoking release.sh. @@ -3416,8 +3416,8 @@ steps: to: /io/git_version - from: /repo to: /io/repo - - from: /derived/release/hail/out/assembly.dest/out.jar - to: /io/repo/hail/out/assembly.dest/out.jar + - from: /derived/release/hail/out/hail/assembly.dest/out.jar + to: /io/repo/hail/out/hail/assembly.dest/out.jar - from: /azure-wheel to: /io/azure-wheel - from: /www.tar.gz @@ -3664,7 +3664,7 @@ steps: inputs: - from: /resources.tar.gz to: /io/resources.tar.gz - - from: /derived/debug/hail/out/test/assembly.dest/out.jar + - from: /derived/debug/hail/out/hail/test/assembly.dest/out.jar to: /io/hail-test.jar - from: /repo/hail/testng-fs.xml to: /io/testng-fs.xml @@ -3706,7 +3706,7 @@ steps: inputs: - from: /resources.tar.gz to: /io/resources.tar.gz - - from: /derived/debug/hail/out/test/assembly.dest/out.jar + - from: /derived/debug/hail/out/hail/test/assembly.dest/out.jar to: /io/hail-test.jar - from: /repo/hail/testng-services.xml to: /io/testng-services.xml diff --git a/hail/Makefile b/hail/Makefile index fa06d1eec31..8308b9243eb 100644 --- a/hail/Makefile +++ b/hail/Makefile @@ -62,50 +62,50 @@ mill-clean: # be recomputed. FORCE: -SHADOW_JAR := out/assembly.dest/out.jar +SHADOW_JAR := out/hail/assembly.dest/out.jar ifdef HAIL_COMPILE_NATIVES $(SHADOW_JAR): native-lib-prebuilt endif $(SHADOW_JAR): FORCE - $(MILL) $(MILLOPTS) assembly + $(MILL) $(MILLOPTS) hail.assembly .PHONY: shadowJar shadowJar: $(SHADOW_JAR) -NON_SHADOW_JAR := out/jar.dest/out.jar +NON_SHADOW_JAR := out/hail/jar.dest/out.jar ifdef HAIL_COMPILE_NATIVES $(NON_SHADOW_JAR): native-lib-prebuilt endif $(NON_SHADOW_JAR): FORCE - $(MILL) $(MILLOPTS) jar + $(MILL) $(MILLOPTS) hail.jar -SHADOW_TEST_JAR := out/test/assembly.dest/out.jar +SHADOW_TEST_JAR := out/hail/test/assembly.dest/out.jar ifdef HAIL_COMPILE_NATIVES $(SHADOW_TEST_JAR): native-lib-prebuilt endif $(SHADOW_TEST_JAR): FORCE - $(MILL) $(MILLOPTS) test.assembly + $(MILL) $(MILLOPTS) hail.test.assembly .PHONY: shadowTestJar shadowTestJar: $(SHADOW_TEST_JAR) -EXTRA_CLASSPATH := out/writeRunClasspath.dest/runClasspath +EXTRA_CLASSPATH := out/hail/writeRunClasspath.dest/runClasspath $(EXTRA_CLASSPATH): FORCE - $(MILL) $(MILLOPTS) writeRunClasspath + $(MILL) $(MILLOPTS) hail.writeRunClasspath .PHONY: jvm-test ifdef HAIL_COMPILE_NATIVES jvm-test: native-lib-prebuilt endif jvm-test: - $(MILL) $(MILLOPTS) test testng.xml + $(MILL) $(MILLOPTS) hail.test testng.xml .PHONY: services-jvm-test ifdef HAIL_COMPILE_NATIVES services-jvm-test: native-lib-prebuilt endif services-jvm-test: - $(MILL) $(MILLOPTS) test testng-services.xml + $(MILL) $(MILLOPTS) hail.test testng-services.xml .PHONY: fs-jvm-test ifdef HAIL_COMPILE_NATIVES @@ -118,7 +118,7 @@ fs-jvm-test: upload-remote-test-resources HAIL_DEFAULT_NAMESPACE=$(NAMESPACE) \ HAIL_FS_TEST_CLOUD_RESOURCES_URI=$(CLOUD_HAIL_TEST_RESOURCES_DIR)fs \ HAIL_TEST_STORAGE_URI=$(TEST_STORAGE_URI) \ - $(MILL) $(MILLOPTS) test testng-fs.xml + $(MILL) $(MILLOPTS) hail.test testng-fs.xml # end mill integration diff --git a/hail/build.mill b/hail/build.mill index 35f3e2be318..6a14da4d4b3 100644 --- a/hail/build.mill +++ b/hail/build.mill @@ -72,7 +72,35 @@ object Deps { } } -trait HailScalaModule extends SbtModule with ScalafmtModule with ScalafixModule { outer => +object env extends Module { + def scalaVersion: T[String] = Task.Input { + val v = T.ctx().env.getOrElse("SCALA_VERSION", "2.12.20") + if (!v.startsWith("2.12")) + Result.Failure("Hail currently supports only Scala 2.12") + else + v + } + + def javaVersion: T[String] = Task.Input { + System.getProperty("java.version") + } + + def sparkVersion: T[String] = Task.Input { + Result.Success(T.ctx().env.getOrElse("SPARK_VERSION", "3.5.0")) + } + + def debugMode: T[Boolean] = Task.Input { + val isDebug = !T.ctx().env.contains("HAIL_RELEASE_MODE") + T.log.info(s"Building in ${if (isDebug) "debug" else "release"} mode") + isDebug + } + + def debugOrRelease: Task[String] = Task.Anon { + if (debugMode()) "debug" else "release" + } +} + +trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { outer => override def scalaVersion: T[String] = build.env.scalaVersion() override def javacOptions: T[Seq[String]] = Seq( @@ -106,7 +134,7 @@ trait HailScalaModule extends SbtModule with ScalafmtModule with ScalafixModule override def bspCompileClasspath: T[Agg[UnresolvedPath]] = super.bspCompileClasspath() ++ resources().map(p => UnresolvedPath.ResolvedPath(p.path)) - trait HailTests extends SbtTests with TestNg with ScalafmtModule with ScalafixModule { + trait HailTests extends ScalaTests with TestNg with ScalafmtModule with ScalafixModule { override def forkArgs: T[Seq[String]] = Seq("-Xss4m", "-Xmx4096M") override def ivyDeps: T[Agg[Dep]] = @@ -124,35 +152,7 @@ trait HailScalaModule extends SbtModule with ScalafmtModule with ScalafixModule } } -object `package` extends RootModule with HailScalaModule { outer => - - object env extends Module { - def scalaVersion: T[String] = Task.Input { - val v = T.ctx().env.getOrElse("SCALA_VERSION", "2.12.20") - if (!v.startsWith("2.12")) - Result.Failure("Hail currently supports only Scala 2.12") - else - v - } - - def javaVersion: T[String] = Task.Input { - System.getProperty("java.version") - } - - def sparkVersion: T[String] = Task.Input { - Result.Success(T.ctx().env.getOrElse("SPARK_VERSION", "3.5.0")) - } - - def debugMode: T[Boolean] = Task.Input { - val isDebug = !T.ctx().env.contains("HAIL_RELEASE_MODE") - T.log.info(s"Building in ${if (isDebug) "debug" else "release"} mode") - isDebug - } - - def debugOrRelease: Task[String] = Task.Anon { - if (debugMode()) "debug" else "release" - } - } +object hail extends HailModule { outer => def buildInfo: T[PathRef] = T { val revision = VcsVersion.vcsState().currentRevision @@ -170,8 +170,7 @@ object `package` extends RootModule with HailScalaModule { outer => override def moduleDeps: Seq[JavaModule] = Seq(memory) - override def resources: T[Seq[PathRef]] = Seq( - PathRef(millSourcePath / "src" / "main" / "resources"), + override def resources: T[Seq[PathRef]] = super.resources() ++ Seq( PathRef(millSourcePath / "prebuilt" / "lib"), buildInfo(), ) @@ -260,7 +259,7 @@ object `package` extends RootModule with HailScalaModule { outer => ) override def sources: T[Seq[PathRef]] = Task.Sources { - Seq(PathRef(this.millSourcePath / os.up / "src" / env.debugOrRelease() / "java")) + Seq(PathRef(this.millSourcePath / env.debugOrRelease() / "src")) } } diff --git a/hail/src/main/c/ApproximateQuantiles_test.cpp b/hail/c/ApproximateQuantiles_test.cpp similarity index 100% rename from hail/src/main/c/ApproximateQuantiles_test.cpp rename to hail/c/ApproximateQuantiles_test.cpp diff --git a/hail/src/main/c/Decoder.cpp b/hail/c/Decoder.cpp similarity index 100% rename from hail/src/main/c/Decoder.cpp rename to hail/c/Decoder.cpp diff --git a/hail/src/main/c/Encoder.cpp b/hail/c/Encoder.cpp similarity index 100% rename from hail/src/main/c/Encoder.cpp rename to hail/c/Encoder.cpp diff --git a/hail/src/main/c/FS.cpp b/hail/c/FS.cpp similarity index 100% rename from hail/src/main/c/FS.cpp rename to hail/c/FS.cpp diff --git a/hail/src/main/c/Logging.cpp b/hail/c/Logging.cpp similarity index 100% rename from hail/src/main/c/Logging.cpp rename to hail/c/Logging.cpp diff --git a/hail/src/main/c/Makefile b/hail/c/Makefile similarity index 100% rename from hail/src/main/c/Makefile rename to hail/c/Makefile diff --git a/hail/src/main/c/NativeBoot.cpp b/hail/c/NativeBoot.cpp similarity index 100% rename from hail/src/main/c/NativeBoot.cpp rename to hail/c/NativeBoot.cpp diff --git a/hail/src/main/c/NativeCodeSuite.cpp b/hail/c/NativeCodeSuite.cpp similarity index 100% rename from hail/src/main/c/NativeCodeSuite.cpp rename to hail/c/NativeCodeSuite.cpp diff --git a/hail/src/main/c/NativeLongFunc.cpp b/hail/c/NativeLongFunc.cpp similarity index 100% rename from hail/src/main/c/NativeLongFunc.cpp rename to hail/c/NativeLongFunc.cpp diff --git a/hail/src/main/c/NativeModule.cpp b/hail/c/NativeModule.cpp similarity index 100% rename from hail/src/main/c/NativeModule.cpp rename to hail/c/NativeModule.cpp diff --git a/hail/src/main/c/NativePtr.cpp b/hail/c/NativePtr.cpp similarity index 100% rename from hail/src/main/c/NativePtr.cpp rename to hail/c/NativePtr.cpp diff --git a/hail/src/main/c/NativeStatus.cpp b/hail/c/NativeStatus.cpp similarity index 100% rename from hail/src/main/c/NativeStatus.cpp rename to hail/c/NativeStatus.cpp diff --git a/hail/src/main/c/ObjectArray.cpp b/hail/c/ObjectArray.cpp similarity index 100% rename from hail/src/main/c/ObjectArray.cpp rename to hail/c/ObjectArray.cpp diff --git a/hail/src/main/c/PartitionIterators.cpp b/hail/c/PartitionIterators.cpp similarity index 100% rename from hail/src/main/c/PartitionIterators.cpp rename to hail/c/PartitionIterators.cpp diff --git a/hail/src/main/c/README.md b/hail/c/README.md similarity index 100% rename from hail/src/main/c/README.md rename to hail/c/README.md diff --git a/hail/src/main/c/Region.cpp b/hail/c/Region.cpp similarity index 100% rename from hail/src/main/c/Region.cpp rename to hail/c/Region.cpp diff --git a/hail/src/main/c/Region_test.cpp b/hail/c/Region_test.cpp similarity index 100% rename from hail/src/main/c/Region_test.cpp rename to hail/c/Region_test.cpp diff --git a/hail/src/main/c/Upcalls.cpp b/hail/c/Upcalls.cpp similarity index 100% rename from hail/src/main/c/Upcalls.cpp rename to hail/c/Upcalls.cpp diff --git a/hail/src/main/c/cache-tests.cpp b/hail/c/cache-tests.cpp similarity index 100% rename from hail/src/main/c/cache-tests.cpp rename to hail/c/cache-tests.cpp diff --git a/hail/src/main/c/ibs.cpp b/hail/c/ibs.cpp similarity index 100% rename from hail/src/main/c/ibs.cpp rename to hail/c/ibs.cpp diff --git a/hail/src/main/c/ibs.h b/hail/c/ibs.h similarity index 100% rename from hail/src/main/c/ibs.h rename to hail/c/ibs.h diff --git a/hail/src/main/c/test.cpp b/hail/c/test.cpp similarity index 100% rename from hail/src/main/c/test.cpp rename to hail/c/test.cpp diff --git a/hail/src/main/c/testutils/style.css b/hail/c/testutils/style.css similarity index 100% rename from hail/src/main/c/testutils/style.css rename to hail/c/testutils/style.css diff --git a/hail/src/main/c/testutils/test-reporter.xslt b/hail/c/testutils/test-reporter.xslt similarity index 100% rename from hail/src/main/c/testutils/test-reporter.xslt rename to hail/c/testutils/test-reporter.xslt diff --git a/hail/src/main/c/testutils/unit-tests.cpp b/hail/c/testutils/unit-tests.cpp similarity index 100% rename from hail/src/main/c/testutils/unit-tests.cpp rename to hail/c/testutils/unit-tests.cpp diff --git a/hail/generate_splits.py b/hail/generate_splits.py index 88aa6f1bc11..4ea4907b19e 100644 --- a/hail/generate_splits.py +++ b/hail/generate_splits.py @@ -23,14 +23,14 @@ def partition(k: int, ls: List[T]) -> List[List[T]]: return out -sp.run("find src/test \\( -name \"*.scala\" -o -name \"*.java\" \\) -type f > classes", shell=True, check=True) +sp.run("find hail/test/src \\( -name \"*.scala\" -o -name \"*.java\" \\) -type f > classes", shell=True, check=True) n_splits = int(os.environ['TESTNG_SPLITS']) with open('classes', 'r') as f: foo = f.readlines() classes = [ - x.replace('src/test/scala/', '').replace('.scala\n', '').replace('.java\n', '').replace('/', '.') for x in foo + x.replace('hail/test/src/', '').replace('.scala\n', '').replace('.java\n', '').replace('/', '.') for x in foo ] classes = [cls for cls in classes if not cls.startswith('is.hail.services') if not cls.startswith('is.hail.io.fs')] diff --git a/hail/src/dist/scripts/Plot_gq20bydp.R b/hail/hail/dist/scripts/Plot_gq20bydp.R similarity index 100% rename from hail/src/dist/scripts/Plot_gq20bydp.R rename to hail/hail/dist/scripts/Plot_gq20bydp.R diff --git a/hail/src/debug/java/is/hail/annotations/Memory.java b/hail/hail/memory/debug/src/is/hail/annotations/Memory.java similarity index 100% rename from hail/src/debug/java/is/hail/annotations/Memory.java rename to hail/hail/memory/debug/src/is/hail/annotations/Memory.java diff --git a/hail/src/release/java/is/hail/annotations/Memory.java b/hail/hail/memory/release/src/is/hail/annotations/Memory.java similarity index 100% rename from hail/src/release/java/is/hail/annotations/Memory.java rename to hail/hail/memory/release/src/is/hail/annotations/Memory.java diff --git a/hail/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider b/hail/hail/resources/META-INF/services/com.azure.core.http.HttpClientProvider similarity index 100% rename from hail/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider rename to hail/hail/resources/META-INF/services/com.azure.core.http.HttpClientProvider diff --git a/hail/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory b/hail/hail/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory rename to hail/hail/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory diff --git a/hail/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory b/hail/hail/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory rename to hail/hail/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory b/hail/hail/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory rename to hail/hail/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec b/hail/hail/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec similarity index 100% rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec rename to hail/hail/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module b/hail/hail/resources/META-INF/services/com.fasterxml.jackson.databind.Module similarity index 100% rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module rename to hail/hail/resources/META-INF/services/com.fasterxml.jackson.databind.Module diff --git a/hail/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor b/hail/hail/resources/META-INF/services/io.micrometer.context.ContextAccessor similarity index 100% rename from hail/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor rename to hail/hail/resources/META-INF/services/io.micrometer.context.ContextAccessor diff --git a/hail/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider b/hail/hail/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider similarity index 100% rename from hail/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider rename to hail/hail/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory b/hail/hail/resources/META-INF/services/javax.xml.stream.XMLEventFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory rename to hail/hail/resources/META-INF/services/javax.xml.stream.XMLEventFactory diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory b/hail/hail/resources/META-INF/services/javax.xml.stream.XMLInputFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory rename to hail/hail/resources/META-INF/services/javax.xml.stream.XMLInputFactory diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory b/hail/hail/resources/META-INF/services/javax.xml.stream.XMLOutputFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory rename to hail/hail/resources/META-INF/services/javax.xml.stream.XMLOutputFactory diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory b/hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory similarity index 100% rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory rename to hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd b/hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd similarity index 100% rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd rename to hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng b/hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng similarity index 100% rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng rename to hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c b/hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c similarity index 100% rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c rename to hail/hail/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c diff --git a/hail/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration b/hail/hail/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration similarity index 100% rename from hail/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration rename to hail/hail/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration diff --git a/hail/src/main/resources/include/README b/hail/hail/resources/include/README similarity index 100% rename from hail/src/main/resources/include/README rename to hail/hail/resources/include/README diff --git a/hail/src/main/resources/include/hail/ApproximateQuantiles.h b/hail/hail/resources/include/hail/ApproximateQuantiles.h similarity index 100% rename from hail/src/main/resources/include/hail/ApproximateQuantiles.h rename to hail/hail/resources/include/hail/ApproximateQuantiles.h diff --git a/hail/src/main/resources/include/hail/ArrayBuilder.h b/hail/hail/resources/include/hail/ArrayBuilder.h similarity index 100% rename from hail/src/main/resources/include/hail/ArrayBuilder.h rename to hail/hail/resources/include/hail/ArrayBuilder.h diff --git a/hail/src/main/resources/include/hail/ArraySorter.h b/hail/hail/resources/include/hail/ArraySorter.h similarity index 100% rename from hail/src/main/resources/include/hail/ArraySorter.h rename to hail/hail/resources/include/hail/ArraySorter.h diff --git a/hail/src/main/resources/include/hail/Decoder.h b/hail/hail/resources/include/hail/Decoder.h similarity index 100% rename from hail/src/main/resources/include/hail/Decoder.h rename to hail/hail/resources/include/hail/Decoder.h diff --git a/hail/src/main/resources/include/hail/Encoder.h b/hail/hail/resources/include/hail/Encoder.h similarity index 100% rename from hail/src/main/resources/include/hail/Encoder.h rename to hail/hail/resources/include/hail/Encoder.h diff --git a/hail/src/main/resources/include/hail/FS.h b/hail/hail/resources/include/hail/FS.h similarity index 100% rename from hail/src/main/resources/include/hail/FS.h rename to hail/hail/resources/include/hail/FS.h diff --git a/hail/src/main/resources/include/hail/Logging.h b/hail/hail/resources/include/hail/Logging.h similarity index 100% rename from hail/src/main/resources/include/hail/Logging.h rename to hail/hail/resources/include/hail/Logging.h diff --git a/hail/src/main/resources/include/hail/NDArray.h b/hail/hail/resources/include/hail/NDArray.h similarity index 100% rename from hail/src/main/resources/include/hail/NDArray.h rename to hail/hail/resources/include/hail/NDArray.h diff --git a/hail/src/main/resources/include/hail/NativeMethod.h b/hail/hail/resources/include/hail/NativeMethod.h similarity index 100% rename from hail/src/main/resources/include/hail/NativeMethod.h rename to hail/hail/resources/include/hail/NativeMethod.h diff --git a/hail/src/main/resources/include/hail/NativeModule.h b/hail/hail/resources/include/hail/NativeModule.h similarity index 100% rename from hail/src/main/resources/include/hail/NativeModule.h rename to hail/hail/resources/include/hail/NativeModule.h diff --git a/hail/src/main/resources/include/hail/NativeObj.h b/hail/hail/resources/include/hail/NativeObj.h similarity index 100% rename from hail/src/main/resources/include/hail/NativeObj.h rename to hail/hail/resources/include/hail/NativeObj.h diff --git a/hail/src/main/resources/include/hail/NativePtr.h b/hail/hail/resources/include/hail/NativePtr.h similarity index 100% rename from hail/src/main/resources/include/hail/NativePtr.h rename to hail/hail/resources/include/hail/NativePtr.h diff --git a/hail/src/main/resources/include/hail/NativeStatus.h b/hail/hail/resources/include/hail/NativeStatus.h similarity index 100% rename from hail/src/main/resources/include/hail/NativeStatus.h rename to hail/hail/resources/include/hail/NativeStatus.h diff --git a/hail/src/main/resources/include/hail/ObjectArray.h b/hail/hail/resources/include/hail/ObjectArray.h similarity index 100% rename from hail/src/main/resources/include/hail/ObjectArray.h rename to hail/hail/resources/include/hail/ObjectArray.h diff --git a/hail/src/main/resources/include/hail/Ordering.h b/hail/hail/resources/include/hail/Ordering.h similarity index 100% rename from hail/src/main/resources/include/hail/Ordering.h rename to hail/hail/resources/include/hail/Ordering.h diff --git a/hail/src/main/resources/include/hail/PartitionIterators.h b/hail/hail/resources/include/hail/PartitionIterators.h similarity index 100% rename from hail/src/main/resources/include/hail/PartitionIterators.h rename to hail/hail/resources/include/hail/PartitionIterators.h diff --git a/hail/src/main/resources/include/hail/Region.h b/hail/hail/resources/include/hail/Region.h similarity index 100% rename from hail/src/main/resources/include/hail/Region.h rename to hail/hail/resources/include/hail/Region.h diff --git a/hail/src/main/resources/include/hail/RegionPool.h b/hail/hail/resources/include/hail/RegionPool.h similarity index 100% rename from hail/src/main/resources/include/hail/RegionPool.h rename to hail/hail/resources/include/hail/RegionPool.h diff --git a/hail/src/main/resources/include/hail/SparkUtils.h b/hail/hail/resources/include/hail/SparkUtils.h similarity index 100% rename from hail/src/main/resources/include/hail/SparkUtils.h rename to hail/hail/resources/include/hail/SparkUtils.h diff --git a/hail/src/main/resources/include/hail/Upcalls.h b/hail/hail/resources/include/hail/Upcalls.h similarity index 100% rename from hail/src/main/resources/include/hail/Upcalls.h rename to hail/hail/resources/include/hail/Upcalls.h diff --git a/hail/src/main/resources/include/hail/Utils.h b/hail/hail/resources/include/hail/Utils.h similarity index 100% rename from hail/src/main/resources/include/hail/Utils.h rename to hail/hail/resources/include/hail/Utils.h diff --git a/hail/src/main/resources/include/hail/hail.h b/hail/hail/resources/include/hail/hail.h similarity index 100% rename from hail/src/main/resources/include/hail/hail.h rename to hail/hail/resources/include/hail/hail.h diff --git a/hail/src/main/resources/log4j.properties b/hail/hail/resources/log4j.properties similarity index 100% rename from hail/src/main/resources/log4j.properties rename to hail/hail/resources/log4j.properties diff --git a/hail/src/main/resources/reference/canfam3.json b/hail/hail/resources/reference/canfam3.json similarity index 100% rename from hail/src/main/resources/reference/canfam3.json rename to hail/hail/resources/reference/canfam3.json diff --git a/hail/src/main/resources/reference/grch37.json b/hail/hail/resources/reference/grch37.json similarity index 100% rename from hail/src/main/resources/reference/grch37.json rename to hail/hail/resources/reference/grch37.json diff --git a/hail/src/main/resources/reference/grch38.json b/hail/hail/resources/reference/grch38.json similarity index 100% rename from hail/src/main/resources/reference/grch38.json rename to hail/hail/resources/reference/grch38.json diff --git a/hail/src/main/resources/reference/grcm38.json b/hail/hail/resources/reference/grcm38.json similarity index 100% rename from hail/src/main/resources/reference/grcm38.json rename to hail/hail/resources/reference/grcm38.json diff --git a/hail/src/main/scala/is/hail/HailContext.scala b/hail/hail/src/is/hail/HailContext.scala similarity index 100% rename from hail/src/main/scala/is/hail/HailContext.scala rename to hail/hail/src/is/hail/HailContext.scala diff --git a/hail/src/main/scala/is/hail/HailFeatureFlags.scala b/hail/hail/src/is/hail/HailFeatureFlags.scala similarity index 100% rename from hail/src/main/scala/is/hail/HailFeatureFlags.scala rename to hail/hail/src/is/hail/HailFeatureFlags.scala diff --git a/hail/src/main/scala/is/hail/annotations/Annotation.scala b/hail/hail/src/is/hail/annotations/Annotation.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/Annotation.scala rename to hail/hail/src/is/hail/annotations/Annotation.scala diff --git a/hail/src/main/scala/is/hail/annotations/BroadcastValue.scala b/hail/hail/src/is/hail/annotations/BroadcastValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/BroadcastValue.scala rename to hail/hail/src/is/hail/annotations/BroadcastValue.scala diff --git a/hail/src/main/scala/is/hail/annotations/ChunkCache.scala b/hail/hail/src/is/hail/annotations/ChunkCache.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/ChunkCache.scala rename to hail/hail/src/is/hail/annotations/ChunkCache.scala diff --git a/hail/src/main/scala/is/hail/annotations/ExtendedOrdering.scala b/hail/hail/src/is/hail/annotations/ExtendedOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/ExtendedOrdering.scala rename to hail/hail/src/is/hail/annotations/ExtendedOrdering.scala diff --git a/hail/src/main/scala/is/hail/annotations/JoinedRegionValue.scala b/hail/hail/src/is/hail/annotations/JoinedRegionValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/JoinedRegionValue.scala rename to hail/hail/src/is/hail/annotations/JoinedRegionValue.scala diff --git a/hail/src/main/scala/is/hail/annotations/OrderedRVIterator.scala b/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/OrderedRVIterator.scala rename to hail/hail/src/is/hail/annotations/OrderedRVIterator.scala diff --git a/hail/src/main/scala/is/hail/annotations/Region.scala b/hail/hail/src/is/hail/annotations/Region.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/Region.scala rename to hail/hail/src/is/hail/annotations/Region.scala diff --git a/hail/src/main/scala/is/hail/annotations/RegionMemory.scala b/hail/hail/src/is/hail/annotations/RegionMemory.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/RegionMemory.scala rename to hail/hail/src/is/hail/annotations/RegionMemory.scala diff --git a/hail/src/main/scala/is/hail/annotations/RegionPool.scala b/hail/hail/src/is/hail/annotations/RegionPool.