Update to htsjdk 4.1.0 (#8620)

* update to htsjdk 4.1.0 which enables http-nio in more cases * remove several test cases handling genomicsdb path parsing which were testing nonsensical paths that are now illegal
broadinstitute · Dec 13, 2023 · 23c8071 · 23c8071
1 parent 75f5104
commit 23c8071
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Showing 3 changed files with 1 addition and 6 deletions.
diff --git a/build.gradle b/build.gradle
@@ -57,7 +57,7 @@ repositories {
     mavenLocal()
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version','4.0.2')
+final htsjdkVersion = System.getProperty('htsjdk.version','4.1.0')
 final picardVersion = System.getProperty('picard.version','3.1.1')
 final barclayVersion = System.getProperty('barclay.version','5.0.0')
 final sparkVersion = System.getProperty('spark.version', '3.3.1')

diff --git a/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java
@@ -91,19 +91,16 @@ public Object[][] genDbPathAndNameData() {
                 {"argName:myname", "gendb://myJsons", "gendb://myJsons", "myname"},
                 {"argName:myname,key1=value1", "gendb://myJsons", "gendb://myJsons", "myname"},
                 {"argName:myname//", "gendb://myJsons", "gendb://myJsons", "myname//"},
-                {"argName:myname", "gendb://", "gendb://", "myname"},
 
                 {"argName", "gendb.gs://myBucket/myJsons", "gendb.gs://myBucket/myJsons", "gendb.gs://myBucket/myJsons"},
                 {"argName:myname", "gendb.gs://myJsons", "gendb.gs://myJsons", "myname"},
                 {"argName:myname,key1=value1", "gendb.gs://myJsons", "gendb.gs://myJsons", "myname"},
                 {"argName:myname//", "gendb.gs://myJsons", "gendb.gs://myJsons", "myname//"},
-                {"argName:myname", "gendb.gs://", "gendb.gs://", "myname"},
 
                 {"argName", "gendb.hdfs://localhost/myJsons", "gendb.hdfs://localhost/myJsons", "gendb.hdfs://localhost/myJsons"},
                 {"argName:myname", "gendb.hdfs://myJsons", "gendb.hdfs://myJsons", "myname"},
                 {"argName:myname,key1=value1", "gendb.hdfs://myJsons", "gendb.hdfs://myJsons", "myname"},
                 {"argName:myname//", "gendb.hdfs://myJsons", "gendb.hdfs://myJsons", "myname//"},
-                {"argName:myname", "gendb.hdfs://", "gendb.hdfs://", "myname"}
         };
     }
 

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java
@@ -687,7 +687,6 @@ public Object[][] genomicsDBTestPathData() {
                 {"fdfdf", null, null, false},
                 {"gendbdfdfdf://fdfdf", null, null, false},
                 {"gendb-dfdfdf://fdfdf", null, null, false},
-                {"gendb-dfdfdf://", null, null, false},
                 {"gendb", null, null, false},
                 {"gendbdfdf", null, null, false},
                 {"agendb://dfdfd", null, null, false},
@@ -696,7 +695,6 @@ public Object[][] genomicsDBTestPathData() {
 
                 {"gendb.dfdfdf://fdfdf", "dfdfdf://fdfdf", "gendb.dfdfdf://fdfdf", true},
                 {"gendb://fdfdf", "fdfdf", "gendb://" + new File("fdfdf").getAbsolutePath(), true},
-                {"gendb://", "", "gendb://" + new File("").getAbsolutePath(), true},
                 {"gendb:///fdfd", "/fdfd", "gendb:///fdfd", true},
                 {"gendb:///", "/", "gendb:///", true},
                 {"gendb.hdfs://this-node:9000/dir", "hdfs://this-node:9000/dir", "gendb.hdfs://this-node:9000/dir", true},