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/RegionPool.scala rename to hail/hail/src/is/hail/annotations/RegionPool.scala diff --git a/hail/src/main/scala/is/hail/annotations/RegionValue.scala b/hail/hail/src/is/hail/annotations/RegionValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/RegionValue.scala rename to hail/hail/src/is/hail/annotations/RegionValue.scala diff --git a/hail/src/main/scala/is/hail/annotations/RegionValueBuilder.scala b/hail/hail/src/is/hail/annotations/RegionValueBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/RegionValueBuilder.scala rename to hail/hail/src/is/hail/annotations/RegionValueBuilder.scala diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeOrdering.scala b/hail/hail/src/is/hail/annotations/UnsafeOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/UnsafeOrdering.scala rename to hail/hail/src/is/hail/annotations/UnsafeOrdering.scala diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeRow.scala b/hail/hail/src/is/hail/annotations/UnsafeRow.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/UnsafeRow.scala rename to hail/hail/src/is/hail/annotations/UnsafeRow.scala diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeUtils.scala b/hail/hail/src/is/hail/annotations/UnsafeUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/UnsafeUtils.scala rename to hail/hail/src/is/hail/annotations/UnsafeUtils.scala diff --git a/hail/src/main/scala/is/hail/annotations/ValueVisitor.scala b/hail/hail/src/is/hail/annotations/ValueVisitor.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/ValueVisitor.scala rename to hail/hail/src/is/hail/annotations/ValueVisitor.scala diff --git a/hail/src/main/scala/is/hail/annotations/WritableRegionValue.scala b/hail/hail/src/is/hail/annotations/WritableRegionValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/WritableRegionValue.scala rename to hail/hail/src/is/hail/annotations/WritableRegionValue.scala diff --git a/hail/src/main/scala/is/hail/annotations/package.scala b/hail/hail/src/is/hail/annotations/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/annotations/package.scala rename to hail/hail/src/is/hail/annotations/package.scala diff --git a/hail/src/main/scala/is/hail/asm4s/AsmFunction.scala b/hail/hail/src/is/hail/asm4s/AsmFunction.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/AsmFunction.scala rename to hail/hail/src/is/hail/asm4s/AsmFunction.scala diff --git a/hail/src/main/scala/is/hail/asm4s/ClassBuilder.scala b/hail/hail/src/is/hail/asm4s/ClassBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/ClassBuilder.scala rename to hail/hail/src/is/hail/asm4s/ClassBuilder.scala diff --git a/hail/src/main/scala/is/hail/asm4s/Code.scala b/hail/hail/src/is/hail/asm4s/Code.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/Code.scala rename to hail/hail/src/is/hail/asm4s/Code.scala diff --git a/hail/src/main/scala/is/hail/asm4s/CodeBuilder.scala b/hail/hail/src/is/hail/asm4s/CodeBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/CodeBuilder.scala rename to hail/hail/src/is/hail/asm4s/CodeBuilder.scala diff --git a/hail/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala b/hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala rename to hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala diff --git a/hail/src/main/scala/is/hail/asm4s/HailClassLoader.scala b/hail/hail/src/is/hail/asm4s/HailClassLoader.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/HailClassLoader.scala rename to hail/hail/src/is/hail/asm4s/HailClassLoader.scala diff --git a/hail/src/main/scala/is/hail/asm4s/package.scala b/hail/hail/src/is/hail/asm4s/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/asm4s/package.scala rename to hail/hail/src/is/hail/asm4s/package.scala diff --git a/hail/src/main/scala/is/hail/backend/Backend.scala b/hail/hail/src/is/hail/backend/Backend.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/Backend.scala rename to hail/hail/src/is/hail/backend/Backend.scala diff --git a/hail/src/main/scala/is/hail/backend/BackendServer.scala b/hail/hail/src/is/hail/backend/BackendServer.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/BackendServer.scala rename to hail/hail/src/is/hail/backend/BackendServer.scala diff --git a/hail/src/main/scala/is/hail/backend/BackendUtils.scala b/hail/hail/src/is/hail/backend/BackendUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/BackendUtils.scala rename to hail/hail/src/is/hail/backend/BackendUtils.scala diff --git a/hail/src/main/scala/is/hail/backend/ExecuteContext.scala b/hail/hail/src/is/hail/backend/ExecuteContext.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/ExecuteContext.scala rename to hail/hail/src/is/hail/backend/ExecuteContext.scala diff --git a/hail/src/main/scala/is/hail/backend/ExecutionCache.scala b/hail/hail/src/is/hail/backend/ExecutionCache.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/ExecutionCache.scala rename to hail/hail/src/is/hail/backend/ExecutionCache.scala diff --git a/hail/src/main/scala/is/hail/backend/HailStateManager.scala b/hail/hail/src/is/hail/backend/HailStateManager.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/HailStateManager.scala rename to hail/hail/src/is/hail/backend/HailStateManager.scala diff --git a/hail/src/main/scala/is/hail/backend/HailTaskContext.scala b/hail/hail/src/is/hail/backend/HailTaskContext.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/HailTaskContext.scala rename to hail/hail/src/is/hail/backend/HailTaskContext.scala diff --git a/hail/src/main/scala/is/hail/backend/local/LocalBackend.scala b/hail/hail/src/is/hail/backend/local/LocalBackend.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/local/LocalBackend.scala rename to hail/hail/src/is/hail/backend/local/LocalBackend.scala diff --git a/hail/src/main/scala/is/hail/backend/service/Main.scala b/hail/hail/src/is/hail/backend/service/Main.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/service/Main.scala rename to hail/hail/src/is/hail/backend/service/Main.scala diff --git a/hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala b/hail/hail/src/is/hail/backend/service/ServiceBackend.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala rename to hail/hail/src/is/hail/backend/service/ServiceBackend.scala diff --git a/hail/src/main/scala/is/hail/backend/service/Worker.scala b/hail/hail/src/is/hail/backend/service/Worker.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/service/Worker.scala rename to hail/hail/src/is/hail/backend/service/Worker.scala diff --git a/hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala b/hail/hail/src/is/hail/backend/spark/SparkBackend.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala rename to hail/hail/src/is/hail/backend/spark/SparkBackend.scala diff --git a/hail/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala b/hail/hail/src/is/hail/backend/spark/SparkBlockMatrixCache.scala similarity index 100% rename from hail/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala rename to hail/hail/src/is/hail/backend/spark/SparkBlockMatrixCache.scala diff --git a/hail/src/main/scala/is/hail/check/Arbitrary.scala b/hail/hail/src/is/hail/check/Arbitrary.scala similarity index 100% rename from hail/src/main/scala/is/hail/check/Arbitrary.scala rename to hail/hail/src/is/hail/check/Arbitrary.scala diff --git a/hail/src/main/scala/is/hail/check/Gen.scala b/hail/hail/src/is/hail/check/Gen.scala similarity index 100% rename from hail/src/main/scala/is/hail/check/Gen.scala rename to hail/hail/src/is/hail/check/Gen.scala diff --git a/hail/src/main/scala/is/hail/check/Prop.scala b/hail/hail/src/is/hail/check/Prop.scala similarity index 100% rename from hail/src/main/scala/is/hail/check/Prop.scala rename to hail/hail/src/is/hail/check/Prop.scala diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala b/hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala similarity index 100% rename from hail/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala rename to hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala b/hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala similarity index 100% rename from hail/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala rename to hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala b/hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala similarity index 100% rename from hail/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala rename to hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala diff --git a/hail/src/main/scala/is/hail/cxx/RegionValueIterator.scala b/hail/hail/src/is/hail/cxx/RegionValueIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/cxx/RegionValueIterator.scala rename to hail/hail/src/is/hail/cxx/RegionValueIterator.scala diff --git a/hail/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala b/hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala rename to hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala diff --git a/hail/src/main/scala/is/hail/experimental/package.scala b/hail/hail/src/is/hail/experimental/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/experimental/package.scala rename to hail/hail/src/is/hail/experimental/package.scala diff --git a/hail/src/main/scala/is/hail/expr/AnnotationImpex.scala b/hail/hail/src/is/hail/expr/AnnotationImpex.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/AnnotationImpex.scala rename to hail/hail/src/is/hail/expr/AnnotationImpex.scala diff --git a/hail/src/main/scala/is/hail/expr/NatBase.scala b/hail/hail/src/is/hail/expr/NatBase.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/NatBase.scala rename to hail/hail/src/is/hail/expr/NatBase.scala diff --git a/hail/src/main/scala/is/hail/expr/Parser.scala b/hail/hail/src/is/hail/expr/Parser.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/Parser.scala rename to hail/hail/src/is/hail/expr/Parser.scala diff --git a/hail/src/main/scala/is/hail/expr/Validate.scala b/hail/hail/src/is/hail/expr/Validate.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/Validate.scala rename to hail/hail/src/is/hail/expr/Validate.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala b/hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala rename to hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala b/hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala rename to hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/AggOp.scala b/hail/hail/src/is/hail/expr/ir/AggOp.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/AggOp.scala rename to hail/hail/src/is/hail/expr/ir/AggOp.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ArraySorter.scala b/hail/hail/src/is/hail/expr/ir/ArraySorter.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ArraySorter.scala rename to hail/hail/src/is/hail/expr/ir/ArraySorter.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/BaseIR.scala b/hail/hail/src/is/hail/expr/ir/BaseIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/BaseIR.scala rename to hail/hail/src/is/hail/expr/ir/BaseIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/BinaryOp.scala b/hail/hail/src/is/hail/expr/ir/BinaryOp.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/BinaryOp.scala rename to hail/hail/src/is/hail/expr/ir/BinaryOp.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/BinarySearch.scala b/hail/hail/src/is/hail/expr/ir/BinarySearch.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/BinarySearch.scala rename to hail/hail/src/is/hail/expr/ir/BinarySearch.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Binds.scala b/hail/hail/src/is/hail/expr/ir/Binds.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Binds.scala rename to hail/hail/src/is/hail/expr/ir/Binds.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala rename to hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala b/hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala rename to hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Casts.scala b/hail/hail/src/is/hail/expr/ir/Casts.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Casts.scala rename to hail/hail/src/is/hail/expr/ir/Casts.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Children.scala b/hail/hail/src/is/hail/expr/ir/Children.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Children.scala rename to hail/hail/src/is/hail/expr/ir/Children.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala b/hail/hail/src/is/hail/expr/ir/ComparisonOp.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala rename to hail/hail/src/is/hail/expr/ir/ComparisonOp.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Compilable.scala b/hail/hail/src/is/hail/expr/ir/Compilable.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Compilable.scala rename to hail/hail/src/is/hail/expr/ir/Compilable.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Compile.scala b/hail/hail/src/is/hail/expr/ir/Compile.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Compile.scala rename to hail/hail/src/is/hail/expr/ir/Compile.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala b/hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala rename to hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala b/hail/hail/src/is/hail/expr/ir/ComputeUsesAndDefs.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala rename to hail/hail/src/is/hail/expr/ir/ComputeUsesAndDefs.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Copy.scala b/hail/hail/src/is/hail/expr/ir/Copy.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Copy.scala rename to hail/hail/src/is/hail/expr/ir/Copy.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala b/hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala rename to hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala b/hail/hail/src/is/hail/expr/ir/DistinctlyKeyed.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala rename to hail/hail/src/is/hail/expr/ir/DistinctlyKeyed.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Emit.scala b/hail/hail/src/is/hail/expr/ir/Emit.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Emit.scala rename to hail/hail/src/is/hail/expr/ir/Emit.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala b/hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala rename to hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala b/hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala rename to hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala b/hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala rename to hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Env.scala b/hail/hail/src/is/hail/expr/ir/Env.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Env.scala rename to hail/hail/src/is/hail/expr/ir/Env.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Exists.scala b/hail/hail/src/is/hail/expr/ir/Exists.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Exists.scala rename to hail/hail/src/is/hail/expr/ir/Exists.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala rename to hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/FoldConstants.scala b/hail/hail/src/is/hail/expr/ir/FoldConstants.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/FoldConstants.scala rename to hail/hail/src/is/hail/expr/ir/FoldConstants.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ForwardLets.scala b/hail/hail/src/is/hail/expr/ir/ForwardLets.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ForwardLets.scala rename to hail/hail/src/is/hail/expr/ir/ForwardLets.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala b/hail/hail/src/is/hail/expr/ir/ForwardRelationalLets.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala rename to hail/hail/src/is/hail/expr/ir/ForwardRelationalLets.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/FreeVariables.scala b/hail/hail/src/is/hail/expr/ir/FreeVariables.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/FreeVariables.scala rename to hail/hail/src/is/hail/expr/ir/FreeVariables.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/GenericLines.scala b/hail/hail/src/is/hail/expr/ir/GenericLines.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/GenericLines.scala rename to hail/hail/src/is/hail/expr/ir/GenericLines.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/GenericTableValue.scala b/hail/hail/src/is/hail/expr/ir/GenericTableValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/GenericTableValue.scala rename to hail/hail/src/is/hail/expr/ir/GenericTableValue.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IR.scala b/hail/hail/src/is/hail/expr/ir/IR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IR.scala rename to hail/hail/src/is/hail/expr/ir/IR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IRBuilder.scala b/hail/hail/src/is/hail/expr/ir/IRBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IRBuilder.scala rename to hail/hail/src/is/hail/expr/ir/IRBuilder.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IRSize.scala b/hail/hail/src/is/hail/expr/ir/IRSize.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IRSize.scala rename to hail/hail/src/is/hail/expr/ir/IRSize.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IRTraversal.scala b/hail/hail/src/is/hail/expr/ir/IRTraversal.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IRTraversal.scala rename to hail/hail/src/is/hail/expr/ir/IRTraversal.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/InTailPosition.scala b/hail/hail/src/is/hail/expr/ir/InTailPosition.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/InTailPosition.scala rename to hail/hail/src/is/hail/expr/ir/InTailPosition.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/InferPType.scala b/hail/hail/src/is/hail/expr/ir/InferPType.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/InferPType.scala rename to hail/hail/src/is/hail/expr/ir/InferPType.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/InferType.scala b/hail/hail/src/is/hail/expr/ir/InferType.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/InferType.scala rename to hail/hail/src/is/hail/expr/ir/InferType.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Interpret.scala b/hail/hail/src/is/hail/expr/ir/Interpret.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Interpret.scala rename to hail/hail/src/is/hail/expr/ir/Interpret.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Interpretable.scala b/hail/hail/src/is/hail/expr/ir/Interpretable.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Interpretable.scala rename to hail/hail/src/is/hail/expr/ir/Interpretable.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IsConstant.scala b/hail/hail/src/is/hail/expr/ir/IsConstant.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IsConstant.scala rename to hail/hail/src/is/hail/expr/ir/IsConstant.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/IsPure.scala b/hail/hail/src/is/hail/expr/ir/IsPure.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/IsPure.scala rename to hail/hail/src/is/hail/expr/ir/IsPure.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala b/hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala rename to hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala rename to hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala b/hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala rename to hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala b/hail/hail/src/is/hail/expr/ir/LoweringAnalyses.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala rename to hail/hail/src/is/hail/expr/ir/LoweringAnalyses.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/MapIR.scala b/hail/hail/src/is/hail/expr/ir/MapIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/MapIR.scala rename to hail/hail/src/is/hail/expr/ir/MapIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixIR.scala b/hail/hail/src/is/hail/expr/ir/MatrixIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/MatrixIR.scala rename to hail/hail/src/is/hail/expr/ir/MatrixIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixValue.scala b/hail/hail/src/is/hail/expr/ir/MatrixValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/MatrixValue.scala rename to hail/hail/src/is/hail/expr/ir/MatrixValue.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixWriter.scala b/hail/hail/src/is/hail/expr/ir/MatrixWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/MatrixWriter.scala rename to hail/hail/src/is/hail/expr/ir/MatrixWriter.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Mentions.scala b/hail/hail/src/is/hail/expr/ir/Mentions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Mentions.scala rename to hail/hail/src/is/hail/expr/ir/Mentions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala b/hail/hail/src/is/hail/expr/ir/NativeReaderOptions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala rename to hail/hail/src/is/hail/expr/ir/NativeReaderOptions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/NestingDepth.scala b/hail/hail/src/is/hail/expr/ir/NestingDepth.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/NestingDepth.scala rename to hail/hail/src/is/hail/expr/ir/NestingDepth.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/NormalizeNames.scala b/hail/hail/src/is/hail/expr/ir/NormalizeNames.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/NormalizeNames.scala rename to hail/hail/src/is/hail/expr/ir/NormalizeNames.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala b/hail/hail/src/is/hail/expr/ir/NumericPrimitives.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala rename to hail/hail/src/is/hail/expr/ir/NumericPrimitives.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Optimize.scala b/hail/hail/src/is/hail/expr/ir/Optimize.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Optimize.scala rename to hail/hail/src/is/hail/expr/ir/Optimize.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Param.scala b/hail/hail/src/is/hail/expr/ir/Param.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Param.scala rename to hail/hail/src/is/hail/expr/ir/Param.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Parser.scala b/hail/hail/src/is/hail/expr/ir/Parser.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Parser.scala rename to hail/hail/src/is/hail/expr/ir/Parser.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Pretty.scala b/hail/hail/src/is/hail/expr/ir/Pretty.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Pretty.scala rename to hail/hail/src/is/hail/expr/ir/Pretty.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala b/hail/hail/src/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala rename to hail/hail/src/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala b/hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala rename to hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Random.scala b/hail/hail/src/is/hail/expr/ir/Random.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Random.scala rename to hail/hail/src/is/hail/expr/ir/Random.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/RefEquality.scala b/hail/hail/src/is/hail/expr/ir/RefEquality.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/RefEquality.scala rename to hail/hail/src/is/hail/expr/ir/RefEquality.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Requiredness.scala b/hail/hail/src/is/hail/expr/ir/Requiredness.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Requiredness.scala rename to hail/hail/src/is/hail/expr/ir/Requiredness.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala b/hail/hail/src/is/hail/expr/ir/RewriteBottomUp.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala rename to hail/hail/src/is/hail/expr/ir/RewriteBottomUp.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala b/hail/hail/src/is/hail/expr/ir/RewriteTopDown.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala rename to hail/hail/src/is/hail/expr/ir/RewriteTopDown.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Scope.scala b/hail/hail/src/is/hail/expr/ir/Scope.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Scope.scala rename to hail/hail/src/is/hail/expr/ir/Scope.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Simplify.scala b/hail/hail/src/is/hail/expr/ir/Simplify.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Simplify.scala rename to hail/hail/src/is/hail/expr/ir/Simplify.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala b/hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala rename to hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/StringTableReader.scala b/hail/hail/src/is/hail/expr/ir/StringTableReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/StringTableReader.scala rename to hail/hail/src/is/hail/expr/ir/StringTableReader.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Subst.scala b/hail/hail/src/is/hail/expr/ir/Subst.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Subst.scala rename to hail/hail/src/is/hail/expr/ir/Subst.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/Sym.scala b/hail/hail/src/is/hail/expr/ir/Sym.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/Sym.scala rename to hail/hail/src/is/hail/expr/ir/Sym.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/TableIR.scala b/hail/hail/src/is/hail/expr/ir/TableIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/TableIR.scala rename to hail/hail/src/is/hail/expr/ir/TableIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/TableValue.scala b/hail/hail/src/is/hail/expr/ir/TableValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/TableValue.scala rename to hail/hail/src/is/hail/expr/ir/TableValue.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/TableWriter.scala b/hail/hail/src/is/hail/expr/ir/TableWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/TableWriter.scala rename to hail/hail/src/is/hail/expr/ir/TableWriter.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/TypeCheck.scala b/hail/hail/src/is/hail/expr/ir/TypeCheck.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/TypeCheck.scala rename to hail/hail/src/is/hail/expr/ir/TypeCheck.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/UnaryOp.scala b/hail/hail/src/is/hail/expr/ir/UnaryOp.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/UnaryOp.scala rename to hail/hail/src/is/hail/expr/ir/UnaryOp.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ValueReader.scala b/hail/hail/src/is/hail/expr/ir/ValueReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ValueReader.scala rename to hail/hail/src/is/hail/expr/ir/ValueReader.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ValueWriter.scala b/hail/hail/src/is/hail/expr/ir/ValueWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ValueWriter.scala rename to hail/hail/src/is/hail/expr/ir/ValueWriter.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt b/hail/hail/src/is/hail/expr/ir/add-ir-checklist.txt similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt rename to hail/hail/src/is/hail/expr/ir/add-ir-checklist.txt diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala b/hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala rename to hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala b/hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala rename to hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala rename to hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/Extract.scala b/hail/hail/src/is/hail/expr/ir/agg/Extract.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/Extract.scala rename to hail/hail/src/is/hail/expr/ir/agg/Extract.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/FoldAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/FoldAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/StagedAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/StagedAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala b/hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala rename to hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala b/hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala rename to hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala rename to hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala b/hail/hail/src/is/hail/expr/ir/analyses/ComputeMethodSplits.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala rename to hail/hail/src/is/hail/expr/ir/analyses/ComputeMethodSplits.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala b/hail/hail/src/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala rename to hail/hail/src/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala b/hail/hail/src/is/hail/expr/ir/analyses/ParentPointers.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala rename to hail/hail/src/is/hail/expr/ir/analyses/ParentPointers.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala b/hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala rename to hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/Functions.scala b/hail/hail/src/is/hail/expr/ir/functions/Functions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/Functions.scala rename to hail/hail/src/is/hail/expr/ir/functions/Functions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/GetElement.scala b/hail/hail/src/is/hail/expr/ir/functions/GetElement.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/GetElement.scala rename to hail/hail/src/is/hail/expr/ir/functions/GetElement.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala b/hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala rename to hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala b/hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala rename to hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala rename to hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala b/hail/hail/src/is/hail/expr/ir/lowering/CanLowerEfficiently.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala rename to hail/hail/src/is/hail/expr/ir/lowering/CanLowerEfficiently.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala b/hail/hail/src/is/hail/expr/ir/lowering/EvalRelationalLets.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala rename to hail/hail/src/is/hail/expr/ir/lowering/EvalRelationalLets.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/IRState.scala b/hail/hail/src/is/hail/expr/ir/lowering/IRState.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/IRState.scala rename to hail/hail/src/is/hail/expr/ir/lowering/IRState.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerToCDA.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LowerToCDA.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala b/hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala b/hail/hail/src/is/hail/expr/ir/lowering/LoweringPipeline.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala rename to hail/hail/src/is/hail/expr/ir/lowering/LoweringPipeline.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala b/hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala rename to hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/Rule.scala b/hail/hail/src/is/hail/expr/ir/lowering/Rule.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/Rule.scala rename to hail/hail/src/is/hail/expr/ir/lowering/Rule.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala b/hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala rename to hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala b/hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala rename to hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/CallOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/CallOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/IntervalOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/IntervalOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/IterableOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/IterableOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/LocusOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/LocusOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/PrimitiveOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/PrimitiveOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/StringOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/StringOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/StructOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala rename to hail/hail/src/is/hail/expr/ir/orderings/StructOrdering.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/package.scala b/hail/hail/src/is/hail/expr/ir/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/package.scala rename to hail/hail/src/is/hail/expr/ir/package.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala b/hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala rename to hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala b/hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala rename to hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala b/hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala rename to hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala diff --git a/hail/src/main/scala/is/hail/expr/package.scala b/hail/hail/src/is/hail/expr/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/expr/package.scala rename to hail/hail/src/is/hail/expr/package.scala diff --git a/hail/src/main/scala/is/hail/io/AbstractBinaryReader.scala b/hail/hail/src/is/hail/io/AbstractBinaryReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/AbstractBinaryReader.scala rename to hail/hail/src/is/hail/io/AbstractBinaryReader.scala diff --git a/hail/src/main/scala/is/hail/io/BufferSpecs.scala b/hail/hail/src/is/hail/io/BufferSpecs.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/BufferSpecs.scala rename to hail/hail/src/is/hail/io/BufferSpecs.scala diff --git a/hail/src/main/scala/is/hail/io/ByteArrayReader.scala b/hail/hail/src/is/hail/io/ByteArrayReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/ByteArrayReader.scala rename to hail/hail/src/is/hail/io/ByteArrayReader.scala diff --git a/hail/src/main/scala/is/hail/io/CodecSpec.scala b/hail/hail/src/is/hail/io/CodecSpec.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/CodecSpec.scala rename to hail/hail/src/is/hail/io/CodecSpec.scala diff --git a/hail/src/main/scala/is/hail/io/Decoder.scala b/hail/hail/src/is/hail/io/Decoder.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/Decoder.scala rename to hail/hail/src/is/hail/io/Decoder.scala diff --git a/hail/src/main/scala/is/hail/io/DoubleInputBuffer.scala b/hail/hail/src/is/hail/io/DoubleInputBuffer.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/DoubleInputBuffer.scala rename to hail/hail/src/is/hail/io/DoubleInputBuffer.scala diff --git a/hail/src/main/scala/is/hail/io/ElasticsearchConnector.scala b/hail/hail/src/is/hail/io/ElasticsearchConnector.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/ElasticsearchConnector.scala rename to hail/hail/src/is/hail/io/ElasticsearchConnector.scala diff --git a/hail/src/main/scala/is/hail/io/Encoder.scala b/hail/hail/src/is/hail/io/Encoder.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/Encoder.scala rename to hail/hail/src/is/hail/io/Encoder.scala diff --git a/hail/src/main/scala/is/hail/io/FileWriteMetadata.scala b/hail/hail/src/is/hail/io/FileWriteMetadata.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/FileWriteMetadata.scala rename to hail/hail/src/is/hail/io/FileWriteMetadata.scala diff --git a/hail/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala b/hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala rename to hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala diff --git a/hail/src/main/scala/is/hail/io/IndexBTree.scala b/hail/hail/src/is/hail/io/IndexBTree.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/IndexBTree.scala rename to hail/hail/src/is/hail/io/IndexBTree.scala diff --git a/hail/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala b/hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala rename to hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala diff --git a/hail/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala b/hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala rename to hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala diff --git a/hail/src/main/scala/is/hail/io/InputBuffers.scala b/hail/hail/src/is/hail/io/InputBuffers.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/InputBuffers.scala rename to hail/hail/src/is/hail/io/InputBuffers.scala diff --git a/hail/src/main/scala/is/hail/io/MemoryBuffer.scala b/hail/hail/src/is/hail/io/MemoryBuffer.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/MemoryBuffer.scala rename to hail/hail/src/is/hail/io/MemoryBuffer.scala diff --git a/hail/src/main/scala/is/hail/io/OutputBuffers.scala b/hail/hail/src/is/hail/io/OutputBuffers.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/OutputBuffers.scala rename to hail/hail/src/is/hail/io/OutputBuffers.scala diff --git a/hail/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala b/hail/hail/src/is/hail/io/RichContextRDDRegionValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala rename to hail/hail/src/is/hail/io/RichContextRDDRegionValue.scala diff --git a/hail/src/main/scala/is/hail/io/Spec.scala b/hail/hail/src/is/hail/io/Spec.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/Spec.scala rename to hail/hail/src/is/hail/io/Spec.scala diff --git a/hail/src/main/scala/is/hail/io/TypedCodecSpec.scala b/hail/hail/src/is/hail/io/TypedCodecSpec.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/TypedCodecSpec.scala rename to hail/hail/src/is/hail/io/TypedCodecSpec.scala diff --git a/hail/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala b/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala rename to hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala diff --git a/hail/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala b/hail/hail/src/is/hail/io/avro/AvroSchemaSerializer.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala rename to hail/hail/src/is/hail/io/avro/AvroSchemaSerializer.scala diff --git a/hail/src/main/scala/is/hail/io/avro/AvroTableReader.scala b/hail/hail/src/is/hail/io/avro/AvroTableReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/avro/AvroTableReader.scala rename to hail/hail/src/is/hail/io/avro/AvroTableReader.scala diff --git a/hail/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala b/hail/hail/src/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala rename to hail/hail/src/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala b/hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala rename to hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala b/hail/hail/src/is/hail/io/bgen/BgenSettings.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala rename to hail/hail/src/is/hail/io/bgen/BgenSettings.scala diff --git a/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala b/hail/hail/src/is/hail/io/bgen/LoadBgen.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala rename to hail/hail/src/is/hail/io/bgen/LoadBgen.scala diff --git a/hail/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala b/hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala rename to hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala diff --git a/hail/src/main/scala/is/hail/io/compress/BGzipLineReader.scala b/hail/hail/src/is/hail/io/compress/BGzipLineReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/compress/BGzipLineReader.scala rename to hail/hail/src/is/hail/io/compress/BGzipLineReader.scala diff --git a/hail/src/main/scala/is/hail/io/compress/LZ4.scala b/hail/hail/src/is/hail/io/compress/LZ4.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/compress/LZ4.scala rename to hail/hail/src/is/hail/io/compress/LZ4.scala diff --git a/hail/src/main/scala/is/hail/io/fs/AzureStorageFS.scala b/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/AzureStorageFS.scala rename to hail/hail/src/is/hail/io/fs/AzureStorageFS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/FS.scala b/hail/hail/src/is/hail/io/fs/FS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/FS.scala rename to hail/hail/src/is/hail/io/fs/FS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala b/hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala rename to hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/HadoopFS.scala b/hail/hail/src/is/hail/io/fs/HadoopFS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/HadoopFS.scala rename to hail/hail/src/is/hail/io/fs/HadoopFS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/README b/hail/hail/src/is/hail/io/fs/README similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/README rename to hail/hail/src/is/hail/io/fs/README diff --git a/hail/src/main/scala/is/hail/io/fs/RouterFS.scala b/hail/hail/src/is/hail/io/fs/RouterFS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/RouterFS.scala rename to hail/hail/src/is/hail/io/fs/RouterFS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala b/hail/hail/src/is/hail/io/fs/TerraAzureStorageFS.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala rename to hail/hail/src/is/hail/io/fs/TerraAzureStorageFS.scala diff --git a/hail/src/main/scala/is/hail/io/fs/package.scala b/hail/hail/src/is/hail/io/fs/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/fs/package.scala rename to hail/hail/src/is/hail/io/fs/package.scala diff --git a/hail/src/main/scala/is/hail/io/gen/ExportBGEN.scala b/hail/hail/src/is/hail/io/gen/ExportBGEN.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/gen/ExportBGEN.scala rename to hail/hail/src/is/hail/io/gen/ExportBGEN.scala diff --git a/hail/src/main/scala/is/hail/io/gen/ExportGen.scala b/hail/hail/src/is/hail/io/gen/ExportGen.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/gen/ExportGen.scala rename to hail/hail/src/is/hail/io/gen/ExportGen.scala diff --git a/hail/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala b/hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala rename to hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala diff --git a/hail/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala b/hail/hail/src/is/hail/io/hadoop/BytesOnlyWritable.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala rename to hail/hail/src/is/hail/io/hadoop/BytesOnlyWritable.scala diff --git a/hail/src/main/scala/is/hail/io/index/IndexReader.scala b/hail/hail/src/is/hail/io/index/IndexReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/index/IndexReader.scala rename to hail/hail/src/is/hail/io/index/IndexReader.scala diff --git a/hail/src/main/scala/is/hail/io/index/IndexWriter.scala b/hail/hail/src/is/hail/io/index/IndexWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/index/IndexWriter.scala rename to hail/hail/src/is/hail/io/index/IndexWriter.scala diff --git a/hail/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala b/hail/hail/src/is/hail/io/index/InternalNodeBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala rename to hail/hail/src/is/hail/io/index/InternalNodeBuilder.scala diff --git a/hail/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala b/hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala rename to hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala diff --git a/hail/src/main/scala/is/hail/io/index/StagedIndexReader.scala b/hail/hail/src/is/hail/io/index/StagedIndexReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/index/StagedIndexReader.scala rename to hail/hail/src/is/hail/io/index/StagedIndexReader.scala diff --git a/hail/src/main/scala/is/hail/io/package.scala b/hail/hail/src/is/hail/io/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/package.scala rename to hail/hail/src/is/hail/io/package.scala diff --git a/hail/src/main/scala/is/hail/io/plink/ExportPlink.scala b/hail/hail/src/is/hail/io/plink/ExportPlink.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/plink/ExportPlink.scala rename to hail/hail/src/is/hail/io/plink/ExportPlink.scala diff --git a/hail/src/main/scala/is/hail/io/plink/LoadPlink.scala b/hail/hail/src/is/hail/io/plink/LoadPlink.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/plink/LoadPlink.scala rename to hail/hail/src/is/hail/io/plink/LoadPlink.scala diff --git a/hail/src/main/scala/is/hail/io/reference/FASTAReader.scala b/hail/hail/src/is/hail/io/reference/FASTAReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/reference/FASTAReader.scala rename to hail/hail/src/is/hail/io/reference/FASTAReader.scala diff --git a/hail/src/main/scala/is/hail/io/reference/LiftOver.scala b/hail/hail/src/is/hail/io/reference/LiftOver.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/reference/LiftOver.scala rename to hail/hail/src/is/hail/io/reference/LiftOver.scala diff --git a/hail/src/main/scala/is/hail/io/tabix/TabixReader.scala b/hail/hail/src/is/hail/io/tabix/TabixReader.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/tabix/TabixReader.scala rename to hail/hail/src/is/hail/io/tabix/TabixReader.scala diff --git a/hail/src/main/scala/is/hail/io/vcf/ExportVCF.scala b/hail/hail/src/is/hail/io/vcf/ExportVCF.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/vcf/ExportVCF.scala rename to hail/hail/src/is/hail/io/vcf/ExportVCF.scala diff --git a/hail/src/main/scala/is/hail/io/vcf/LoadVCF.scala b/hail/hail/src/is/hail/io/vcf/LoadVCF.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/vcf/LoadVCF.scala rename to hail/hail/src/is/hail/io/vcf/LoadVCF.scala diff --git a/hail/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala b/hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala rename to hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala diff --git a/hail/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala b/hail/hail/src/is/hail/kryo/HailKryoRegistrator.scala similarity index 100% rename from hail/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala rename to hail/hail/src/is/hail/kryo/HailKryoRegistrator.scala diff --git a/hail/src/main/scala/is/hail/linalg/BLAS.scala b/hail/hail/src/is/hail/linalg/BLAS.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/BLAS.scala rename to hail/hail/src/is/hail/linalg/BLAS.scala diff --git a/hail/src/main/scala/is/hail/linalg/BlockMatrix.scala b/hail/hail/src/is/hail/linalg/BlockMatrix.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/BlockMatrix.scala rename to hail/hail/src/is/hail/linalg/BlockMatrix.scala diff --git a/hail/src/main/scala/is/hail/linalg/GridPartitioner.scala b/hail/hail/src/is/hail/linalg/GridPartitioner.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/GridPartitioner.scala rename to hail/hail/src/is/hail/linalg/GridPartitioner.scala diff --git a/hail/src/main/scala/is/hail/linalg/LAPACK.scala b/hail/hail/src/is/hail/linalg/LAPACK.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/LAPACK.scala rename to hail/hail/src/is/hail/linalg/LAPACK.scala diff --git a/hail/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala b/hail/hail/src/is/hail/linalg/LinalgCodeUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala rename to hail/hail/src/is/hail/linalg/LinalgCodeUtils.scala diff --git a/hail/src/main/scala/is/hail/linalg/RowMatrix.scala b/hail/hail/src/is/hail/linalg/RowMatrix.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/RowMatrix.scala rename to hail/hail/src/is/hail/linalg/RowMatrix.scala diff --git a/hail/src/main/scala/is/hail/linalg/RowPartitioner.scala b/hail/hail/src/is/hail/linalg/RowPartitioner.scala similarity index 100% rename from hail/src/main/scala/is/hail/linalg/RowPartitioner.scala rename to hail/hail/src/is/hail/linalg/RowPartitioner.scala diff --git a/hail/src/main/scala/is/hail/lir/Blocks.scala b/hail/hail/src/is/hail/lir/Blocks.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/Blocks.scala rename to hail/hail/src/is/hail/lir/Blocks.scala diff --git a/hail/src/main/scala/is/hail/lir/CFG.scala b/hail/hail/src/is/hail/lir/CFG.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/CFG.scala rename to hail/hail/src/is/hail/lir/CFG.scala diff --git a/hail/src/main/scala/is/hail/lir/Emit.scala b/hail/hail/src/is/hail/lir/Emit.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/Emit.scala rename to hail/hail/src/is/hail/lir/Emit.scala diff --git a/hail/src/main/scala/is/hail/lir/InitializeLocals.scala b/hail/hail/src/is/hail/lir/InitializeLocals.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/InitializeLocals.scala rename to hail/hail/src/is/hail/lir/InitializeLocals.scala diff --git a/hail/src/main/scala/is/hail/lir/Liveness.scala b/hail/hail/src/is/hail/lir/Liveness.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/Liveness.scala rename to hail/hail/src/is/hail/lir/Liveness.scala diff --git a/hail/src/main/scala/is/hail/lir/Locals.scala b/hail/hail/src/is/hail/lir/Locals.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/Locals.scala rename to hail/hail/src/is/hail/lir/Locals.scala diff --git a/hail/src/main/scala/is/hail/lir/PST.scala b/hail/hail/src/is/hail/lir/PST.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/PST.scala rename to hail/hail/src/is/hail/lir/PST.scala diff --git a/hail/src/main/scala/is/hail/lir/Pretty.scala b/hail/hail/src/is/hail/lir/Pretty.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/Pretty.scala rename to hail/hail/src/is/hail/lir/Pretty.scala diff --git a/hail/src/main/scala/is/hail/lir/SimplifyControl.scala b/hail/hail/src/is/hail/lir/SimplifyControl.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/SimplifyControl.scala rename to hail/hail/src/is/hail/lir/SimplifyControl.scala diff --git a/hail/src/main/scala/is/hail/lir/SplitLargeBlocks.scala b/hail/hail/src/is/hail/lir/SplitLargeBlocks.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/SplitLargeBlocks.scala rename to hail/hail/src/is/hail/lir/SplitLargeBlocks.scala diff --git a/hail/src/main/scala/is/hail/lir/SplitMethod.scala b/hail/hail/src/is/hail/lir/SplitMethod.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/SplitMethod.scala rename to hail/hail/src/is/hail/lir/SplitMethod.scala diff --git a/hail/src/main/scala/is/hail/lir/X.scala b/hail/hail/src/is/hail/lir/X.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/X.scala rename to hail/hail/src/is/hail/lir/X.scala diff --git a/hail/src/main/scala/is/hail/lir/package.scala b/hail/hail/src/is/hail/lir/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/lir/package.scala rename to hail/hail/src/is/hail/lir/package.scala diff --git a/hail/src/main/scala/is/hail/methods/FilterPartitions.scala b/hail/hail/src/is/hail/methods/FilterPartitions.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/FilterPartitions.scala rename to hail/hail/src/is/hail/methods/FilterPartitions.scala diff --git a/hail/src/main/scala/is/hail/methods/ForceCount.scala b/hail/hail/src/is/hail/methods/ForceCount.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/ForceCount.scala rename to hail/hail/src/is/hail/methods/ForceCount.scala diff --git a/hail/src/main/scala/is/hail/methods/IBD.scala b/hail/hail/src/is/hail/methods/IBD.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/IBD.scala rename to hail/hail/src/is/hail/methods/IBD.scala diff --git a/hail/src/main/scala/is/hail/methods/IBSFFI.scala b/hail/hail/src/is/hail/methods/IBSFFI.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/IBSFFI.scala rename to hail/hail/src/is/hail/methods/IBSFFI.scala diff --git a/hail/src/main/scala/is/hail/methods/LinearRegression.scala b/hail/hail/src/is/hail/methods/LinearRegression.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/LinearRegression.scala rename to hail/hail/src/is/hail/methods/LinearRegression.scala diff --git a/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala b/hail/hail/src/is/hail/methods/LocalLDPrune.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/LocalLDPrune.scala rename to hail/hail/src/is/hail/methods/LocalLDPrune.scala diff --git a/hail/src/main/scala/is/hail/methods/LocalWhitening.scala b/hail/hail/src/is/hail/methods/LocalWhitening.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/LocalWhitening.scala rename to hail/hail/src/is/hail/methods/LocalWhitening.scala diff --git a/hail/src/main/scala/is/hail/methods/LogisticRegression.scala b/hail/hail/src/is/hail/methods/LogisticRegression.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/LogisticRegression.scala rename to hail/hail/src/is/hail/methods/LogisticRegression.scala diff --git a/hail/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala b/hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala rename to hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala diff --git a/hail/src/main/scala/is/hail/methods/NPartitions.scala b/hail/hail/src/is/hail/methods/NPartitions.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/NPartitions.scala rename to hail/hail/src/is/hail/methods/NPartitions.scala diff --git a/hail/src/main/scala/is/hail/methods/Nirvana.scala b/hail/hail/src/is/hail/methods/Nirvana.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/Nirvana.scala rename to hail/hail/src/is/hail/methods/Nirvana.scala diff --git a/hail/src/main/scala/is/hail/methods/PCA.scala b/hail/hail/src/is/hail/methods/PCA.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/PCA.scala rename to hail/hail/src/is/hail/methods/PCA.scala diff --git a/hail/src/main/scala/is/hail/methods/PCRelate.scala b/hail/hail/src/is/hail/methods/PCRelate.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/PCRelate.scala rename to hail/hail/src/is/hail/methods/PCRelate.scala diff --git a/hail/src/main/scala/is/hail/methods/PoissonRegression.scala b/hail/hail/src/is/hail/methods/PoissonRegression.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/PoissonRegression.scala rename to hail/hail/src/is/hail/methods/PoissonRegression.scala diff --git a/hail/src/main/scala/is/hail/methods/Skat.scala b/hail/hail/src/is/hail/methods/Skat.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/Skat.scala rename to hail/hail/src/is/hail/methods/Skat.scala diff --git a/hail/src/main/scala/is/hail/methods/VEP.scala b/hail/hail/src/is/hail/methods/VEP.scala similarity index 100% rename from hail/src/main/scala/is/hail/methods/VEP.scala rename to hail/hail/src/is/hail/methods/VEP.scala diff --git a/hail/src/main/scala/is/hail/misc/BGZipBlocks.scala b/hail/hail/src/is/hail/misc/BGZipBlocks.scala similarity index 100% rename from hail/src/main/scala/is/hail/misc/BGZipBlocks.scala rename to hail/hail/src/is/hail/misc/BGZipBlocks.scala diff --git a/hail/src/main/scala/is/hail/package.scala b/hail/hail/src/is/hail/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/package.scala rename to hail/hail/src/is/hail/package.scala diff --git a/hail/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala b/hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala rename to hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala diff --git a/hail/src/main/scala/is/hail/rvd/KeyedRVD.scala b/hail/hail/src/is/hail/rvd/KeyedRVD.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/KeyedRVD.scala rename to hail/hail/src/is/hail/rvd/KeyedRVD.scala diff --git a/hail/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala b/hail/hail/src/is/hail/rvd/PartitionBoundOrdering.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala rename to hail/hail/src/is/hail/rvd/PartitionBoundOrdering.scala diff --git a/hail/src/main/scala/is/hail/rvd/RVD.scala b/hail/hail/src/is/hail/rvd/RVD.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/RVD.scala rename to hail/hail/src/is/hail/rvd/RVD.scala diff --git a/hail/src/main/scala/is/hail/rvd/RVDContext.scala b/hail/hail/src/is/hail/rvd/RVDContext.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/RVDContext.scala rename to hail/hail/src/is/hail/rvd/RVDContext.scala diff --git a/hail/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala b/hail/hail/src/is/hail/rvd/RVDPartitionInfo.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala rename to hail/hail/src/is/hail/rvd/RVDPartitionInfo.scala diff --git a/hail/src/main/scala/is/hail/rvd/RVDPartitioner.scala b/hail/hail/src/is/hail/rvd/RVDPartitioner.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/RVDPartitioner.scala rename to hail/hail/src/is/hail/rvd/RVDPartitioner.scala diff --git a/hail/src/main/scala/is/hail/rvd/RVDType.scala b/hail/hail/src/is/hail/rvd/RVDType.scala similarity index 100% rename from hail/src/main/scala/is/hail/rvd/RVDType.scala rename to hail/hail/src/is/hail/rvd/RVDType.scala diff --git a/hail/src/main/scala/is/hail/services/BatchClient.scala b/hail/hail/src/is/hail/services/BatchClient.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/BatchClient.scala rename to hail/hail/src/is/hail/services/BatchClient.scala diff --git a/hail/src/main/scala/is/hail/services/BatchConfig.scala b/hail/hail/src/is/hail/services/BatchConfig.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/BatchConfig.scala rename to hail/hail/src/is/hail/services/BatchConfig.scala diff --git a/hail/src/main/scala/is/hail/services/DeployConfig.scala b/hail/hail/src/is/hail/services/DeployConfig.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/DeployConfig.scala rename to hail/hail/src/is/hail/services/DeployConfig.scala diff --git a/hail/src/main/scala/is/hail/services/JSONLogLayout.scala b/hail/hail/src/is/hail/services/JSONLogLayout.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/JSONLogLayout.scala rename to hail/hail/src/is/hail/services/JSONLogLayout.scala diff --git a/hail/src/main/scala/is/hail/services/NettyProxy.scala b/hail/hail/src/is/hail/services/NettyProxy.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/NettyProxy.scala rename to hail/hail/src/is/hail/services/NettyProxy.scala diff --git a/hail/src/main/scala/is/hail/services/README b/hail/hail/src/is/hail/services/README similarity index 100% rename from hail/src/main/scala/is/hail/services/README rename to hail/hail/src/is/hail/services/README diff --git a/hail/src/main/scala/is/hail/services/oauth2.scala b/hail/hail/src/is/hail/services/oauth2.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/oauth2.scala rename to hail/hail/src/is/hail/services/oauth2.scala diff --git a/hail/src/main/scala/is/hail/services/package.scala b/hail/hail/src/is/hail/services/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/package.scala rename to hail/hail/src/is/hail/services/package.scala diff --git a/hail/src/main/scala/is/hail/services/requests.scala b/hail/hail/src/is/hail/services/requests.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/requests.scala rename to hail/hail/src/is/hail/services/requests.scala diff --git a/hail/src/main/scala/is/hail/services/tls/package.scala b/hail/hail/src/is/hail/services/tls/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/services/tls/package.scala rename to hail/hail/src/is/hail/services/tls/package.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/BlockedRDD.scala b/hail/hail/src/is/hail/sparkextras/BlockedRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/BlockedRDD.scala rename to hail/hail/src/is/hail/sparkextras/BlockedRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala b/hail/hail/src/is/hail/sparkextras/ContextPairRDDFunctions.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala rename to hail/hail/src/is/hail/sparkextras/ContextPairRDDFunctions.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/ContextRDD.scala b/hail/hail/src/is/hail/sparkextras/ContextRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/ContextRDD.scala rename to hail/hail/src/is/hail/sparkextras/ContextRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala b/hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala rename to hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala b/hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala rename to hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala b/hail/hail/src/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala rename to hail/hail/src/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala b/hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala rename to hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala b/hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala rename to hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala diff --git a/hail/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala b/hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala similarity index 100% rename from hail/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala rename to hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala diff --git a/hail/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala b/hail/hail/src/is/hail/stats/GeneralizedChiSquaredDistribution.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala rename to hail/hail/src/is/hail/stats/GeneralizedChiSquaredDistribution.scala diff --git a/hail/src/main/scala/is/hail/stats/LeveneHaldane.scala b/hail/hail/src/is/hail/stats/LeveneHaldane.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/LeveneHaldane.scala rename to hail/hail/src/is/hail/stats/LeveneHaldane.scala diff --git a/hail/src/main/scala/is/hail/stats/LinearMixedModel.scala b/hail/hail/src/is/hail/stats/LinearMixedModel.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/LinearMixedModel.scala rename to hail/hail/src/is/hail/stats/LinearMixedModel.scala diff --git a/hail/src/main/scala/is/hail/stats/LinearRegressionModel.scala b/hail/hail/src/is/hail/stats/LinearRegressionModel.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/LinearRegressionModel.scala rename to hail/hail/src/is/hail/stats/LinearRegressionModel.scala diff --git a/hail/src/main/scala/is/hail/stats/LogisticRegressionModel.scala b/hail/hail/src/is/hail/stats/LogisticRegressionModel.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/LogisticRegressionModel.scala rename to hail/hail/src/is/hail/stats/LogisticRegressionModel.scala diff --git a/hail/src/main/scala/is/hail/stats/PoissonRegressionModel.scala b/hail/hail/src/is/hail/stats/PoissonRegressionModel.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/PoissonRegressionModel.scala rename to hail/hail/src/is/hail/stats/PoissonRegressionModel.scala diff --git a/hail/src/main/scala/is/hail/stats/RegressionUtils.scala b/hail/hail/src/is/hail/stats/RegressionUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/RegressionUtils.scala rename to hail/hail/src/is/hail/stats/RegressionUtils.scala diff --git a/hail/src/main/scala/is/hail/stats/eigSymD.scala b/hail/hail/src/is/hail/stats/eigSymD.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/eigSymD.scala rename to hail/hail/src/is/hail/stats/eigSymD.scala diff --git a/hail/src/main/scala/is/hail/stats/package.scala b/hail/hail/src/is/hail/stats/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/stats/package.scala rename to hail/hail/src/is/hail/stats/package.scala diff --git a/hail/src/main/scala/is/hail/types/BaseType.scala b/hail/hail/src/is/hail/types/BaseType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/BaseType.scala rename to hail/hail/src/is/hail/types/BaseType.scala diff --git a/hail/src/main/scala/is/hail/types/Box.scala b/hail/hail/src/is/hail/types/Box.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/Box.scala rename to hail/hail/src/is/hail/types/Box.scala diff --git a/hail/src/main/scala/is/hail/types/MapTypes.scala b/hail/hail/src/is/hail/types/MapTypes.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/MapTypes.scala rename to hail/hail/src/is/hail/types/MapTypes.scala diff --git a/hail/src/main/scala/is/hail/types/TypeWithRequiredness.scala b/hail/hail/src/is/hail/types/TypeWithRequiredness.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/TypeWithRequiredness.scala rename to hail/hail/src/is/hail/types/TypeWithRequiredness.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EArray.scala b/hail/hail/src/is/hail/types/encoded/EArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EArray.scala rename to hail/hail/src/is/hail/types/encoded/EArray.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EBaseStruct.scala b/hail/hail/src/is/hail/types/encoded/EBaseStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EBaseStruct.scala rename to hail/hail/src/is/hail/types/encoded/EBaseStruct.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EBinary.scala b/hail/hail/src/is/hail/types/encoded/EBinary.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EBinary.scala rename to hail/hail/src/is/hail/types/encoded/EBinary.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala b/hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala rename to hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EBoolean.scala b/hail/hail/src/is/hail/types/encoded/EBoolean.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EBoolean.scala rename to hail/hail/src/is/hail/types/encoded/EBoolean.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EContainer.scala b/hail/hail/src/is/hail/types/encoded/EContainer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EContainer.scala rename to hail/hail/src/is/hail/types/encoded/EContainer.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala b/hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala rename to hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EFloat32.scala b/hail/hail/src/is/hail/types/encoded/EFloat32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EFloat32.scala rename to hail/hail/src/is/hail/types/encoded/EFloat32.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EFloat64.scala b/hail/hail/src/is/hail/types/encoded/EFloat64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EFloat64.scala rename to hail/hail/src/is/hail/types/encoded/EFloat64.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EInt32.scala b/hail/hail/src/is/hail/types/encoded/EInt32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EInt32.scala rename to hail/hail/src/is/hail/types/encoded/EInt32.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EInt64.scala b/hail/hail/src/is/hail/types/encoded/EInt64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EInt64.scala rename to hail/hail/src/is/hail/types/encoded/EInt64.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala b/hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala rename to hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala b/hail/hail/src/is/hail/types/encoded/ENumpyBinaryNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala rename to hail/hail/src/is/hail/types/encoded/ENumpyBinaryNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/ERNGState.scala b/hail/hail/src/is/hail/types/encoded/ERNGState.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/ERNGState.scala rename to hail/hail/src/is/hail/types/encoded/ERNGState.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala b/hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala rename to hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EType.scala b/hail/hail/src/is/hail/types/encoded/EType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EType.scala rename to hail/hail/src/is/hail/types/encoded/EType.scala diff --git a/hail/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala b/hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala rename to hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala diff --git a/hail/src/main/scala/is/hail/types/package.scala b/hail/hail/src/is/hail/types/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/package.scala rename to hail/hail/src/is/hail/types/package.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PArray.scala b/hail/hail/src/is/hail/types/physical/PArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PArray.scala rename to hail/hail/src/is/hail/types/physical/PArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala b/hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala rename to hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PBaseStruct.scala b/hail/hail/src/is/hail/types/physical/PBaseStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PBaseStruct.scala rename to hail/hail/src/is/hail/types/physical/PBaseStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PBinary.scala b/hail/hail/src/is/hail/types/physical/PBinary.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PBinary.scala rename to hail/hail/src/is/hail/types/physical/PBinary.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PBoolean.scala b/hail/hail/src/is/hail/types/physical/PBoolean.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PBoolean.scala rename to hail/hail/src/is/hail/types/physical/PBoolean.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCall.scala b/hail/hail/src/is/hail/types/physical/PCall.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCall.scala rename to hail/hail/src/is/hail/types/physical/PCall.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalArray.scala b/hail/hail/src/is/hail/types/physical/PCanonicalArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalArray.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala b/hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala b/hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalCall.scala b/hail/hail/src/is/hail/types/physical/PCanonicalCall.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalCall.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalCall.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalDict.scala b/hail/hail/src/is/hail/types/physical/PCanonicalDict.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalDict.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalDict.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala b/hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala b/hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala b/hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalSet.scala b/hail/hail/src/is/hail/types/physical/PCanonicalSet.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalSet.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalSet.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalString.scala b/hail/hail/src/is/hail/types/physical/PCanonicalString.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalString.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalString.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala b/hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala b/hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala rename to hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PContainer.scala b/hail/hail/src/is/hail/types/physical/PContainer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PContainer.scala rename to hail/hail/src/is/hail/types/physical/PContainer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PDict.scala b/hail/hail/src/is/hail/types/physical/PDict.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PDict.scala rename to hail/hail/src/is/hail/types/physical/PDict.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PField.scala b/hail/hail/src/is/hail/types/physical/PField.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PField.scala rename to hail/hail/src/is/hail/types/physical/PField.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PFloat32.scala b/hail/hail/src/is/hail/types/physical/PFloat32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PFloat32.scala rename to hail/hail/src/is/hail/types/physical/PFloat32.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PFloat64.scala b/hail/hail/src/is/hail/types/physical/PFloat64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PFloat64.scala rename to hail/hail/src/is/hail/types/physical/PFloat64.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PInt32.scala b/hail/hail/src/is/hail/types/physical/PInt32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PInt32.scala rename to hail/hail/src/is/hail/types/physical/PInt32.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PInt64.scala b/hail/hail/src/is/hail/types/physical/PInt64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PInt64.scala rename to hail/hail/src/is/hail/types/physical/PInt64.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PInterval.scala b/hail/hail/src/is/hail/types/physical/PInterval.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PInterval.scala rename to hail/hail/src/is/hail/types/physical/PInterval.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PIterable.scala b/hail/hail/src/is/hail/types/physical/PIterable.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PIterable.scala rename to hail/hail/src/is/hail/types/physical/PIterable.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PLocus.scala b/hail/hail/src/is/hail/types/physical/PLocus.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PLocus.scala rename to hail/hail/src/is/hail/types/physical/PLocus.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PNDArray.scala b/hail/hail/src/is/hail/types/physical/PNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PNDArray.scala rename to hail/hail/src/is/hail/types/physical/PNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PNumeric.scala b/hail/hail/src/is/hail/types/physical/PNumeric.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PNumeric.scala rename to hail/hail/src/is/hail/types/physical/PNumeric.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PPrimitive.scala b/hail/hail/src/is/hail/types/physical/PPrimitive.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PPrimitive.scala rename to hail/hail/src/is/hail/types/physical/PPrimitive.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PSet.scala b/hail/hail/src/is/hail/types/physical/PSet.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PSet.scala rename to hail/hail/src/is/hail/types/physical/PSet.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PString.scala b/hail/hail/src/is/hail/types/physical/PString.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PString.scala rename to hail/hail/src/is/hail/types/physical/PString.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PStruct.scala b/hail/hail/src/is/hail/types/physical/PStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PStruct.scala rename to hail/hail/src/is/hail/types/physical/PStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PSubsetStruct.scala b/hail/hail/src/is/hail/types/physical/PSubsetStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PSubsetStruct.scala rename to hail/hail/src/is/hail/types/physical/PSubsetStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PTuple.scala b/hail/hail/src/is/hail/types/physical/PTuple.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PTuple.scala rename to hail/hail/src/is/hail/types/physical/PTuple.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PType.scala b/hail/hail/src/is/hail/types/physical/PType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PType.scala rename to hail/hail/src/is/hail/types/physical/PType.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PUnrealizable.scala b/hail/hail/src/is/hail/types/physical/PUnrealizable.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PUnrealizable.scala rename to hail/hail/src/is/hail/types/physical/PUnrealizable.scala diff --git a/hail/src/main/scala/is/hail/types/physical/PVoid.scala b/hail/hail/src/is/hail/types/physical/PVoid.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/PVoid.scala rename to hail/hail/src/is/hail/types/physical/PVoid.scala diff --git a/hail/src/main/scala/is/hail/types/physical/StoredSTypePType.scala b/hail/hail/src/is/hail/types/physical/StoredSTypePType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/StoredSTypePType.scala rename to hail/hail/src/is/hail/types/physical/StoredSTypePType.scala diff --git a/hail/src/main/scala/is/hail/types/physical/package.scala b/hail/hail/src/is/hail/types/physical/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/package.scala rename to hail/hail/src/is/hail/types/physical/package.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SCode.scala b/hail/hail/src/is/hail/types/physical/stypes/SCode.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/SCode.scala rename to hail/hail/src/is/hail/types/physical/stypes/SCode.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SType.scala b/hail/hail/src/is/hail/types/physical/stypes/SType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/SType.scala rename to hail/hail/src/is/hail/types/physical/stypes/SType.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala b/hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala rename to hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala rename to hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBinary.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SBinary.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SCall.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SCall.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SLocus.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SLocus.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SString.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SString.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala rename to hail/hail/src/is/hail/types/physical/stypes/interfaces/package.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala rename to hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala b/hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala rename to hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/Field.scala b/hail/hail/src/is/hail/types/virtual/Field.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/Field.scala rename to hail/hail/src/is/hail/types/virtual/Field.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/MatrixType.scala b/hail/hail/src/is/hail/types/virtual/MatrixType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/MatrixType.scala rename to hail/hail/src/is/hail/types/virtual/MatrixType.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TArray.scala b/hail/hail/src/is/hail/types/virtual/TArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TArray.scala rename to hail/hail/src/is/hail/types/virtual/TArray.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TBaseStruct.scala b/hail/hail/src/is/hail/types/virtual/TBaseStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TBaseStruct.scala rename to hail/hail/src/is/hail/types/virtual/TBaseStruct.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TBinary.scala b/hail/hail/src/is/hail/types/virtual/TBinary.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TBinary.scala rename to hail/hail/src/is/hail/types/virtual/TBinary.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TBoolean.scala b/hail/hail/src/is/hail/types/virtual/TBoolean.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TBoolean.scala rename to hail/hail/src/is/hail/types/virtual/TBoolean.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TCall.scala b/hail/hail/src/is/hail/types/virtual/TCall.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TCall.scala rename to hail/hail/src/is/hail/types/virtual/TCall.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TContainer.scala b/hail/hail/src/is/hail/types/virtual/TContainer.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TContainer.scala rename to hail/hail/src/is/hail/types/virtual/TContainer.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TDict.scala b/hail/hail/src/is/hail/types/virtual/TDict.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TDict.scala rename to hail/hail/src/is/hail/types/virtual/TDict.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TFloat32.scala b/hail/hail/src/is/hail/types/virtual/TFloat32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TFloat32.scala rename to hail/hail/src/is/hail/types/virtual/TFloat32.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TFloat64.scala b/hail/hail/src/is/hail/types/virtual/TFloat64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TFloat64.scala rename to hail/hail/src/is/hail/types/virtual/TFloat64.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TInt32.scala b/hail/hail/src/is/hail/types/virtual/TInt32.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TInt32.scala rename to hail/hail/src/is/hail/types/virtual/TInt32.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TInt64.scala b/hail/hail/src/is/hail/types/virtual/TInt64.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TInt64.scala rename to hail/hail/src/is/hail/types/virtual/TInt64.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TIntegral.scala b/hail/hail/src/is/hail/types/virtual/TIntegral.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TIntegral.scala rename to hail/hail/src/is/hail/types/virtual/TIntegral.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TInterval.scala b/hail/hail/src/is/hail/types/virtual/TInterval.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TInterval.scala rename to hail/hail/src/is/hail/types/virtual/TInterval.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TIterable.scala b/hail/hail/src/is/hail/types/virtual/TIterable.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TIterable.scala rename to hail/hail/src/is/hail/types/virtual/TIterable.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TLocus.scala b/hail/hail/src/is/hail/types/virtual/TLocus.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TLocus.scala rename to hail/hail/src/is/hail/types/virtual/TLocus.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TNDArray.scala b/hail/hail/src/is/hail/types/virtual/TNDArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TNDArray.scala rename to hail/hail/src/is/hail/types/virtual/TNDArray.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TNumeric.scala b/hail/hail/src/is/hail/types/virtual/TNumeric.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TNumeric.scala rename to hail/hail/src/is/hail/types/virtual/TNumeric.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TRNGState.scala b/hail/hail/src/is/hail/types/virtual/TRNGState.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TRNGState.scala rename to hail/hail/src/is/hail/types/virtual/TRNGState.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TSet.scala b/hail/hail/src/is/hail/types/virtual/TSet.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TSet.scala rename to hail/hail/src/is/hail/types/virtual/TSet.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TStream.scala b/hail/hail/src/is/hail/types/virtual/TStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TStream.scala rename to hail/hail/src/is/hail/types/virtual/TStream.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TString.scala b/hail/hail/src/is/hail/types/virtual/TString.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TString.scala rename to hail/hail/src/is/hail/types/virtual/TString.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TStruct.scala b/hail/hail/src/is/hail/types/virtual/TStruct.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TStruct.scala rename to hail/hail/src/is/hail/types/virtual/TStruct.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TTuple.scala b/hail/hail/src/is/hail/types/virtual/TTuple.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TTuple.scala rename to hail/hail/src/is/hail/types/virtual/TTuple.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TUnion.scala b/hail/hail/src/is/hail/types/virtual/TUnion.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TUnion.scala rename to hail/hail/src/is/hail/types/virtual/TUnion.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TVariable.scala b/hail/hail/src/is/hail/types/virtual/TVariable.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TVariable.scala rename to hail/hail/src/is/hail/types/virtual/TVariable.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TVoid.scala b/hail/hail/src/is/hail/types/virtual/TVoid.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TVoid.scala rename to hail/hail/src/is/hail/types/virtual/TVoid.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/TableType.scala b/hail/hail/src/is/hail/types/virtual/TableType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/TableType.scala rename to hail/hail/src/is/hail/types/virtual/TableType.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/Type.scala b/hail/hail/src/is/hail/types/virtual/Type.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/Type.scala rename to hail/hail/src/is/hail/types/virtual/Type.scala diff --git a/hail/src/main/scala/is/hail/types/virtual/VType.scala b/hail/hail/src/is/hail/types/virtual/VType.scala similarity index 100% rename from hail/src/main/scala/is/hail/types/virtual/VType.scala rename to hail/hail/src/is/hail/types/virtual/VType.scala diff --git a/hail/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala b/hail/hail/src/is/hail/utils/AbsoluteFuzzyComparable.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala rename to hail/hail/src/is/hail/utils/AbsoluteFuzzyComparable.scala diff --git a/hail/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala b/hail/hail/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala rename to hail/hail/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/ArrayStack.scala b/hail/hail/src/is/hail/utils/ArrayStack.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ArrayStack.scala rename to hail/hail/src/is/hail/utils/ArrayStack.scala diff --git a/hail/src/main/scala/is/hail/utils/BinaryHeap.scala b/hail/hail/src/is/hail/utils/BinaryHeap.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/BinaryHeap.scala rename to hail/hail/src/is/hail/utils/BinaryHeap.scala diff --git a/hail/src/main/scala/is/hail/utils/BitVector.scala b/hail/hail/src/is/hail/utils/BitVector.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/BitVector.scala rename to hail/hail/src/is/hail/utils/BitVector.scala diff --git a/hail/src/main/scala/is/hail/utils/Bitstring.scala b/hail/hail/src/is/hail/utils/Bitstring.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Bitstring.scala rename to hail/hail/src/is/hail/utils/Bitstring.scala diff --git a/hail/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala b/hail/hail/src/is/hail/utils/BoxedArrayBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala rename to hail/hail/src/is/hail/utils/BoxedArrayBuilder.scala diff --git a/hail/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala b/hail/hail/src/is/hail/utils/BufferedAggregatorIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala rename to hail/hail/src/is/hail/utils/BufferedAggregatorIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/BytePacker.scala b/hail/hail/src/is/hail/utils/BytePacker.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/BytePacker.scala rename to hail/hail/src/is/hail/utils/BytePacker.scala diff --git a/hail/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala b/hail/hail/src/is/hail/utils/ByteTrackingInputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala rename to hail/hail/src/is/hail/utils/ByteTrackingInputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/Cache.scala b/hail/hail/src/is/hail/utils/Cache.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Cache.scala rename to hail/hail/src/is/hail/utils/Cache.scala diff --git a/hail/src/main/scala/is/hail/utils/CompressionUtils.scala b/hail/hail/src/is/hail/utils/CompressionUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/CompressionUtils.scala rename to hail/hail/src/is/hail/utils/CompressionUtils.scala diff --git a/hail/src/main/scala/is/hail/utils/Context.scala b/hail/hail/src/is/hail/utils/Context.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Context.scala rename to hail/hail/src/is/hail/utils/Context.scala diff --git a/hail/src/main/scala/is/hail/utils/DateFormatUtils.scala b/hail/hail/src/is/hail/utils/DateFormatUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/DateFormatUtils.scala rename to hail/hail/src/is/hail/utils/DateFormatUtils.scala diff --git a/hail/src/main/scala/is/hail/utils/DoubleNumericConversion.scala b/hail/hail/src/is/hail/utils/DoubleNumericConversion.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/DoubleNumericConversion.scala rename to hail/hail/src/is/hail/utils/DoubleNumericConversion.scala diff --git a/hail/src/main/scala/is/hail/utils/EitherIsAMonad.scala b/hail/hail/src/is/hail/utils/EitherIsAMonad.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/EitherIsAMonad.scala rename to hail/hail/src/is/hail/utils/EitherIsAMonad.scala diff --git a/hail/src/main/scala/is/hail/utils/ErrorHandling.scala b/hail/hail/src/is/hail/utils/ErrorHandling.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ErrorHandling.scala rename to hail/hail/src/is/hail/utils/ErrorHandling.scala diff --git a/hail/src/main/scala/is/hail/utils/ExecutionTimer.scala b/hail/hail/src/is/hail/utils/ExecutionTimer.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ExecutionTimer.scala rename to hail/hail/src/is/hail/utils/ExecutionTimer.scala diff --git a/hail/src/main/scala/is/hail/utils/ExportType.scala b/hail/hail/src/is/hail/utils/ExportType.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ExportType.scala rename to hail/hail/src/is/hail/utils/ExportType.scala diff --git a/hail/src/main/scala/is/hail/utils/FastSeq.scala b/hail/hail/src/is/hail/utils/FastSeq.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/FastSeq.scala rename to hail/hail/src/is/hail/utils/FastSeq.scala diff --git a/hail/src/main/scala/is/hail/utils/FlipbookIterator.scala b/hail/hail/src/is/hail/utils/FlipbookIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/FlipbookIterator.scala rename to hail/hail/src/is/hail/utils/FlipbookIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/Graph.scala b/hail/hail/src/is/hail/utils/Graph.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Graph.scala rename to hail/hail/src/is/hail/utils/Graph.scala diff --git a/hail/src/main/scala/is/hail/utils/HTTPClient.scala b/hail/hail/src/is/hail/utils/HTTPClient.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/HTTPClient.scala rename to hail/hail/src/is/hail/utils/HTTPClient.scala diff --git a/hail/src/main/scala/is/hail/utils/HailIterator.scala b/hail/hail/src/is/hail/utils/HailIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/HailIterator.scala rename to hail/hail/src/is/hail/utils/HailIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/HashMethods.scala b/hail/hail/src/is/hail/utils/HashMethods.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/HashMethods.scala rename to hail/hail/src/is/hail/utils/HashMethods.scala diff --git a/hail/src/main/scala/is/hail/utils/Interval.scala b/hail/hail/src/is/hail/utils/Interval.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Interval.scala rename to hail/hail/src/is/hail/utils/Interval.scala diff --git a/hail/src/main/scala/is/hail/utils/JSON.scala b/hail/hail/src/is/hail/utils/JSON.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/JSON.scala rename to hail/hail/src/is/hail/utils/JSON.scala diff --git a/hail/src/main/scala/is/hail/utils/LoggerOutputStream.scala b/hail/hail/src/is/hail/utils/LoggerOutputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/LoggerOutputStream.scala rename to hail/hail/src/is/hail/utils/LoggerOutputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/Logging.scala b/hail/hail/src/is/hail/utils/Logging.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Logging.scala rename to hail/hail/src/is/hail/utils/Logging.scala diff --git a/hail/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala b/hail/hail/src/is/hail/utils/MemoryBufferWrapper.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala rename to hail/hail/src/is/hail/utils/MemoryBufferWrapper.scala diff --git a/hail/src/main/scala/is/hail/utils/MissingArrayBuilder.scala b/hail/hail/src/is/hail/utils/MissingArrayBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/MissingArrayBuilder.scala rename to hail/hail/src/is/hail/utils/MissingArrayBuilder.scala diff --git a/hail/src/main/scala/is/hail/utils/MultiArray2.scala b/hail/hail/src/is/hail/utils/MultiArray2.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/MultiArray2.scala rename to hail/hail/src/is/hail/utils/MultiArray2.scala diff --git a/hail/src/main/scala/is/hail/utils/Muple.scala b/hail/hail/src/is/hail/utils/Muple.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Muple.scala rename to hail/hail/src/is/hail/utils/Muple.scala diff --git a/hail/src/main/scala/is/hail/utils/NumericImplicits.scala b/hail/hail/src/is/hail/utils/NumericImplicits.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/NumericImplicits.scala rename to hail/hail/src/is/hail/utils/NumericImplicits.scala diff --git a/hail/src/main/scala/is/hail/utils/NumericPair.scala b/hail/hail/src/is/hail/utils/NumericPair.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/NumericPair.scala rename to hail/hail/src/is/hail/utils/NumericPair.scala diff --git a/hail/src/main/scala/is/hail/utils/OrderingView.scala b/hail/hail/src/is/hail/utils/OrderingView.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/OrderingView.scala rename to hail/hail/src/is/hail/utils/OrderingView.scala diff --git a/hail/src/main/scala/is/hail/utils/ParseTrieNode.scala b/hail/hail/src/is/hail/utils/ParseTrieNode.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/ParseTrieNode.scala rename to hail/hail/src/is/hail/utils/ParseTrieNode.scala diff --git a/hail/src/main/scala/is/hail/utils/PartitionCounts.scala b/hail/hail/src/is/hail/utils/PartitionCounts.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/PartitionCounts.scala rename to hail/hail/src/is/hail/utils/PartitionCounts.scala diff --git a/hail/src/main/scala/is/hail/utils/Py4jUtils.scala b/hail/hail/src/is/hail/utils/Py4jUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Py4jUtils.scala rename to hail/hail/src/is/hail/utils/Py4jUtils.scala diff --git a/hail/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala b/hail/hail/src/is/hail/utils/RelativeFuzzyComparable.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala rename to hail/hail/src/is/hail/utils/RelativeFuzzyComparable.scala diff --git a/hail/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala b/hail/hail/src/is/hail/utils/RestartableByteArrayInputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala rename to hail/hail/src/is/hail/utils/RestartableByteArrayInputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/SemanticVersion.scala b/hail/hail/src/is/hail/utils/SemanticVersion.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/SemanticVersion.scala rename to hail/hail/src/is/hail/utils/SemanticVersion.scala diff --git a/hail/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala b/hail/hail/src/is/hail/utils/SerializableHadoopConfiguration.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala rename to hail/hail/src/is/hail/utils/SerializableHadoopConfiguration.scala diff --git a/hail/src/main/scala/is/hail/utils/SpillingCollectIterator.scala b/hail/hail/src/is/hail/utils/SpillingCollectIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/SpillingCollectIterator.scala rename to hail/hail/src/is/hail/utils/SpillingCollectIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/StackSafe.scala b/hail/hail/src/is/hail/utils/StackSafe.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/StackSafe.scala rename to hail/hail/src/is/hail/utils/StackSafe.scala diff --git a/hail/src/main/scala/is/hail/utils/StringEscapeUtils.scala b/hail/hail/src/is/hail/utils/StringEscapeUtils.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/StringEscapeUtils.scala rename to hail/hail/src/is/hail/utils/StringEscapeUtils.scala diff --git a/hail/src/main/scala/is/hail/utils/StringSocketAppender.scala b/hail/hail/src/is/hail/utils/StringSocketAppender.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/StringSocketAppender.scala rename to hail/hail/src/is/hail/utils/StringSocketAppender.scala diff --git a/hail/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala b/hail/hail/src/is/hail/utils/TextInputFilterAndReplace.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala rename to hail/hail/src/is/hail/utils/TextInputFilterAndReplace.scala diff --git a/hail/src/main/scala/is/hail/utils/Traceback.scala b/hail/hail/src/is/hail/utils/Traceback.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/Traceback.scala rename to hail/hail/src/is/hail/utils/Traceback.scala diff --git a/hail/src/main/scala/is/hail/utils/TracingInputStream.scala b/hail/hail/src/is/hail/utils/TracingInputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TracingInputStream.scala rename to hail/hail/src/is/hail/utils/TracingInputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/TracingOutputStream.scala b/hail/hail/src/is/hail/utils/TracingOutputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TracingOutputStream.scala rename to hail/hail/src/is/hail/utils/TracingOutputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/TreeTraversal.scala b/hail/hail/src/is/hail/utils/TreeTraversal.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TreeTraversal.scala rename to hail/hail/src/is/hail/utils/TreeTraversal.scala diff --git a/hail/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala b/hail/hail/src/is/hail/utils/TruncatedArrayIndexedSeq.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala rename to hail/hail/src/is/hail/utils/TruncatedArrayIndexedSeq.scala diff --git a/hail/src/main/scala/is/hail/utils/TryAll.scala b/hail/hail/src/is/hail/utils/TryAll.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/TryAll.scala rename to hail/hail/src/is/hail/utils/TryAll.scala diff --git a/hail/src/main/scala/is/hail/utils/UnionFind.scala b/hail/hail/src/is/hail/utils/UnionFind.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/UnionFind.scala rename to hail/hail/src/is/hail/utils/UnionFind.scala diff --git a/hail/src/main/scala/is/hail/utils/package.scala b/hail/hail/src/is/hail/utils/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/package.scala rename to hail/hail/src/is/hail/utils/package.scala diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala b/hail/hail/src/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala rename to hail/hail/src/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala b/hail/hail/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala rename to hail/hail/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/package.scala b/hail/hail/src/is/hail/utils/prettyPrint/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/prettyPrint/package.scala rename to hail/hail/src/is/hail/utils/prettyPrint/package.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala b/hail/hail/src/is/hail/utils/richUtils/ByteTrackingOutputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala rename to hail/hail/src/is/hail/utils/richUtils/ByteTrackingOutputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/Implicits.scala b/hail/hail/src/is/hail/utils/richUtils/Implicits.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/Implicits.scala rename to hail/hail/src/is/hail/utils/richUtils/Implicits.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichArray.scala b/hail/hail/src/is/hail/utils/richUtils/RichArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichArray.scala rename to hail/hail/src/is/hail/utils/richUtils/RichArray.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala b/hail/hail/src/is/hail/utils/richUtils/RichBoolean.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala rename to hail/hail/src/is/hail/utils/richUtils/RichBoolean.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala b/hail/hail/src/is/hail/utils/richUtils/RichCodeInputBuffer.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala rename to hail/hail/src/is/hail/utils/richUtils/RichCodeInputBuffer.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala b/hail/hail/src/is/hail/utils/richUtils/RichCodeIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala rename to hail/hail/src/is/hail/utils/richUtils/RichCodeIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala b/hail/hail/src/is/hail/utils/richUtils/RichCodeOutputBuffer.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala rename to hail/hail/src/is/hail/utils/richUtils/RichCodeOutputBuffer.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala b/hail/hail/src/is/hail/utils/richUtils/RichCodeRegion.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala rename to hail/hail/src/is/hail/utils/richUtils/RichCodeRegion.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala b/hail/hail/src/is/hail/utils/richUtils/RichContextIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala rename to hail/hail/src/is/hail/utils/richUtils/RichContextIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala b/hail/hail/src/is/hail/utils/richUtils/RichContextRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala rename to hail/hail/src/is/hail/utils/richUtils/RichContextRDD.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala b/hail/hail/src/is/hail/utils/richUtils/RichContextRDDRow.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala rename to hail/hail/src/is/hail/utils/richUtils/RichContextRDDRow.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala b/hail/hail/src/is/hail/utils/richUtils/RichDenseMatrixDouble.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala rename to hail/hail/src/is/hail/utils/richUtils/RichDenseMatrixDouble.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala b/hail/hail/src/is/hail/utils/richUtils/RichEnumeration.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala rename to hail/hail/src/is/hail/utils/richUtils/RichEnumeration.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala b/hail/hail/src/is/hail/utils/richUtils/RichIndexedRowMatrix.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala rename to hail/hail/src/is/hail/utils/richUtils/RichIndexedRowMatrix.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIndexedSeq.scala b/hail/hail/src/is/hail/utils/richUtils/RichIndexedSeq.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichIndexedSeq.scala rename to hail/hail/src/is/hail/utils/richUtils/RichIndexedSeq.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichInputStream.scala b/hail/hail/src/is/hail/utils/richUtils/RichInputStream.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichInputStream.scala rename to hail/hail/src/is/hail/utils/richUtils/RichInputStream.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIntPairTraversableOnce.scala b/hail/hail/src/is/hail/utils/richUtils/RichIntPairTraversableOnce.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichIntPairTraversableOnce.scala rename to hail/hail/src/is/hail/utils/richUtils/RichIntPairTraversableOnce.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIterable.scala b/hail/hail/src/is/hail/utils/richUtils/RichIterable.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichIterable.scala rename to hail/hail/src/is/hail/utils/richUtils/RichIterable.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIterator.scala b/hail/hail/src/is/hail/utils/richUtils/RichIterator.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichIterator.scala rename to hail/hail/src/is/hail/utils/richUtils/RichIterator.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichJoinedRegionValue.scala b/hail/hail/src/is/hail/utils/richUtils/RichJoinedRegionValue.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichJoinedRegionValue.scala rename to hail/hail/src/is/hail/utils/richUtils/RichJoinedRegionValue.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichMap.scala b/hail/hail/src/is/hail/utils/richUtils/RichMap.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichMap.scala rename to hail/hail/src/is/hail/utils/richUtils/RichMap.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichMultiArray2Numeric.scala b/hail/hail/src/is/hail/utils/richUtils/RichMultiArray2Numeric.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichMultiArray2Numeric.scala rename to hail/hail/src/is/hail/utils/richUtils/RichMultiArray2Numeric.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichMutableMap.scala b/hail/hail/src/is/hail/utils/richUtils/RichMutableMap.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichMutableMap.scala rename to hail/hail/src/is/hail/utils/richUtils/RichMutableMap.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichOption.scala b/hail/hail/src/is/hail/utils/richUtils/RichOption.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichOption.scala rename to hail/hail/src/is/hail/utils/richUtils/RichOption.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichOrderedArray.scala b/hail/hail/src/is/hail/utils/richUtils/RichOrderedArray.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichOrderedArray.scala rename to hail/hail/src/is/hail/utils/richUtils/RichOrderedArray.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichOrderedSeq.scala b/hail/hail/src/is/hail/utils/richUtils/RichOrderedSeq.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichOrderedSeq.scala rename to hail/hail/src/is/hail/utils/richUtils/RichOrderedSeq.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichPairRDD.scala b/hail/hail/src/is/hail/utils/richUtils/RichPairRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichPairRDD.scala rename to hail/hail/src/is/hail/utils/richUtils/RichPairRDD.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala b/hail/hail/src/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala rename to hail/hail/src/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichRDD.scala b/hail/hail/src/is/hail/utils/richUtils/RichRDD.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichRDD.scala rename to hail/hail/src/is/hail/utils/richUtils/RichRDD.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichRegex.scala b/hail/hail/src/is/hail/utils/richUtils/RichRegex.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichRegex.scala rename to hail/hail/src/is/hail/utils/richUtils/RichRegex.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichRow.scala b/hail/hail/src/is/hail/utils/richUtils/RichRow.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichRow.scala rename to hail/hail/src/is/hail/utils/richUtils/RichRow.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichSparkContext.scala b/hail/hail/src/is/hail/utils/richUtils/RichSparkContext.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichSparkContext.scala rename to hail/hail/src/is/hail/utils/richUtils/RichSparkContext.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichString.scala b/hail/hail/src/is/hail/utils/richUtils/RichString.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichString.scala rename to hail/hail/src/is/hail/utils/richUtils/RichString.scala diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichStringBuilder.scala b/hail/hail/src/is/hail/utils/richUtils/RichStringBuilder.scala similarity index 100% rename from hail/src/main/scala/is/hail/utils/richUtils/RichStringBuilder.scala rename to hail/hail/src/is/hail/utils/richUtils/RichStringBuilder.scala diff --git a/hail/src/main/scala/is/hail/variant/Call.scala b/hail/hail/src/is/hail/variant/Call.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/Call.scala rename to hail/hail/src/is/hail/variant/Call.scala diff --git a/hail/src/main/scala/is/hail/variant/Genotype.scala b/hail/hail/src/is/hail/variant/Genotype.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/Genotype.scala rename to hail/hail/src/is/hail/variant/Genotype.scala diff --git a/hail/src/main/scala/is/hail/variant/HardCallView.scala b/hail/hail/src/is/hail/variant/HardCallView.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/HardCallView.scala rename to hail/hail/src/is/hail/variant/HardCallView.scala diff --git a/hail/src/main/scala/is/hail/variant/Locus.scala b/hail/hail/src/is/hail/variant/Locus.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/Locus.scala rename to hail/hail/src/is/hail/variant/Locus.scala diff --git a/hail/src/main/scala/is/hail/variant/ReferenceGenome.scala b/hail/hail/src/is/hail/variant/ReferenceGenome.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/ReferenceGenome.scala rename to hail/hail/src/is/hail/variant/ReferenceGenome.scala diff --git a/hail/src/main/scala/is/hail/variant/RegionValueVariant.scala b/hail/hail/src/is/hail/variant/RegionValueVariant.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/RegionValueVariant.scala rename to hail/hail/src/is/hail/variant/RegionValueVariant.scala diff --git a/hail/src/main/scala/is/hail/variant/Sex.scala b/hail/hail/src/is/hail/variant/Sex.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/Sex.scala rename to hail/hail/src/is/hail/variant/Sex.scala diff --git a/hail/src/main/scala/is/hail/variant/VariantMethods.scala b/hail/hail/src/is/hail/variant/VariantMethods.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/VariantMethods.scala rename to hail/hail/src/is/hail/variant/VariantMethods.scala diff --git a/hail/src/main/scala/is/hail/variant/View.scala b/hail/hail/src/is/hail/variant/View.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/View.scala rename to hail/hail/src/is/hail/variant/View.scala diff --git a/hail/src/main/scala/is/hail/variant/package.scala b/hail/hail/src/is/hail/variant/package.scala similarity index 100% rename from hail/src/main/scala/is/hail/variant/package.scala rename to hail/hail/src/is/hail/variant/package.scala diff --git a/hail/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java b/hail/hail/src/java/is/hail/expr/ir/MatrixWriterConstants.java similarity index 100% rename from hail/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java rename to hail/hail/src/java/is/hail/expr/ir/MatrixWriterConstants.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodec.java b/hail/hail/src/java/is/hail/io/compress/BGzipCodec.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipCodec.java rename to hail/hail/src/java/is/hail/io/compress/BGzipCodec.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodecGZ.java b/hail/hail/src/java/is/hail/io/compress/BGzipCodecGZ.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipCodecGZ.java rename to hail/hail/src/java/is/hail/io/compress/BGzipCodecGZ.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodecTbi.java b/hail/hail/src/java/is/hail/io/compress/BGzipCodecTbi.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipCodecTbi.java rename to hail/hail/src/java/is/hail/io/compress/BGzipCodecTbi.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipConstants.java b/hail/hail/src/java/is/hail/io/compress/BGzipConstants.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipConstants.java rename to hail/hail/src/java/is/hail/io/compress/BGzipConstants.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipInputStream.java b/hail/hail/src/java/is/hail/io/compress/BGzipInputStream.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipInputStream.java rename to hail/hail/src/java/is/hail/io/compress/BGzipInputStream.java diff --git a/hail/src/main/java/is/hail/io/compress/BGzipOutputStream.java b/hail/hail/src/java/is/hail/io/compress/BGzipOutputStream.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/BGzipOutputStream.java rename to hail/hail/src/java/is/hail/io/compress/BGzipOutputStream.java diff --git a/hail/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java b/hail/hail/src/java/is/hail/io/compress/ComposableBGzipCodec.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java rename to hail/hail/src/java/is/hail/io/compress/ComposableBGzipCodec.java diff --git a/hail/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java b/hail/hail/src/java/is/hail/io/compress/ComposableBGzipOutputStream.java similarity index 100% rename from hail/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java rename to hail/hail/src/java/is/hail/io/compress/ComposableBGzipOutputStream.java diff --git a/hail/src/main/java/is/hail/io/fs/Positioned.java b/hail/hail/src/java/is/hail/io/fs/Positioned.java similarity index 100% rename from hail/src/main/java/is/hail/io/fs/Positioned.java rename to hail/hail/src/java/is/hail/io/fs/Positioned.java diff --git a/hail/src/main/java/is/hail/io/fs/Seekable.java b/hail/hail/src/java/is/hail/io/fs/Seekable.java similarity index 100% rename from hail/src/main/java/is/hail/io/fs/Seekable.java rename to hail/hail/src/java/is/hail/io/fs/Seekable.java diff --git a/hail/src/main/scala/org/apache/spark/ExposedMetrics.scala b/hail/hail/src/org/apache/spark/ExposedMetrics.scala similarity index 100% rename from hail/src/main/scala/org/apache/spark/ExposedMetrics.scala rename to hail/hail/src/org/apache/spark/ExposedMetrics.scala diff --git a/hail/src/main/scala/org/apache/spark/ExposedUtils.scala b/hail/hail/src/org/apache/spark/ExposedUtils.scala similarity index 100% rename from hail/src/main/scala/org/apache/spark/ExposedUtils.scala rename to hail/hail/src/org/apache/spark/ExposedUtils.scala diff --git a/hail/src/main/scala/org/apache/spark/ProgressBarBuilder.scala b/hail/hail/src/org/apache/spark/ProgressBarBuilder.scala similarity index 100% rename from hail/src/main/scala/org/apache/spark/ProgressBarBuilder.scala rename to hail/hail/src/org/apache/spark/ProgressBarBuilder.scala diff --git 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similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/parts/part-0 b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/parts/part-0 similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/parts/part-0 rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/cols/rows/parts/part-0 diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/_SUCCESS b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/_SUCCESS similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/_SUCCESS rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/_SUCCESS diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/entries/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/_SUCCESS b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/_SUCCESS similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/_SUCCESS rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/_SUCCESS diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/parts/part-0 b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/parts/part-0 similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/parts/part-0 rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/globals/parts/part-0 diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/parts/part-0 b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/parts/part-0 similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/parts/part-0 rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/globals/rows/parts/part-0 diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/_SUCCESS b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/_SUCCESS similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/_SUCCESS rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/_SUCCESS diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 b/hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 similarity index 100% rename from hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 rename to hail/hail/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 diff --git a/hail/src/test/resources/vep_grch38_input_req_indexed_cache.tsv b/hail/hail/test/resources/vep_grch38_input_req_indexed_cache.tsv similarity index 100% rename from hail/src/test/resources/vep_grch38_input_req_indexed_cache.tsv rename to hail/hail/test/resources/vep_grch38_input_req_indexed_cache.tsv diff --git a/hail/src/test/resources/width_scale_tests/1024.tsv b/hail/hail/test/resources/width_scale_tests/1024.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/1024.tsv rename to hail/hail/test/resources/width_scale_tests/1024.tsv diff --git a/hail/src/test/resources/width_scale_tests/16384.tsv b/hail/hail/test/resources/width_scale_tests/16384.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/16384.tsv rename to hail/hail/test/resources/width_scale_tests/16384.tsv diff --git a/hail/src/test/resources/width_scale_tests/2048.tsv b/hail/hail/test/resources/width_scale_tests/2048.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/2048.tsv rename to hail/hail/test/resources/width_scale_tests/2048.tsv diff --git a/hail/src/test/resources/width_scale_tests/256.tsv b/hail/hail/test/resources/width_scale_tests/256.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/256.tsv rename to hail/hail/test/resources/width_scale_tests/256.tsv diff --git a/hail/src/test/resources/width_scale_tests/3072.tsv b/hail/hail/test/resources/width_scale_tests/3072.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/3072.tsv rename to hail/hail/test/resources/width_scale_tests/3072.tsv diff --git a/hail/src/test/resources/width_scale_tests/4096.tsv b/hail/hail/test/resources/width_scale_tests/4096.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/4096.tsv rename to hail/hail/test/resources/width_scale_tests/4096.tsv diff --git a/hail/src/test/resources/width_scale_tests/512.tsv b/hail/hail/test/resources/width_scale_tests/512.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/512.tsv rename to hail/hail/test/resources/width_scale_tests/512.tsv diff --git a/hail/src/test/resources/width_scale_tests/8192.tsv b/hail/hail/test/resources/width_scale_tests/8192.tsv similarity index 100% rename from hail/src/test/resources/width_scale_tests/8192.tsv rename to hail/hail/test/resources/width_scale_tests/8192.tsv diff --git a/hail/src/test/resources/x-chromosome.vcf b/hail/hail/test/resources/x-chromosome.vcf similarity index 100% rename from hail/src/test/resources/x-chromosome.vcf rename to hail/hail/test/resources/x-chromosome.vcf diff --git a/hail/src/test/scala/is/hail/HailContextSuite.scala b/hail/hail/test/src/is/hail/HailContextSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/HailContextSuite.scala rename to hail/hail/test/src/is/hail/HailContextSuite.scala diff --git a/hail/src/test/scala/is/hail/HailSuite.scala b/hail/hail/test/src/is/hail/HailSuite.scala similarity index 99% rename from hail/src/test/scala/is/hail/HailSuite.scala rename to hail/hail/test/src/is/hail/HailSuite.scala index af4da3ce3ff..66a9abbeb03 100644 --- a/hail/src/test/scala/is/hail/HailSuite.scala +++ b/hail/hail/test/src/is/hail/HailSuite.scala @@ -71,7 +71,7 @@ class HailSuite extends TestNGSuite { var pool: RegionPool = _ - def getTestResource(localPath: String): String = s"src/test/resources/$localPath" + def getTestResource(localPath: String): String = s"hail/test/resources/$localPath" @BeforeMethod def setupContext(context: ITestContext): Unit = { diff --git a/hail/src/test/scala/is/hail/LogTestListener.scala b/hail/hail/test/src/is/hail/LogTestListener.scala similarity index 100% rename from hail/src/test/scala/is/hail/LogTestListener.scala rename to hail/hail/test/src/is/hail/LogTestListener.scala diff --git a/hail/src/test/scala/is/hail/TestUtils.scala b/hail/hail/test/src/is/hail/TestUtils.scala similarity index 100% rename from hail/src/test/scala/is/hail/TestUtils.scala rename to hail/hail/test/src/is/hail/TestUtils.scala diff --git a/hail/src/test/scala/is/hail/TestUtilsSuite.scala b/hail/hail/test/src/is/hail/TestUtilsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/TestUtilsSuite.scala rename to hail/hail/test/src/is/hail/TestUtilsSuite.scala diff --git a/hail/src/test/scala/is/hail/annotations/AnnotationsSuite.scala b/hail/hail/test/src/is/hail/annotations/AnnotationsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/AnnotationsSuite.scala rename to hail/hail/test/src/is/hail/annotations/AnnotationsSuite.scala diff --git a/hail/src/test/scala/is/hail/annotations/ApproxCDFAggregatorSuite.scala b/hail/hail/test/src/is/hail/annotations/ApproxCDFAggregatorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/ApproxCDFAggregatorSuite.scala rename to hail/hail/test/src/is/hail/annotations/ApproxCDFAggregatorSuite.scala diff --git a/hail/src/test/scala/is/hail/annotations/RegionSuite.scala b/hail/hail/test/src/is/hail/annotations/RegionSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/RegionSuite.scala rename to hail/hail/test/src/is/hail/annotations/RegionSuite.scala diff --git a/hail/src/test/scala/is/hail/annotations/ScalaToRegionValue.scala b/hail/hail/test/src/is/hail/annotations/ScalaToRegionValue.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/ScalaToRegionValue.scala rename to hail/hail/test/src/is/hail/annotations/ScalaToRegionValue.scala diff --git a/hail/src/test/scala/is/hail/annotations/StagedConstructorSuite.scala b/hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/StagedConstructorSuite.scala rename to hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala diff --git a/hail/src/test/scala/is/hail/annotations/UnsafeSuite.scala b/hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/annotations/UnsafeSuite.scala rename to hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala diff --git a/hail/src/test/scala/is/hail/asm4s/ASM4SSuite.scala b/hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/asm4s/ASM4SSuite.scala rename to hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala diff --git a/hail/src/test/scala/is/hail/asm4s/CodeSuite.scala b/hail/hail/test/src/is/hail/asm4s/CodeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/asm4s/CodeSuite.scala rename to hail/hail/test/src/is/hail/asm4s/CodeSuite.scala diff --git a/hail/src/test/scala/is/hail/asm4s/Foo.java b/hail/hail/test/src/is/hail/asm4s/Foo.java similarity index 100% rename from hail/src/test/scala/is/hail/asm4s/Foo.java rename to hail/hail/test/src/is/hail/asm4s/Foo.java diff --git a/hail/src/test/scala/is/hail/backend/ServiceBackendSuite.scala b/hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/backend/ServiceBackendSuite.scala rename to hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ParserSuite.scala b/hail/hail/test/src/is/hail/expr/ParserSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ParserSuite.scala rename to hail/hail/test/src/is/hail/expr/ParserSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala b/hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala rename to hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/AggregatorsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/AggregatorsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/ArrayDeforestationSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/ArrayDeforestationSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/ArrayFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/ArrayFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/BlockMatrixIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/BlockMatrixIRSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/CallFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/CallFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/CallFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/CallFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/DictFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/DictFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/DistinctlyKeyedSuite.scala b/hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/DistinctlyKeyedSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/EmitStreamSuite.scala b/hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/EmitStreamSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/EncodedLiteralSuite.scala b/hail/hail/test/src/is/hail/expr/ir/EncodedLiteralSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/EncodedLiteralSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/EncodedLiteralSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/FakeTableReader.scala b/hail/hail/test/src/is/hail/expr/ir/FakeTableReader.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/FakeTableReader.scala rename to hail/hail/test/src/is/hail/expr/ir/FakeTableReader.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/FoldConstantsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/FoldConstantsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/ForwardLetsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/ForwardLetsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/FunctionSuite.scala b/hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/FunctionSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/GenotypeFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/GenotypeFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/IRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/IRSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/IRSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/IRSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/IntervalSuite.scala b/hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/IntervalSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/LiftLiteralsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/LiftLiteralsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/LocusFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/LocusFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/LoweringPipelineSuite.scala b/hail/hail/test/src/is/hail/expr/ir/LoweringPipelineSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/LoweringPipelineSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/LoweringPipelineSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/MathFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MathFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/MathFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/MathFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/MatrixIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/MatrixIRSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/MemoryLeakSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/MemoryLeakSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/MissingArrayBuilderSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/MissingArrayBuilderSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/OrderingSuite.scala b/hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/OrderingSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/PruneSuite.scala b/hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/PruneSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/RandomSuite.scala b/hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/RandomSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/RequirednessSuite.scala b/hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/RequirednessSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/SetFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/SetFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/SetFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/SetFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/SimplifySuite.scala b/hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/SimplifySuite.scala rename to hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/StagedBTreeSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/StagedBTreeSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/StagedMinHeapSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/StagedMinHeapSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/StringFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/StringFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/StringLengthSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StringLengthSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/StringLengthSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/StringLengthSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/StringSliceSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/StringSliceSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/TableIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala similarity index 99% rename from hail/src/test/scala/is/hail/expr/ir/TableIRSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala index 5041df1e705..0cde18c3bf1 100644 --- a/hail/src/test/scala/is/hail/expr/ir/TableIRSuite.scala +++ b/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala @@ -672,10 +672,10 @@ class TableIRSuite extends HailSuite { // Catches a bug in the partitioner created by the importer. @Test def testTableJoinOfImport(): Unit = { - val mnr = MatrixNativeReader(fs, "src/test/resources/sample.vcf.mt") + val mnr = MatrixNativeReader(fs, "hail/test/resources/sample.vcf.mt") val mt2 = MatrixRead(mnr.fullMatrixType, false, false, mnr) val t2 = MatrixRowsTable(mt2) - val mt = importVCF(ctx, "src/test/resources/sample.vcf") + val mt = importVCF(ctx, "hail/test/resources/sample.vcf") var t: TableIR = MatrixRowsTable(mt) t = TableMapRows( t, @@ -686,7 +686,7 @@ class TableIRSuite extends HailSuite { } @Test def testNativeReaderWithOverlappingPartitions(): Unit = { - val path = "src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows" + val path = "hail/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows" // i1 overlaps the first two partitions val i1 = Interval(Row(Locus("20", 10200000)), Row(Locus("20", 10500000)), true, true) diff --git a/hail/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/TestUtils.scala b/hail/hail/test/src/is/hail/expr/ir/TestUtils.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/TestUtils.scala rename to hail/hail/test/src/is/hail/expr/ir/TestUtils.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/UtilFunctionsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/UtilFunctionsSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala b/hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala b/hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala b/hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala b/hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala diff --git a/hail/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala b/hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala rename to hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala diff --git a/hail/src/test/scala/is/hail/io/AvroReaderSuite.scala b/hail/hail/test/src/is/hail/io/AvroReaderSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/AvroReaderSuite.scala rename to hail/hail/test/src/is/hail/io/AvroReaderSuite.scala diff --git a/hail/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala b/hail/hail/test/src/is/hail/io/ByteArrayReaderSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala rename to hail/hail/test/src/is/hail/io/ByteArrayReaderSuite.scala diff --git a/hail/src/test/scala/is/hail/io/IndexBTreeSuite.scala b/hail/hail/test/src/is/hail/io/IndexBTreeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/IndexBTreeSuite.scala rename to hail/hail/test/src/is/hail/io/IndexBTreeSuite.scala diff --git a/hail/src/test/scala/is/hail/io/IndexSuite.scala b/hail/hail/test/src/is/hail/io/IndexSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/IndexSuite.scala rename to hail/hail/test/src/is/hail/io/IndexSuite.scala diff --git a/hail/src/test/scala/is/hail/io/TabixSuite.scala b/hail/hail/test/src/is/hail/io/TabixSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/TabixSuite.scala rename to hail/hail/test/src/is/hail/io/TabixSuite.scala diff --git a/hail/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala b/hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala rename to hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala diff --git a/hail/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala b/hail/hail/test/src/is/hail/io/fs/AzureStorageFSSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala rename to hail/hail/test/src/is/hail/io/fs/AzureStorageFSSuite.scala diff --git a/hail/src/test/scala/is/hail/io/fs/FSSuite.scala b/hail/hail/test/src/is/hail/io/fs/FSSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/fs/FSSuite.scala rename to hail/hail/test/src/is/hail/io/fs/FSSuite.scala diff --git a/hail/src/test/scala/is/hail/io/fs/FakeFS.scala b/hail/hail/test/src/is/hail/io/fs/FakeFS.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/fs/FakeFS.scala rename to hail/hail/test/src/is/hail/io/fs/FakeFS.scala diff --git a/hail/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala b/hail/hail/test/src/is/hail/io/fs/GoogleStorageFSSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala rename to hail/hail/test/src/is/hail/io/fs/GoogleStorageFSSuite.scala diff --git a/hail/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala b/hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala rename to hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala diff --git a/hail/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala b/hail/hail/test/src/is/hail/linalg/GridPartitionerSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala rename to hail/hail/test/src/is/hail/linalg/GridPartitionerSuite.scala diff --git a/hail/src/test/scala/is/hail/linalg/RowMatrixSuite.scala b/hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/linalg/RowMatrixSuite.scala rename to hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala diff --git a/hail/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala b/hail/hail/test/src/is/hail/linalg/RowPartitionerSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala rename to hail/hail/test/src/is/hail/linalg/RowPartitionerSuite.scala diff --git a/hail/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala b/hail/hail/test/src/is/hail/lir/CompileTimeRequirednessSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala rename to hail/hail/test/src/is/hail/lir/CompileTimeRequirednessSuite.scala diff --git a/hail/src/test/scala/is/hail/lir/LIRSplitSuite.scala b/hail/hail/test/src/is/hail/lir/LIRSplitSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/lir/LIRSplitSuite.scala rename to hail/hail/test/src/is/hail/lir/LIRSplitSuite.scala diff --git a/hail/src/test/scala/is/hail/methods/ExprSuite.scala b/hail/hail/test/src/is/hail/methods/ExprSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/methods/ExprSuite.scala rename to hail/hail/test/src/is/hail/methods/ExprSuite.scala diff --git a/hail/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala b/hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala rename to hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala diff --git a/hail/src/test/scala/is/hail/methods/MultiArray2Suite.scala b/hail/hail/test/src/is/hail/methods/MultiArray2Suite.scala similarity index 100% rename from hail/src/test/scala/is/hail/methods/MultiArray2Suite.scala rename to hail/hail/test/src/is/hail/methods/MultiArray2Suite.scala diff --git a/hail/src/test/scala/is/hail/methods/SkatSuite.scala b/hail/hail/test/src/is/hail/methods/SkatSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/methods/SkatSuite.scala rename to hail/hail/test/src/is/hail/methods/SkatSuite.scala diff --git a/hail/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala b/hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala rename to hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala diff --git a/hail/src/test/scala/is/hail/services/BatchClientSuite.scala b/hail/hail/test/src/is/hail/services/BatchClientSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/services/BatchClientSuite.scala rename to hail/hail/test/src/is/hail/services/BatchClientSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/FisherExactTestSuite.scala b/hail/hail/test/src/is/hail/stats/FisherExactTestSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/FisherExactTestSuite.scala rename to hail/hail/test/src/is/hail/stats/FisherExactTestSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala b/hail/hail/test/src/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala rename to hail/hail/test/src/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala b/hail/hail/test/src/is/hail/stats/LeveneHaldaneSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala rename to hail/hail/test/src/is/hail/stats/LeveneHaldaneSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala b/hail/hail/test/src/is/hail/stats/LogisticRegressionModelSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala rename to hail/hail/test/src/is/hail/stats/LogisticRegressionModelSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/StatsSuite.scala b/hail/hail/test/src/is/hail/stats/StatsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/StatsSuite.scala rename to hail/hail/test/src/is/hail/stats/StatsSuite.scala diff --git a/hail/src/test/scala/is/hail/stats/eigSymDSuite.scala b/hail/hail/test/src/is/hail/stats/eigSymDSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/stats/eigSymDSuite.scala rename to hail/hail/test/src/is/hail/stats/eigSymDSuite.scala diff --git a/hail/src/test/scala/is/hail/testUtils/AltAllele.scala b/hail/hail/test/src/is/hail/testUtils/AltAllele.scala similarity index 100% rename from hail/src/test/scala/is/hail/testUtils/AltAllele.scala rename to hail/hail/test/src/is/hail/testUtils/AltAllele.scala diff --git a/hail/src/test/scala/is/hail/testUtils/Variant.scala b/hail/hail/test/src/is/hail/testUtils/Variant.scala similarity index 100% rename from hail/src/test/scala/is/hail/testUtils/Variant.scala rename to hail/hail/test/src/is/hail/testUtils/Variant.scala diff --git a/hail/src/test/scala/is/hail/types/encoded/ETypeSuite.scala b/hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/encoded/ETypeSuite.scala rename to hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala b/hail/hail/test/src/is/hail/types/physical/PBaseStructSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala rename to hail/hail/test/src/is/hail/types/physical/PBaseStructSuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PBinarySuite.scala b/hail/hail/test/src/is/hail/types/physical/PBinarySuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PBinarySuite.scala rename to hail/hail/test/src/is/hail/types/physical/PBinarySuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PCallSuite.scala b/hail/hail/test/src/is/hail/types/physical/PCallSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PCallSuite.scala rename to hail/hail/test/src/is/hail/types/physical/PCallSuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PContainerTest.scala b/hail/hail/test/src/is/hail/types/physical/PContainerTest.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PContainerTest.scala rename to hail/hail/test/src/is/hail/types/physical/PContainerTest.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PIntervalSuite.scala b/hail/hail/test/src/is/hail/types/physical/PIntervalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PIntervalSuite.scala rename to hail/hail/test/src/is/hail/types/physical/PIntervalSuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PNDArraySuite.scala b/hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PNDArraySuite.scala rename to hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PTypeSuite.scala b/hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PTypeSuite.scala rename to hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala diff --git a/hail/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala b/hail/hail/test/src/is/hail/types/physical/PhysicalTestUtils.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala rename to hail/hail/test/src/is/hail/types/physical/PhysicalTestUtils.scala diff --git a/hail/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala b/hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala rename to hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala diff --git a/hail/src/test/scala/is/hail/types/virtual/TStructSuite.scala b/hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/types/virtual/TStructSuite.scala rename to hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala b/hail/hail/test/src/is/hail/utils/ArrayBuilderSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala rename to hail/hail/test/src/is/hail/utils/ArrayBuilderSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/ArrayStackSuite.scala b/hail/hail/test/src/is/hail/utils/ArrayStackSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/ArrayStackSuite.scala rename to hail/hail/test/src/is/hail/utils/ArrayStackSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/BinaryHeapSuite.scala b/hail/hail/test/src/is/hail/utils/BinaryHeapSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/BinaryHeapSuite.scala rename to hail/hail/test/src/is/hail/utils/BinaryHeapSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/BitVectorSuite.scala b/hail/hail/test/src/is/hail/utils/BitVectorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/BitVectorSuite.scala rename to hail/hail/test/src/is/hail/utils/BitVectorSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala b/hail/hail/test/src/is/hail/utils/BufferedAggregatorIteratorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala rename to hail/hail/test/src/is/hail/utils/BufferedAggregatorIteratorSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala b/hail/hail/test/src/is/hail/utils/FlipbookIteratorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala rename to hail/hail/test/src/is/hail/utils/FlipbookIteratorSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/GraphSuite.scala b/hail/hail/test/src/is/hail/utils/GraphSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/GraphSuite.scala rename to hail/hail/test/src/is/hail/utils/GraphSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/HashMethodsSuite.scala b/hail/hail/test/src/is/hail/utils/HashMethodsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/HashMethodsSuite.scala rename to hail/hail/test/src/is/hail/utils/HashMethodsSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/IntervalSuite.scala b/hail/hail/test/src/is/hail/utils/IntervalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/IntervalSuite.scala rename to hail/hail/test/src/is/hail/utils/IntervalSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/PartitionCountsSuite.scala b/hail/hail/test/src/is/hail/utils/PartitionCountsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/PartitionCountsSuite.scala rename to hail/hail/test/src/is/hail/utils/PartitionCountsSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/RichArraySuite.scala b/hail/hail/test/src/is/hail/utils/RichArraySuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/RichArraySuite.scala rename to hail/hail/test/src/is/hail/utils/RichArraySuite.scala diff --git a/hail/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala b/hail/hail/test/src/is/hail/utils/RichDenseMatrixDoubleSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala rename to hail/hail/test/src/is/hail/utils/RichDenseMatrixDoubleSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala b/hail/hail/test/src/is/hail/utils/RichIndexedRowMatrixSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala rename to hail/hail/test/src/is/hail/utils/RichIndexedRowMatrixSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/RichRDDSuite.scala b/hail/hail/test/src/is/hail/utils/RichRDDSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/RichRDDSuite.scala rename to hail/hail/test/src/is/hail/utils/RichRDDSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/RowIntervalSuite.scala b/hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/RowIntervalSuite.scala rename to hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/SemanticVersionSuite.scala b/hail/hail/test/src/is/hail/utils/SemanticVersionSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/SemanticVersionSuite.scala rename to hail/hail/test/src/is/hail/utils/SemanticVersionSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala b/hail/hail/test/src/is/hail/utils/SpillingCollectIteratorSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala rename to hail/hail/test/src/is/hail/utils/SpillingCollectIteratorSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/TreeTraversalSuite.scala b/hail/hail/test/src/is/hail/utils/TreeTraversalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/TreeTraversalSuite.scala rename to hail/hail/test/src/is/hail/utils/TreeTraversalSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/UnionFindSuite.scala b/hail/hail/test/src/is/hail/utils/UnionFindSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/UnionFindSuite.scala rename to hail/hail/test/src/is/hail/utils/UnionFindSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/UtilsSuite.scala b/hail/hail/test/src/is/hail/utils/UtilsSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/UtilsSuite.scala rename to hail/hail/test/src/is/hail/utils/UtilsSuite.scala diff --git a/hail/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala b/hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala rename to hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala diff --git a/hail/src/test/scala/is/hail/variant/GenotypeSuite.scala b/hail/hail/test/src/is/hail/variant/GenotypeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/variant/GenotypeSuite.scala rename to hail/hail/test/src/is/hail/variant/GenotypeSuite.scala diff --git a/hail/src/test/scala/is/hail/variant/LocusIntervalSuite.scala b/hail/hail/test/src/is/hail/variant/LocusIntervalSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/variant/LocusIntervalSuite.scala rename to hail/hail/test/src/is/hail/variant/LocusIntervalSuite.scala diff --git a/hail/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala b/hail/hail/test/src/is/hail/variant/ReferenceGenomeSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala rename to hail/hail/test/src/is/hail/variant/ReferenceGenomeSuite.scala diff --git a/hail/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala b/hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala similarity index 100% rename from hail/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala rename to hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala diff --git a/hail/python/test/hail/helpers.py b/hail/python/test/hail/helpers.py index 1da5bfc7e90..268c58cc15b 100644 --- a/hail/python/test/hail/helpers.py +++ b/hail/python/test/hail/helpers.py @@ -36,7 +36,7 @@ def hl_stop_for_test(): _test_dir = os.environ.get( 'HAIL_TEST_RESOURCES_DIR', - os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(hl.__file__))), 'src/test/resources'), + os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(hl.__file__))), 'hail/test/resources'), ) _doctest_dir = os.environ.get('HAIL_DOCTEST_DATA_DIR', 'hail/docs/data') diff --git a/hail/src/test/resources/backward_compatability/1.1.0/matrix_table/0.hmt/index/part-0-1-0-0-57116ffc-89dc-c5ca-faa1-e77e34afb443.idx/index b/hail/src/test/resources/backward_compatability/1.1.0/matrix_table/0.hmt/index/part-0-1-0-0-57116ffc-89dc-c5ca-faa1-e77e34afb443.idx/index deleted file mode 100644 index 7bbc1325bcf..00000000000 Binary files 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A T oREsa B9 YySqUn6 0 0 82 114 123 0.527777777778 0.02 0.037037037037 36 50 54 0.346153846154 0.999967291659 HIGH_SNV AC=22;AN=816;AF=2.69608e-02;ESP=6.73086e-02 -1 1020207 . A T pBo0A ze79u G 0 0 150 82 86 0.515151515152 0.0 0.0 33 18 19 0.891891891892 0.966351483497 MEDIUM_SNV AC=29;AN=808;AF=3.58911e-02;ESP=8.58836e-03 -1 1020207 . A T A3N1hy D8SOc9a4 TR 0 0 113 168 154 0.64 0.027027027027 0.0 25 37 34 0.352112676056 0.999999998366 HIGH_SNV AC=29;AN=808;AF=3.58911e-02;ESP=8.58836e-03 -1 1281541 . A T hdfAn4k qZc WCJRI9P 0 0 76 93 116 0.521739130435 0.0357142857143 0.0 23 28 35 0.365079365079 0.997651255558 HIGH_SNV AC=34;AN=796;AF=4.27136e-02;ESP=0.00000e+00 -1 3057010 . A AA ou bw7ldn zMnt 0 0 42 63 130 0.5 0.0 0.0232558139535 14 21 43 0.21875 0.157346969226 LOW_indel AC=73;AN=790;AF=9.24051e-02;ESP=1.04241e-01 -1 3057010 . A AA I5Pz iHtaz y 0 0 54 70 118 0.666666666667 0.0 0.025641025641 18 23 39 0.290322580645 0.483429069367 LOW_indel AC=73;AN=790;AF=9.24051e-02;ESP=1.04241e-01 -1 3392108 . A T Eeh5s6tQ OjtGGek4b Dh 0 0 150 114 97 0.622222222222 0.0294117647059 0.0 45 34 29 0.714285714286 0.99898523486 HIGH_SNV AC=2;AN=804;AF=2.48756e-03;ESP=4.44755e-02 -1 5296597 . A T XeqjeZvpN Ju riI2 0 0 94 98 94 0.52 0.0384615384615 0.04 25 26 25 0.490196078431 0.997256483159 HIGH_SNV AC=37;AN=818;AF=4.52323e-02;ESP=3.89619e-03 -1 5296597 . A T f5WJEcL2I p3z cjjzO6h3 0 0 234 136 147 0.387096774194 0.0 0.0 62 36 39 0.826666666667 0.999999865984 HIGH_SNV AC=37;AN=818;AF=4.52323e-02;ESP=3.89619e-03 -1 6252602 . A AA R1tod LSr3DTLXnm yMGScTObr8 0 0 293 253 109 0.525423728814 0.0 0.0 59 51 22 0.808219178082 0.99987017152 LOW_indel AC=66;AN=788;AF=8.37563e-02;ESP=9.99655e-02 -1 6252602 . A AA CqwzHDh iQh v0kXL8 0 0 268 258 69 0.481481481481 0.0192307692308 0.0 54 52 14 0.818181818182 0.435075173245 LOW_indel AC=66;AN=788;AF=8.37563e-02;ESP=9.99655e-02 -1 6559260 . A AA t6M1ZE cHlRpuznS UErxdwA0g 0 0 84 136 96 0.52380952381 0.0 0.0416666666667 21 34 24 0.362068965517 0.998007055335 LOW_indel AC=61;AN=810;AF=7.53086e-02;ESP=4.51986e-02 -1 6559260 . A AA w0 T cvXQaAn 0 0 56 76 104 0.571428571429 0.0 0.0384615384615 14 19 26 0.311111111111 0.83334101757 LOW_indel AC=61;AN=810;AF=7.53086e-02;ESP=4.51986e-02 -1 6559260 . A AA NlS eguHEhm5 JpCu0WQS 0 0 168 152 108 0.547619047619 0.0263157894737 0.037037037037 42 38 27 0.646153846154 0.999874026041 LOW_indel AC=61;AN=810;AF=7.53086e-02;ESP=4.51986e-02 -1 6559260 . A AA HXy2a12pp s2I Fp0a 0 0 108 76 112 0.592592592593 0.0 0.0 27 19 28 0.574468085106 0.833525995426 LOW_indel AC=61;AN=810;AF=7.53086e-02;ESP=4.51986e-02 -1 6559800 . A T oREsa B9 YySqUn6 0 0 96 274 224 0.571428571429 0.0166666666667 0.0204081632653 21 60 49 0.192660550459 1.0 MEDIUM_SNV AC=77;AN=804;AF=9.57711e-02;ESP=6.30567e-02 -1 6559800 . A T Taaq6gTPV HOTvfpz bg 0 0 178 114 160 0.615384615385 0.04 0.0 39 25 35 0.65 0.99996085121 HIGH_SNV AC=77;AN=804;AF=9.57711e-02;ESP=6.30567e-02 -1 6559800 . A T PqKa6PK1V FmEi14ZtZPC Pay3MWpo2ZH 0 0 128 187 169 0.607142857143 0.0487804878049 0.0 28 41 37 0.358974358974 0.999999999874 HIGH_SNV AC=77;AN=804;AF=9.57711e-02;ESP=6.30567e-02 -1 6559800 . A T yPxJCb6Y5 EGC CdExBV 0 0 453 229 151 0.575757575758 0.04 0.0 99 50 33 1.19277108434 0.999999992189 HIGH_SNV AC=77;AN=804;AF=9.57711e-02;ESP=6.30567e-02 -1 6559800 . A T CqwzHDh iQh v0kXL8 0 0 78 183 123 0.470588235294 0.025 0.037037037037 17 40 27 0.253731343284 0.99999507141 HIGH_SNV AC=77;AN=804;AF=9.57711e-02;ESP=6.30567e-02 -1 7548634 . A AA uf sCGa3x zrP9Ew7 0 0 69 100 71 0.621621621622 0.037037037037 0.0263157894737 37 54 38 0.402173913043 0.495273871779 LOW_indel AC=67;AN=796;AF=8.41709e-02;ESP=1.30004e-01 -1 7548634 . A AA I5Pz iHtaz y 0 0 69 119 71 0.405405405405 0.046875 0.0263157894737 37 64 38 0.362745098039 0.49558441702 LOW_indel AC=67;AN=796;AF=8.41709e-02;ESP=1.30004e-01 -1 7548634 . A AA NlS eguHEhm5 JpCu0WQS 0 0 80 108 80 0.604651162791 0.0 0.046511627907 43 58 43 0.425742574257 0.886260078972 LOW_indel AC=67;AN=796;AF=8.41709e-02;ESP=1.30004e-01 -1 8072325 . A T mg28SDQkS jsN9 jP3ms 0 0 61 110 126 0.526315789474 0.0 0.0 19 34 39 0.260273972603 0.99999228795 HIGH_SNV AC=6;AN=790;AF=7.59494e-03;ESP=0.00000e+00 -1 8072325 . A T wN A5pHPhENV RKLQ 0 0 74 65 68 0.608695652174 0.0 0.047619047619 23 20 21 0.560975609756 0.73684574712 HIGH_SNV AC=6;AN=790;AF=7.59494e-03;ESP=0.00000e+00 -1 9833462 . A T HiI6Ng n7wzDoH3KoO VS11 0 0 242 168 128 0.408163265306 0.0294117647059 0.0 49 34 26 0.816666666667 0.999999363902 HIGH_SNV AC=29;AN=794;AF=3.65239e-02;ESP=3.35638e-02 -1 10355790 . A AA q0fIbf Oj Le8nhxcA 0 0 91 87 66 0.575 0.0263157894737 0.0 40 38 29 0.597014925373 0.297819899519 LOW_indel AC=75;AN=834;AF=8.99281e-02;ESP=4.23236e-02 -1 10355790 . A AA R1tod LSr3DTLXnm yMGScTObr8 0 0 52 59 100 0.434782608696 0.0 0.0454545454545 23 26 44 0.328571428571 0.0785887372364 LOW_indel AC=75;AN=834;AF=8.99281e-02;ESP=4.23236e-02 -1 11191983 . A AA EMAzCz iZkQkrF uftzolA 0 0 46 84 104 0.375 0.0344827586207 0.0277777777778 16 29 36 0.246153846154 0.956017000126 LOW_indel AC=80;AN=812;AF=9.85222e-02;ESP=1.13144e-01 -1 11191983 . A AA Ko4 dqkzxIh AR 0 0 32 78 110 0.272727272727 0.0 0.0263157894737 11 27 38 0.169230769231 0.846413101521 LOW_indel AC=80;AN=812;AF=9.85222e-02;ESP=1.13144e-01 -1 12235650 . A T HEx7BZUN aab4NoyV8 DxqNtUAJ0y 0 0 102 57 85 0.638888888889 0.0 0.0 36 20 30 0.72 0.110912317888 LOW_SNV AC=24;AN=808;AF=2.97030e-02;ESP=3.52470e-02 -1 13086728 . A AA qjHUz GrEv5BGRTo uVv 0 0 105 82 132 0.407407407407 0.047619047619 0.0294117647059 27 21 34 0.490909090909 0.944969649035 LOW_indel AC=31;AN=790;AF=3.92405e-02;ESP=8.78186e-02 -1 13086728 . A AA AeaS4jjUx8 iVlc59pr7gM ouWlcjn 0 0 101 78 58 0.423076923077 0.0 0.0 26 20 15 0.742857142857 0.0633950016579 LOW_indel AC=31;AN=790;AF=3.92405e-02;ESP=8.78186e-02 -1 13086728 . A AA hSo07 oJCrVs1ihl Q60L71 0 0 39 140 117 0.4 0.0277777777778 0.0 10 36 30 0.151515151515 0.999981492693 LOW_indel AC=31;AN=790;AF=3.92405e-02;ESP=8.78186e-02 -1 14100747 . A AA Eeh5s6tQ OjtGGek4b Dh 0 0 101 133 117 0.4 0.030303030303 0.0344827586207 25 33 29 0.403225806452 0.999977346338 LOW_indel AC=90;AN=818;AF=1.10024e-01;ESP=7.63232e-02 -1 14795321 . A T Ixll CF E 0 0 61 101 66 0.521739130435 0.0 0.0 23 38 25 0.365079365079 0.360399064388 LOW_SNV AC=44;AN=786;AF=5.59796e-02;ESP=6.49089e-02 -1 14795321 . A T QjL5 EKCjT1P LS6RmDeZ 0 0 56 61 72 0.619047619048 0.0 0.0 21 23 27 0.42 0.141723951257 LOW_SNV AC=44;AN=786;AF=5.59796e-02;ESP=6.49089e-02 -1 16040027 . A T HEx7BZUN aab4NoyV8 DxqNtUAJ0y 0 0 279 72 121 0.486486486486 0.0 0.0 74 19 32 1.45098039216 0.821605756428 MEDIUM_SNV AC=25;AN=800;AF=3.12500e-02;ESP=9.43449e-03 -1 16520318 . A AA NlS eguHEhm5 JpCu0WQS 0 0 66 69 73 0.305555555556 0.0263157894737 0.025 36 38 40 0.461538461538 0.406082392497 LOW_indel AC=54;AN=802;AF=6.73317e-02;ESP=7.78801e-02 -1 16674610 . A T wN A5pHPhENV RKLQ 0 0 30 126 78 0.571428571429 0.0 0.0 7 29 18 0.148936170213 0.879974388408 MEDIUM_SNV AC=66;AN=802;AF=8.22943e-02;ESP=6.04646e-02 -1 16674610 . A T sMYjo0 wXlKNKod pdD 0 0 130 139 100 0.466666666667 0.03125 0.0 30 32 23 0.545454545455 0.999140040404 HIGH_SNV AC=66;AN=802;AF=8.22943e-02;ESP=6.04646e-02 -1 16748786 . A AA ofO667uNsOU ZGoGLCJx2E BhWKlGjVUE 0 0 87 67 77 0.5 0.0 0.0 26 20 23 0.604651162791 0.453672893119 LOW_indel AC=40;AN=792;AF=5.05051e-02;ESP=1.63734e-02 -1 16748786 . A AA zKLRWM PlYNqKUqlpb SZW7lEol9R 0 0 34 124 60 0.5 0.0 0.0 10 37 18 0.181818181818 0.154159733256 LOW_indel AC=40;AN=792;AF=5.05051e-02;ESP=1.63734e-02 -1 16929788 . A T php7FHqhxN fyWBxQJi2 ldO55 0 0 40 117 171 0.444444444444 0.0384615384615 0.0263157894737 9 26 38 0.140625 0.999974577226 MEDIUM_SNV AC=88;AN=816;AF=1.07843e-01;ESP=1.29100e-01 -1 17478977 . A T UJHp AM5eP32WWtV UTxL 0 0 112 77 96 0.51724137931 0.0 0.0 29 20 25 0.644444444444 0.923730066773 MEDIUM_SNV AC=26;AN=784;AF=3.31633e-02;ESP=3.59484e-02 -1 17478977 . A T avrChOq cJVgyEWGR bcL6 0 0 196 119 262 0.588235294118 0.0322580645161 0.0 51 31 68 0.515151515152 0.99999485515 HIGH_SNV AC=26;AN=784;AF=3.31633e-02;ESP=3.59484e-02 -1 17501655 . A AA p8D6Qfi7iC lJjz6B iF 0 0 137 123 119 0.594594594595 0.0 0.03125 37 33 32 0.569230769231 0.999989898307 LOW_indel AC=34;AN=798;AF=4.26065e-02;ESP=5.17004e-02 -1 17501655 . A AA rYZUwaTQXV ltP yPRtluVw 0 0 149 152 256 0.575 0.0 0.0 40 41 69 0.363636363636 0.999999996379 LOW_indel AC=34;AN=798;AF=4.26065e-02;ESP=5.17004e-02 -1 17501655 . A AA aVaoS wLkIi KGuvqVtPal 0 0 197 201 167 0.547169811321 0.037037037037 0.0 53 54 45 0.535353535354 0.999999999885 LOW_indel AC=34;AN=798;AF=4.26065e-02;ESP=5.17004e-02 -1 17501655 . A AA sMYjo0 wXlKNKod pdD 0 0 171 111 93 0.413043478261 0.0 0.0 46 30 25 0.836363636364 0.997086466307 LOW_indel AC=34;AN=798;AF=4.26065e-02;ESP=5.17004e-02 -1 18480996 . A T CqwzHDh iQh v0kXL8 0 0 133 133 106 0.512820512821 0.025641025641 0.0322580645161 39 39 31 0.557142857143 0.999891167601 HIGH_SNV AC=31;AN=786;AF=3.94402e-02;ESP=3.69941e-02 -1 19180292 . A T MxBdoNbVd ZgVITt FcZc 0 0 93 86 141 0.379310344828 0.037037037037 0.0 29 27 44 0.408450704225 0.987661322064 MEDIUM_SNV AC=36;AN=790;AF=4.55696e-02;ESP=4.07424e-02 -1 20535958 . A AA AeaS4jjUx8 iVlc59pr7gM ouWlcjn 0 0 110 103 59 0.59375 0.0 0.0 32 30 17 0.68085106383 0.0804436367028 LOW_indel AC=45;AN=800;AF=5.62500e-02;ESP=8.61774e-02 -1 20944297 . A T wN A5pHPhENV RKLQ 0 0 79 68 84 0.5 0.0416666666667 0.0338983050847 56 48 59 0.523364485981 0.470262330709 LOW_SNV AC=52;AN=802;AF=6.48379e-02;ESP=4.63141e-02 -1 21998163 . A T tEOtgDi3mk pvO Vx8Uupq9E5F 0 0 121 70 78 0.451612903226 0.0 0.0 31 18 20 0.815789473684 0.508415172129 MEDIUM_SNV AC=57;AN=814;AF=7.00246e-02;ESP=7.82709e-02 -1 22098077 . A T w0 T cvXQaAn 0 0 125 181 121 0.413793103448 0.0238095238095 0.0357142857143 29 42 28 0.414285714286 0.999997815547 HIGH_SNV AC=20;AN=800;AF=2.50000e-02;ESP=2.28770e-02 -1 22098077 . A T P7Gk Wmf n8jFlFZ 0 0 164 116 177 0.394736842105 0.037037037037 0.0243902439024 38 27 41 0.558823529412 0.999993092187 HIGH_SNV AC=20;AN=800;AF=2.50000e-02;ESP=2.28770e-02 -1 22429435 . A AA hdfAn4k qZc WCJRI9P 0 0 244 276 120 0.358490566038 0.0 0.0384615384615 53 60 26 0.616279069767 0.999991984712 LOW_indel AC=55;AN=792;AF=6.94444e-02;ESP=7.47703e-02 -1 22829296 . A T qjHUz GrEv5BGRTo uVv 0 0 148 95 159 0.52380952381 0.0 0.0 42 27 45 0.583333333333 0.997825648297 HIGH_SNV AC=34;AN=770;AF=4.41558e-02;ESP=6.31598e-02 -1 24076452 . A AA U QBBcjW oqoydSBU1y5 0 0 113 57 79 0.507462686567 0.0 0.0425531914894 67 34 47 0.827160493827 0.252331283818 LOW_indel AC=11;AN=798;AF=1.37845e-02;ESP=0.00000e+00 -1 24210372 . A T u zxDaU4 UbNePRnK 0 0 197 171 144 0.457627118644 0.0392156862745 0.0232558139535 59 51 43 0.627659574468 0.999999986435 HIGH_SNV AC=25;AN=810;AF=3.08642e-02;ESP=0.00000e+00 -1 24764260 . A T o jlB SwMZo8eP 0 0 50 83 79 0.555555555556 0.0444444444444 0.0232558139535 27 45 43 0.306818181818 0.937667434431 MEDIUM_SNV AC=27;AN=786;AF=3.43511e-02;ESP=1.90822e-02 -1 26226154 . A AA p8D6Qfi7iC lJjz6B iF 0 0 51 69 63 0.485714285714 0.0212765957447 0.0232558139535 35 47 43 0.388888888889 0.236513879863 LOW_indel AC=32;AN=800;AF=4.00000e-02;ESP=4.59725e-02 -1 28258849 . A AA GG9mvG8m bn02mGE9u You3TKfQka 0 0 65 67 85 0.310344827586 0.0 0.0 29 30 38 0.426470588235 0.439332249037 LOW_indel AC=35;AN=806;AF=4.34243e-02;ESP=5.71907e-02 -1 28258849 . A AA avrChOq cJVgyEWGR bcL6 0 0 51 96 76 0.434782608696 0.0 0.0 23 43 34 0.298701298701 0.862264676439 LOW_indel AC=35;AN=806;AF=4.34243e-02;ESP=5.71907e-02 -1 28258849 . A AA PqKa6PK1V FmEi14ZtZPC Pay3MWpo2ZH 0 0 62 69 87 0.535714285714 0.0 0.0 28 31 39 0.4 0.553950275388 LOW_indel AC=35;AN=806;AF=4.34243e-02;ESP=5.71907e-02 -1 28322450 . A AA XeqjeZvpN Ju riI2 0 0 135 71 74 0.35 0.0 0.0454545454545 40 21 22 0.93023255814 0.515016064146 LOW_indel AC=61;AN=816;AF=7.47549e-02;ESP=3.36648e-02 -1 29525996 . A AA Eeh5s6tQ OjtGGek4b Dh 0 0 63 74 106 0.666666666667 0.0357142857143 0.0 24 28 40 0.352941176471 0.732329537534 LOW_indel AC=72;AN=814;AF=8.84521e-02;ESP=7.60600e-02 -1 29525996 . A AA QjL5 EKCjT1P LS6RmDeZ 0 0 79 66 116 0.4 0.04 0.0227272727273 30 25 44 0.434782608696 0.30259451553 LOW_indel AC=72;AN=814;AF=8.84521e-02;ESP=7.60600e-02 -1 29525996 . A AA CqwzHDh iQh v0kXL8 0 0 151 161 103 0.491228070175 0.0 0.0 57 61 39 0.57 0.999540356646 LOW_indel AC=72;AN=814;AF=8.84521e-02;ESP=7.60600e-02 -1 29525996 . A AA MxBdoNbVd ZgVITt FcZc 0 0 55 100 69 0.619047619048 0.0263157894737 0.0384615384615 21 38 26 0.328125 0.46381790426 LOW_indel AC=72;AN=814;AF=8.84521e-02;ESP=7.60600e-02 -1 29622973 . A AA YnE04DPZVC glDTMK2DaV9 qWLM 0 0 227 293 203 0.4375 0.0483870967742 0.046511627907 48 62 43 0.457142857143 1.0 LOW_indel AC=39;AN=796;AF=4.89950e-02;ESP=8.89770e-02 -1 29622973 . A AA NNJAaJ JVcb awI5MW6XS 0 0 265 170 180 0.392857142857 0.0277777777778 0.0263157894737 56 36 38 0.756756756757 0.999999999897 LOW_indel AC=39;AN=796;AF=4.89950e-02;ESP=8.89770e-02 -1 30093522 . A T w0 T cvXQaAn 0 0 184 105 105 0.428571428571 0.0 0.0 42 24 24 0.875 0.999889516169 HIGH_SNV AC=13;AN=806;AF=1.61290e-02;ESP=0.00000e+00 -1 31535257 . A T pBo0A ze79u G 0 0 65 65 60 0.407407407407 0.0 0.0 27 27 25 0.519230769231 0.0665442097764 LOW_SNV AC=65;AN=784;AF=8.29082e-02;ESP=1.03917e-01 -1 31535257 . A T UZlGcu7JzfE iBEYtsek1R0 YaBF 0 0 55 67 96 0.608695652174 0.0 0.025 23 28 40 0.338235294118 0.31957932101 LOW_SNV AC=65;AN=784;AF=8.29082e-02;ESP=1.03917e-01 -1 31535257 . A T f5WJEcL2I p3z cjjzO6h3 0 0 24 74 65 0.5 0.0 0.037037037037 10 31 27 0.172413793103 0.208574291821 LOW_SNV AC=65;AN=784;AF=8.29082e-02;ESP=1.03917e-01 -1 31568942 . A AA DCDoJial CKE0nvz7kGZ aU8PL 0 0 178 136 164 0.394736842105 0.0344827586207 0.0285714285714 38 29 35 0.59375 0.999999704332 LOW_indel AC=81;AN=810;AF=1.00000e-01;ESP=1.16874e-01 -1 31980134 . A AA fDzMU8 kRb cTN 0 0 123 79 133 0.4 0.0 0.0 25 16 27 0.581395348837 0.893953163625 LOW_indel AC=39;AN=772;AF=5.05181e-02;ESP=8.99482e-02 -1 31980134 . A AA iqu1oGpY tQ2Z4 Qxkefj 0 0 197 128 113 0.5 0.0 0.0 40 26 23 0.816326530612 0.99995128295 LOW_indel AC=39;AN=772;AF=5.05181e-02;ESP=8.99482e-02 -1 32265975 . A T GG9mvG8m bn02mGE9u You3TKfQka 0 0 209 93 111 0.422222222222 0.0 0.0416666666667 45 20 24 1.02272727273 0.993455671309 HIGH_SNV AC=86;AN=822;AF=1.04623e-01;ESP=1.31593e-01 -1 32265975 . A T P7Gk Wmf n8jFlFZ 0 0 144 269 93 0.516129032258 0.0172413793103 0.0 31 58 20 0.397435897436 0.993557115881 HIGH_SNV AC=86;AN=822;AF=1.04623e-01;ESP=1.31593e-01 -1 32297379 . A AA StWUjngHw hTjFpJ iim2 0 0 66 239 75 0.266666666667 0.0185185185185 0.0 15 54 17 0.211267605634 0.74596336185 LOW_indel AC=51;AN=794;AF=6.42317e-02;ESP=1.05213e-01 -1 32297379 . A AA GG9mvG8m bn02mGE9u You3TKfQka 0 0 80 248 208 0.333333333333 0.0178571428571 0.0212765957447 18 56 47 0.174757281553 1.0 LOW_indel AC=51;AN=794;AF=6.42317e-02;ESP=1.05213e-01 -1 33862687 . A AA php7FHqhxN fyWBxQJi2 ldO55 0 0 141 106 114 0.461538461538 0.0 0.047619047619 52 39 42 0.641975308642 0.999853996727 LOW_indel AC=15;AN=796;AF=1.88442e-02;ESP=4.47296e-02 -1 33862687 . A AA r FIdIJqCOu mWYD5 0 0 38 136 92 0.714285714286 0.04 0.0294117647059 14 50 34 0.166666666667 0.996843699613 LOW_indel AC=15;AN=796;AF=1.88442e-02;ESP=4.47296e-02 -1 34800398 . A AA StWUjngHw hTjFpJ iim2 0 0 143 84 243 0.477272727273 0.0 0.0 44 26 75 0.435643564356 0.984447477947 LOW_indel AC=21;AN=792;AF=2.65152e-02;ESP=3.48492e-02 -1 36758082 . A AA Ixll CF E 0 0 40 81 92 0.5 0.0 0.0 22 45 51 0.229166666667 0.932787728401 LOW_indel AC=66;AN=824;AF=8.00971e-02;ESP=6.51141e-02 -1 36758082 . A AA DCDoJial CKE0nvz7kGZ aU8PL 0 0 25 76 103 0.428571428571 0.0 0.0175438596491 14 42 57 0.141414141414 0.825414592705 LOW_indel AC=66;AN=824;AF=8.00971e-02;ESP=6.51141e-02 -1 36758082 . A AA HEx7BZUN aab4NoyV8 DxqNtUAJ0y 0 0 43 123 81 0.541666666667 0.0 0.0 24 68 45 0.212389380531 0.937420515023 LOW_indel AC=66;AN=824;AF=8.00971e-02;ESP=6.51141e-02 -1 36758082 . A AA iqu1oGpY tQ2Z4 Qxkefj 0 0 31 65 79 0.352941176471 0.0 0.0 17 36 44 0.2125 0.265725856854 LOW_indel AC=66;AN=824;AF=8.00971e-02;ESP=6.51141e-02 -1 37047125 . A AA EMAzCz iZkQkrF uftzolA 0 0 121 117 90 0.481481481481 0.0384615384615 0.0 27 26 20 0.586956521739 0.989792010445 LOW_indel AC=80;AN=804;AF=9.95025e-02;ESP=9.97227e-02 -1 37047125 . A AA yXi6eb Wa9im XMp 0 0 63 99 63 0.357142857143 0.0454545454545 0.0 14 22 14 0.388888888889 0.162340799915 LOW_indel AC=80;AN=804;AF=9.95025e-02;ESP=9.97227e-02 -1 37070463 . A AA qjHUz GrEv5BGRTo uVv 0 0 234 141 155 0.7 0.0333333333333 0.0 50 30 33 0.793650793651 0.999999919923 LOW_indel AC=72;AN=806;AF=8.93300e-02;ESP=9.29739e-02 -1 37070463 . A AA oREsa B9 YySqUn6 0 0 131 178 155 0.464285714286 0.0 0.0 28 38 33 0.394366197183 0.999999996919 LOW_indel AC=72;AN=806;AF=8.93300e-02;ESP=9.29739e-02 -1 37070463 . A AA aRh4dC4 w1n9xDWTz5X J88Z 0 0 380 291 253 0.530864197531 0.0161290322581 0.0 81 62 54 0.698275862069 1.0 LOW_indel AC=72;AN=806;AF=8.93300e-02;ESP=9.29739e-02 -1 37070463 . A AA php7FHqhxN fyWBxQJi2 ldO55 0 0 178 159 314 0.605263157895 0.0294117647059 0.0 38 34 67 0.376237623762 0.999999998779 LOW_indel AC=72;AN=806;AF=8.93300e-02;ESP=9.29739e-02 -1 37070463 . A AA UZlGcu7JzfE iBEYtsek1R0 YaBF 0 0 258 277 216 0.509090909091 0.0 0.0 55 59 46 0.52380952381 1.0 LOW_indel AC=72;AN=806;AF=8.93300e-02;ESP=9.29739e-02 -1 37231703 . A T u zxDaU4 UbNePRnK 0 0 129 118 69 0.393939393939 0.0166666666667 0.0 66 60 35 0.694736842105 0.60487449915 MEDIUM_SNV AC=38;AN=798;AF=4.76190e-02;ESP=1.51662e-02 -1 37231703 . A T CqwzHDh iQh v0kXL8 0 0 29 96 90 0.666666666667 0.0 0.0434782608696 15 49 46 0.157894736842 0.993549747327 MEDIUM_SNV AC=38;AN=798;AF=4.76190e-02;ESP=1.51662e-02 -1 37231703 . A T jf r6BQTdmkVwW tbpGOIAtdN 0 0 131 82 133 0.388059701493 0.0 0.0 67 42 68 0.609090909091 0.968298696969 MEDIUM_SNV AC=38;AN=798;AF=4.76190e-02;ESP=1.51662e-02 -1 37231703 . A T HXcqZutGNZL Yha AGDAZSW 0 0 108 80 88 0.6 0.0 0.0 55 41 45 0.639534883721 0.943297151859 MEDIUM_SNV AC=38;AN=798;AF=4.76190e-02;ESP=1.51662e-02 -1 40374773 . A T rYZUwaTQXV ltP yPRtluVw 0 0 201 67 62 0.595238095238 0.0 0.0 42 14 13 1.55555555556 0.122507954158 LOW_SNV AC=66;AN=800;AF=8.25000e-02;ESP=6.35326e-02 -1 40374773 . A T we AIt NYGQZQ5tx 0 0 158 134 105 0.454545454545 0.0357142857143 0.0 33 28 22 0.66 0.999726991813 HIGH_SNV AC=66;AN=800;AF=8.25000e-02;ESP=6.35326e-02 -1 40374773 . A T r FIdIJqCOu mWYD5 0 0 48 91 129 0.5 0.0 0.0 10 19 27 0.217391304348 0.993194640909 HIGH_SNV AC=66;AN=800;AF=8.25000e-02;ESP=6.35326e-02 -1 40591404 . A AA SOC3AEPpME AGST9s09a spzDeRQ 0 0 47 109 181 0.533333333333 0.0 0.0 15 35 58 0.161290322581 0.99996479264 LOW_indel AC=10;AN=814;AF=1.22850e-02;ESP=2.41681e-02 -1 40643931 . A AA CqwzHDh iQh v0kXL8 0 0 124 66 87 0.433333333333 0.0 0.047619047619 30 16 21 0.810810810811 0.357487377624 LOW_indel AC=51;AN=766;AF=6.65796e-02;ESP=5.80236e-02 -1 40931831 . A T HiI6Ng n7wzDoH3KoO VS11 0 0 109 67 105 0.472727272727 0.0294117647059 0.0377358490566 55 34 53 0.632183908046 0.389152668555 LOW_SNV AC=60;AN=806;AF=7.44417e-02;ESP=5.77898e-02 -1 40992627 . A T xPt7 mehCDVJBsL qNpaUCBF 0 0 98 84 137 0.560975609756 0.0285714285714 0.0350877192982 41 35 57 0.445652173913 0.970460149466 MEDIUM_SNV AC=55;AN=798;AF=6.89223e-02;ESP=7.09074e-02 -1 46177101 . A AA zKLRWM PlYNqKUqlpb SZW7lEol9R 0 0 88 171 171 0.45 0.0 0.0 20 39 39 0.25641025641 0.999999999778 LOW_indel AC=78;AN=796;AF=9.79899e-02;ESP=1.44739e-01 -1 46177101 . A AA YnE04DPZVC glDTMK2DaV9 qWLM 0 0 74 140 188 0.294117647059 0.03125 0.046511627907 17 32 43 0.226666666667 0.999999860513 LOW_indel AC=78;AN=796;AF=9.79899e-02;ESP=1.44739e-01 -1 47515158 . A AA GG9mvG8m bn02mGE9u You3TKfQka 0 0 128 107 91 0.526315789474 0.03125 0.0 38 32 27 0.64406779661 0.994591604944 LOW_indel AC=36;AN=812;AF=4.43350e-02;ESP=6.10101e-02 -1 47515158 . A AA sktgKDPq zPVAGX iITcwfLMGr 0 0 225 171 74 0.55223880597 0.0392156862745 0.0 67 51 22 0.917808219178 0.789978153014 LOW_indel AC=36;AN=812;AF=4.43350e-02;ESP=6.10101e-02 -1 47515158 . A AA iqu1oGpY tQ2Z4 Qxkefj 0 0 161 198 208 0.5625 0.0 0.0161290322581 48 59 62 0.396694214876 1.0 LOW_indel AC=36;AN=812;AF=4.43350e-02;ESP=6.10101e-02 -1 47892241 . A T zKLRWM PlYNqKUqlpb SZW7lEol9R 0 0 51 105 143 0.333333333333 0.0 0.0238095238095 15 31 42 0.205479452055 0.999769024221 HIGH_SNV AC=52;AN=774;AF=6.71835e-02;ESP=6.73815e-02 -1 47892241 . A T pBo0A ze79u G 0 0 146 136 99 0.511627906977 0.0 0.0 43 40 29 0.623188405797 0.999081063908 HIGH_SNV AC=52;AN=774;AF=6.71835e-02;ESP=6.73815e-02 -1 47892241 . A T r FIdIJqCOu mWYD5 0 0 88 88 75 0.538461538462 0.0384615384615 0.0 26 26 22 0.541666666667 0.804783904939 MEDIUM_SNV AC=52;AN=774;AF=6.71835e-02;ESP=6.73815e-02 -1 47907198 . A T QjL5 EKCjT1P LS6RmDeZ 0 0 90 101 73 0.488372093023 0.0 0.0 43 48 35 0.518072289157 0.710702382258 MEDIUM_SNV AC=61;AN=792;AF=7.70202e-02;ESP=6.04613e-02 -1 49066392 . A AA o jlB SwMZo8eP 0 0 66 71 95 0.36 0.037037037037 0.0 25 27 36 0.396825396825 0.569000393109 LOW_indel AC=39;AN=802;AF=4.86284e-02;ESP=9.07821e-02 -1 50967776 . A AA Fgp n dGG9d5 0 0 153 133 176 0.413043478261 0.0 0.0 46 40 53 0.494623655914 0.999999715892 LOW_indel AC=38;AN=806;AF=4.71464e-02;ESP=5.10086e-02 -1 50967776 . A AA IivrYqEvonZ dyhkOKK yOwsIqZxFE3 0 0 80 246 150 0.541666666667 0.0 0.0444444444444 24 74 45 0.201680672269 0.999999994332 LOW_indel AC=38;AN=806;AF=4.71464e-02;ESP=5.10086e-02 -1 50967776 . A AA MxBdoNbVd ZgVITt FcZc 0 0 140 199 60 0.642857142857 0.0333333333333 0.0 42 60 18 0.538461538462 0.149960623974 LOW_indel AC=38;AN=806;AF=4.71464e-02;ESP=5.10086e-02 -1 51650849 . A T BUd6MlzZ5 UErgeKN ASUw96Pw2u 0 0 42 84 113 0.5 0.0208333333333 0.0153846153846 24 48 65 0.212389380531 0.978889342332 MEDIUM_SNV AC=38;AN=810;AF=4.69136e-02;ESP=4.85018e-02 -1 54305864 . A AA ou bw7ldn zMnt 0 0 114 159 138 0.535714285714 0.0 0.0294117647059 28 39 34 0.383561643836 0.999999966839 LOW_indel AC=15;AN=788;AF=1.90355e-02;ESP=7.89705e-03 -1 54322618 . A AA f5WJEcL2I p3z cjjzO6h3 0 0 165 102 130 0.574468085106 0.0 0.0 47 29 37 0.712121212121 0.999361456888 LOW_indel AC=46;AN=822;AF=5.59611e-02;ESP=9.76506e-02 -1 55573083 . A AA aVaoS wLkIi KGuvqVtPal 0 0 74 97 114 0.444444444444 0.0212765957447 0.0181818181818 36 47 55 0.352941176471 0.998336974683 LOW_indel AC=23;AN=808;AF=2.84653e-02;ESP=7.65650e-02 -1 56233488 . A AA fWaKp7W3ts2 s c00b5R 0 0 70 110 77 0.709677419355 0.0408163265306 0.0 31 49 34 0.373493975904 0.937704387653 LOW_indel AC=24;AN=794;AF=3.02267e-02;ESP=0.00000e+00 -1 56233488 . A AA php7FHqhxN fyWBxQJi2 ldO55 0 0 119 113 56 0.509433962264 0.02 0.0 53 50 25 0.706666666667 0.106844530027 LOW_indel AC=24;AN=794;AF=3.02267e-02;ESP=0.00000e+00 -1 56233488 . A AA WOTVYx Xl73ywFPD Dp 0 0 79 135 88 0.571428571429 0.0 0.025641025641 35 60 39 0.353535353535 0.994753159104 LOW_indel AC=24;AN=794;AF=3.02267e-02;ESP=0.00000e+00 -1 56691088 . A T UZlGcu7JzfE iBEYtsek1R0 YaBF 0 0 111 86 131 0.37037037037 0.047619047619 0.0 27 21 32 0.509433962264 0.970082057641 MEDIUM_SNV AC=79;AN=808;AF=9.77723e-02;ESP=1.23300e-01 -1 56691088 . A T f5WJEcL2I p3z cjjzO6h3 0 0 160 103 127 0.564102564103 0.04 0.0322580645161 39 25 31 0.696428571429 0.999382599717 HIGH_SNV AC=79;AN=808;AF=9.77723e-02;ESP=1.23300e-01 -1 57528249 . A T aWW wGvw1m PuUZJskW 0 0 197 111 90 0.695652173913 0.0 0.0 46 26 21 0.978723404255 0.997096142636 HIGH_SNV AC=21;AN=800;AF=2.62500e-02;ESP=2.19386e-02 -1 57528249 . A T aRh4dC4 w1n9xDWTz5X J88Z 0 0 137 150 94 0.53125 0.0 0.0454545454545 32 35 22 0.561403508772 0.998851042492 HIGH_SNV AC=21;AN=800;AF=2.62500e-02;ESP=2.19386e-02 -1 57528249 . A T HXcqZutGNZL Yha AGDAZSW 0 0 107 128 150 0.32 0.0 0.0285714285714 25 30 35 0.384615384615 0.999999539178 HIGH_SNV AC=21;AN=800;AF=2.62500e-02;ESP=2.19386e-02 -1 59183948 . A T UGq2 WwO gi91 0 0 128 156 143 0.634146341463 0.02 0.0 41 50 46 0.427083333333 0.999999953239 HIGH_SNV AC=66;AN=806;AF=8.18859e-02;ESP=8.40570e-02 -1 59551822 . A T Mw CpgYWWOMv9Q O5e07l56orL 0 0 59 68 136 0.7 0.0 0.0217391304348 20 23 46 0.289855072464 0.485012217163 LOW_SNV AC=46;AN=794;AF=5.79345e-02;ESP=6.12264e-02 -1 59650220 . A T sFyHKW WFOYMh7J aHK 0 0 45 87 76 0.692307692308 0.04 0.0454545454545 13 25 22 0.276595744681 0.888190429892 MEDIUM_SNV AC=35;AN=826;AF=4.23729e-02;ESP=1.95075e-02 -1 59710629 . A T cNsANUG6 ZYdH2goBOWx L5 0 0 46 198 179 0.416666666667 0.0 0.0425531914894 12 52 47 0.121212121212 0.999999999993 MEDIUM_SNV AC=41;AN=798;AF=5.13784e-02;ESP=4.28203e-02 -1 59828423 . A AA GG9mvG8m bn02mGE9u You3TKfQka 0 0 163 100 59 0.681818181818 0.0 0.0 44 27 16 1.02325581395 0.0739953745671 LOW_indel AC=77;AN=794;AF=9.69773e-02;ESP=9.44260e-02 -1 59828423 . A AA HiI6Ng n7wzDoH3KoO VS11 0 0 137 100 189 0.459459459459 0.0 0.0196078431373 37 27 51 0.474358974359 0.999007015143 LOW_indel AC=77;AN=794;AF=9.69773e-02;ESP=9.44260e-02 -1 59828423 . A AA f5WJEcL2I p3z cjjzO6h3 0 0 204 163 111 0.545454545455 0.0227272727273 0.0 55 44 30 0.743243243243 0.999921051744 LOW_indel AC=77;AN=794;AF=9.69773e-02;ESP=9.44260e-02 -1 60194861 . A AA UZlGcu7JzfE iBEYtsek1R0 YaBF 0 0 90 134 70 0.611111111111 0.037037037037 0.0 18 27 14 0.439024390244 0.501069427269 LOW_indel AC=39;AN=818;AF=4.76773e-02;ESP=9.59162e-02 -1 61411005 . A T zKLRWM PlYNqKUqlpb SZW7lEol9R 0 0 34 102 99 0.230769230769 0.025641025641 0.0 13 39 38 0.168831168831 0.998501015599 LOW_SNV AC=52;AN=790;AF=6.58228e-02;ESP=7.40156e-02 -1 61411005 . A T GG9mvG8m bn02mGE9u You3TKfQka 0 0 73 104 78 0.535714285714 0.025 0.0 28 40 30 0.4 0.887931689118 MEDIUM_SNV AC=52;AN=790;AF=6.58228e-02;ESP=7.40156e-02 -1 61411005 . A T HiI6Ng n7wzDoH3KoO VS11 0 0 29 60 63 0.818181818182 0.0 0.0416666666667 11 23 24 0.234042553191 0.0773710474677 LOW_SNV AC=52;AN=790;AF=6.58228e-02;ESP=7.40156e-02 -1 61411005 . A T FyazriIR UTkmvOmA zJDC0YK 0 0 65 141 78 0.36 0.037037037037 0.0 25 54 30 0.297619047619 0.888181038405 MEDIUM_SNV AC=52;AN=790;AF=6.58228e-02;ESP=7.40156e-02 -1 62078605 . A AA Q0oMdGLz MW0FE6B rLAfu 0 0 51 96 153 0.5625 0.0 0.0208333333333 16 30 48 0.205128205128 0.998238649612 LOW_indel AC=53;AN=806;AF=6.57568e-02;ESP=4.63394e-02 -1 63448194 . A AA FyazriIR UTkmvOmA zJDC0YK 0 0 34 86 142 0.888888888889 0.0434782608696 0.0 9 23 38 0.147540983607 0.985836596171 LOW_indel AC=42;AN=796;AF=5.27638e-02;ESP=3.41617e-02 -1 63622369 . A T wN A5pHPhENV RKLQ 0 0 101 121 142 0.457142857143 0.047619047619 0.0408163265306 35 42 49 0.384615384615 0.999995360855 HIGH_SNV AC=43;AN=804;AF=5.34826e-02;ESP=3.65658e-02 -1 64278902 . A T CqwzHDh iQh v0kXL8 0 0 110 77 102 0.555555555556 0.0 0.0 27 19 25 0.613636363636 0.982873570067 HIGH_SNV AC=7;AN=818;AF=8.55746e-03;ESP=0.00000e+00 -1 64346385 . A T n1K ySPO1J ME07O5zUc 0 0 50 163 203 0.272727272727 0.0 0.0222222222222 11 36 45 0.135802469136 0.999999999827 LOW_SNV AC=25;AN=798;AF=3.13283e-02;ESP=1.01123e-02 -1 64346385 . A T U QBBcjW oqoydSBU1y5 0 0 163 59 258 0.583333333333 0.0 0.0175438596491 36 13 57 0.514285714286 0.187174801716 LOW_SNV AC=25;AN=798;AF=3.13283e-02;ESP=1.01123e-02 -1 64808826 . A T t6M1ZE cHlRpuznS UErxdwA0g 0 0 35 92 85 0.222222222222 0.0416666666667 0.0 9 24 22 0.195652173913 0.974541656762 LOW_SNV AC=52;AN=808;AF=6.43564e-02;ESP=6.30506e-02 -1 64808826 . A T r FIdIJqCOu mWYD5 0 0 85 88 81 0.409090909091 0.0434782608696 0.047619047619 22 23 21 0.5 0.938421689829 MEDIUM_SNV AC=52;AN=808;AF=6.43564e-02;ESP=6.30506e-02 -1 64808826 . A T NlS eguHEhm5 JpCu0WQS 0 0 92 134 108 0.708333333333 0.0285714285714 0.0 24 35 28 0.380952380952 0.999890588747 HIGH_SNV AC=52;AN=808;AF=6.43564e-02;ESP=6.30506e-02 -1 64947922 . A T NNJAaJ JVcb awI5MW6XS 0 0 112 104 124 0.53488372093 0.025 0.0208333333333 43 40 48 0.488636363636 0.999606432082 HIGH_SNV AC=63;AN=810;AF=7.77778e-02;ESP=9.40572e-02 -1 65056403 . A AA Ixll CF E 0 0 118 108 270 0.5 0.0 0.0363636363636 24 22 55 0.311688311688 0.999845174913 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65056403 . A AA Ht18G RXWbD3jL5za laEv35rdNU 0 0 103 113 324 0.571428571429 0.0434782608696 0.0151515151515 21 23 66 0.23595505618 0.999951034825 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65056403 . A AA w0 T cvXQaAn 0 0 265 172 236 0.5 0.0285714285714 0.0208333333333 54 35 48 0.650602409639 0.999999999938 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65056403 . A AA we AIt NYGQZQ5tx 0 0 324 251 270 0.545454545455 0.0392156862745 0.0 66 51 55 0.622641509434 1.0 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65056403 . A AA CyocLCY Dth86AGgL K 0 0 216 172 162 0.522727272727 0.0 0.0 44 35 33 0.647058823529 0.999999999322 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65056403 . A AA HXy2a12pp s2I Fp0a 0 0 211 103 138 0.46511627907 0.0 0.0357142857143 43 21 28 0.877551020408 0.999510409239 LOW_indel AC=46;AN=808;AF=5.69307e-02;ESP=9.38148e-02 -1 65411682 . A T AeaS4jjUx8 iVlc59pr7gM ouWlcjn 0 0 218 109 63 0.4375 0.0 0.0 48 24 14 1.26315789474 0.21301088378 LOW_SNV AC=56;AN=808;AF=6.93069e-02;ESP=6.23530e-02 -1 65411682 . A T UGq2 WwO gi91 0 0 154 100 190 0.411764705882 0.0 0.0238095238095 34 22 42 0.53125 0.999263392729 HIGH_SNV AC=56;AN=808;AF=6.93069e-02;ESP=6.23530e-02 -1 65411682 . A T tEOtgDi3mk pvO Vx8Uupq9E5F 0 0 86 95 68 0.526315789474 0.0 0.0 19 21 15 0.527777777778 0.460694574759 LOW_SNV AC=56;AN=808;AF=6.93069e-02;ESP=6.23530e-02 -1 66054893 . A AA u zxDaU4 UbNePRnK 0 0 67 153 82 0.470588235294 0.025641025641 0.047619047619 17 39 21 0.283333333333 0.94898365126 LOW_indel AC=40;AN=810;AF=4.93827e-02;ESP=8.01285e-02 -1 68741737 . A AA Ixll CF E 0 0 95 98 90 0.472222222222 0.0 0.0294117647059 36 37 34 0.507042253521 0.989662264682 LOW_indel AC=34;AN=812;AF=4.18719e-02;ESP=8.54904e-02 -1 68741737 . A AA yPxJCb6Y5 EGC CdExBV 0 0 138 164 122 0.442307692308 0.0161290322581 0.0 52 62 46 0.481481481481 0.999994310537 LOW_indel AC=34;AN=812;AF=4.18719e-02;ESP=8.54904e-02 -1 69091302 . A T A3N1hy D8SOc9a4 TR 0 0 78 59 121 0.448275862069 0.0 0.0222222222222 29 22 45 0.432835820896 0.11036634112 LOW_SNV AC=49;AN=824;AF=5.94660e-02;ESP=5.70427e-02 -1 70775966 . A AA fDzMU8 kRb cTN 0 0 43 57 68 0.428571428571 0.0357142857143 0.0 21 28 33 0.344262295082 0.0579955499004 LOW_indel AC=57;AN=802;AF=7.10723e-02;ESP=3.24346e-02 -1 71392638 . A AA oREsa B9 YySqUn6 0 0 112 139 128 0.48275862069 0.0277777777778 0.0 29 36 33 0.420289855072 0.999999185374 LOW_indel AC=35;AN=804;AF=4.35323e-02;ESP=2.16712e-04 -1 71392638 . A AA rYZUwaTQXV ltP yPRtluVw 0 0 35 143 120 0.333333333333 0.0 0.0 9 37 31 0.132352941176 0.99999521445 LOW_indel AC=35;AN=804;AF=4.35323e-02;ESP=2.16712e-04 -1 71409161 . A T DCDoJial CKE0nvz7kGZ aU8PL 0 0 74 69 120 0.5625 0.0 0.0384615384615 16 15 26 0.390243902439 0.592536622294 MEDIUM_SNV AC=15;AN=798;AF=1.87970e-02;ESP=4.90045e-02 -1 71498178 . A AA FyazriIR UTkmvOmA zJDC0YK 0 0 127 77 164 0.447368421053 0.0 0.0204081632653 38 23 49 0.527777777778 0.823305555116 LOW_indel AC=77;AN=794;AF=9.69773e-02;ESP=1.05064e-01 -1 71710911 . A AA aWW wGvw1m PuUZJskW 0 0 146 76 156 0.45652173913 0.0 0.0 46 24 49 0.630136986301 0.796364430992 LOW_indel AC=46;AN=784;AF=5.86735e-02;ESP=9.84364e-02 -1 71710911 . A AA aVaoS wLkIi KGuvqVtPal 0 0 76 73 137 0.375 0.0 0.0 24 23 43 0.363636363636 0.66216317998 LOW_indel AC=46;AN=784;AF=5.86735e-02;ESP=9.84364e-02 -1 73557674 . A T w0 T cvXQaAn 0 0 161 110 86 0.512195121951 0.0357142857143 0.0 41 28 22 0.82 0.992455089566 HIGH_SNV AC=3;AN=806;AF=3.72208e-03;ESP=2.61272e-02 -1 73675328 . A T sMYjo0 wXlKNKod pdD 0 0 220 101 124 0.583333333333 0.0454545454545 0.0 48 22 27 0.979591836735 0.999137260777 HIGH_SNV AC=64;AN=820;AF=7.80488e-02;ESP=1.05764e-01 -1 74410955 . A AA UZlGcu7JzfE iBEYtsek1R0 YaBF 0 0 61 89 57 0.51724137931 0.047619047619 0.037037037037 29 42 27 0.420289855072 0.170294467023 LOW_indel AC=18;AN=810;AF=2.22222e-02;ESP=0.00000e+00 -1 74464602 . A T aWW wGvw1m PuUZJskW 0 0 66 66 115 0.37037037037 0.037037037037 0.0425531914894 27 27 47 0.364864864865 0.347752874492 LOW_SNV AC=48;AN=800;AF=6.00000e-02;ESP=6.90523e-02 -1 75395964 . A T Ko4 dqkzxIh AR 0 0 49 82 64 0.545454545455 0.0 0.0 22 37 29 0.333333333333 0.19981463678 LOW_SNV AC=57;AN=786;AF=7.25191e-02;ESP=9.52960e-02 -1 75395964 . A T h5zgnm DwKrxpp6Hy7 ItFL6J6 0 0 75 64 66 0.411764705882 0.0 0.0333333333333 34 29 30 0.576271186441 0.134598672701 LOW_SNV AC=57;AN=786;AF=7.25191e-02;ESP=9.52960e-02 -1 75937097 . A T aWW wGvw1m PuUZJskW 0 0 88 129 137 0.393939393939 0.0416666666667 0.0196078431373 33 48 51 0.333333333333 0.999999145216 HIGH_SNV AC=31;AN=818;AF=3.78973e-02;ESP=5.28911e-02 -1 75937097 . A T Ht18G RXWbD3jL5za laEv35rdNU 0 0 67 115 123 0.48 0.0232558139535 0.0217391304348 25 43 46 0.280898876404 0.999978529229 HIGH_SNV AC=31;AN=818;AF=3.78973e-02;ESP=5.28911e-02 -1 77971139 . A AA fDzMU8 kRb cTN 0 0 145 136 73 0.65625 0.0333333333333 0.0 32 30 16 0.695652173913 0.719873482057 LOW_indel AC=59;AN=804;AF=7.33831e-02;ESP=5.46689e-02 -1 77971139 . A AA we AIt NYGQZQ5tx 0 0 132 259 136 0.448275862069 0.0175438596491 0.0 29 57 30 0.333333333333 0.999999804972 LOW_indel AC=59;AN=804;AF=7.33831e-02;ESP=5.46689e-02 -1 77971139 . A AA DFbMPu5HA fe9XjJLofwz f 0 0 82 59 213 0.666666666667 0.0 0.0425531914894 18 13 47 0.3 0.0928110957926 LOW_indel AC=59;AN=804;AF=7.33831e-02;ESP=5.46689e-02 -1 78288013 . A AA GG9mvG8m bn02mGE9u You3TKfQka 0 0 210 184 169 0.464285714286 0.0204081632653 0.0222222222222 56 49 45 0.595744680851 0.999999999945 LOW_indel AC=31;AN=810;AF=3.82716e-02;ESP=1.53336e-02 -1 79576644 . A AA Q0oMdGLz MW0FE6B rLAfu 0 0 51 103 159 0.727272727273 0.0454545454545 0.0 11 22 34 0.196428571429 0.999626541761 LOW_indel AC=56;AN=798;AF=7.01754e-02;ESP=4.89485e-02 -1 79576644 . A AA SOC3AEPpME AGST9s09a spzDeRQ 0 0 243 187 234 0.557692307692 0.0 0.02 52 40 50 0.577777777778 0.999999999999 LOW_indel AC=56;AN=798;AF=7.01754e-02;ESP=4.89485e-02 -1 80096320 . 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