Fix toFile call that prevents IntervalListWriter from writing to Paths (

#1298) * Removing IntervalListWriter toFile call * fixes #1297 * nitpicky formatting and cleanup
samtools · Mar 1, 2019 · b1cb410 · b1cb410
1 parent 37b2e87
commit b1cb410
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Showing 7 changed files with 99 additions and 59 deletions.
diff --git a/src/main/java/htsjdk/samtools/liftover/LiftOver.java b/src/main/java/htsjdk/samtools/liftover/LiftOver.java
@@ -346,7 +346,7 @@ public String toString() {
                 // Matched a chain, but entirely within a gap.
                 return fromInterval.toString() + " (len " + fromInterval.length() + ")=>null using chain " + chainId;
             }
-            final String strand = toInterval.isNegativeStrand()? "-": "+";
+            final String strand = toInterval.getStrand().encode();
             return fromInterval.toString() + " (len " + fromInterval.length() + ")=>" + toInterval + "(" + strand
                     + ") using chain " + chainId + " ; pct matched " + percentLiftedOver;
         }

diff --git a/src/main/java/htsjdk/samtools/util/Interval.java b/src/main/java/htsjdk/samtools/util/Interval.java
@@ -24,6 +24,7 @@
 package htsjdk.samtools.util;
 
 import htsjdk.samtools.SAMException;
+import htsjdk.tribble.annotation.Strand;
 
 import java.util.Collection;
 
@@ -101,6 +102,13 @@ public boolean isPositiveStrand() {
         return !this.negativeStrand;
     }
 
+    /**
+     * Return the {@link Strand} this interval is on.
+     */
+    public Strand getStrand(){
+        return isNegativeStrand() ? Strand.NEGATIVE : Strand.FORWARD;
+    }
+
     /**
      * Returns the name of the interval, possibly null.
      */
@@ -210,7 +218,7 @@ public int hashCode() {
     }
 
     public String toString() {
-        return getContig() + ":" + getStart() + "-" + getEnd() + "\t" + (negativeStrand ? '-' : '+') + "\t" + ((null == name) ? '.' : name);
+        return getContig() + ":" + getStart() + "-" + getEnd() + "\t" + getStrand().encode() + "\t" + ((null == name) ? '.' : name);
     }
 
     @Override

diff --git a/src/main/java/htsjdk/samtools/util/IntervalCodec.java b/src/main/java/htsjdk/samtools/util/IntervalCodec.java
@@ -43,7 +43,7 @@ public IntervalCodec(final SAMSequenceDictionary dict) {
 
     @Override
     public IntervalCodec clone() {
-        return new IntervalCodec(this.dict);
+        return new IntervalCodec(dict);
     }
 
 
@@ -52,31 +52,31 @@ public IntervalCodec clone() {
      */
     @Override
     public void setOutputStream(final OutputStream os) {
-        this.binaryCodec.setOutputStream(os);
+        binaryCodec.setOutputStream(os);
     }
 
     /**
      * Sets the output stream that records will be written to.
      */
     public void setOutputStream(final OutputStream os, final String filename) {
-        this.binaryCodec.setOutputStream(os);
-        this.binaryCodec.setOutputFileName(filename);
+        binaryCodec.setOutputStream(os);
+        binaryCodec.setOutputFileName(filename);
     }
 
     /**
      * Sets the input stream that records will be read from.
      */
     @Override
     public void setInputStream(final InputStream is) {
-        this.binaryCodec.setInputStream(is);
+        binaryCodec.setInputStream(is);
     }
 
     /**
      * Sets the input stream that records will be read from.
      */
     public void setInputStream(final InputStream is, final String filename) {
-        this.binaryCodec.setInputStream(is);
-        this.binaryCodec.setInputFileName(filename);
+        binaryCodec.setInputStream(is);
+        binaryCodec.setInputFileName(filename);
     }
 
     /**
@@ -86,13 +86,13 @@ public void setInputStream(final InputStream is, final String filename) {
     @Override
     public void encode(final Interval interval) {
         final String name = interval.getName();
-        this.binaryCodec.writeInt(this.dict.getSequenceIndex(interval.getContig()));
-        this.binaryCodec.writeInt(interval.getStart());
-        this.binaryCodec.writeInt(interval.getEnd());
-        this.binaryCodec.writeBoolean(interval.isNegativeStrand());
-        this.binaryCodec.writeBoolean(name != null);
+        binaryCodec.writeInt(dict.getSequenceIndex(interval.getContig()));
+        binaryCodec.writeInt(interval.getStart());
+        binaryCodec.writeInt(interval.getEnd());
+        binaryCodec.writeBoolean(interval.isNegativeStrand());
+        binaryCodec.writeBoolean(name != null);
         if (name != null) {
-            this.binaryCodec.writeString(name, false, true);
+            binaryCodec.writeString(name, false, true);
         }
     }
 
@@ -104,16 +104,16 @@ public void encode(final Interval interval) {
     public Interval decode() {
         final int sequenceIndex;
         try {
-            sequenceIndex = this.binaryCodec.readInt();
+            sequenceIndex = binaryCodec.readInt();
         } catch (final RuntimeEOFException e) {
             return null;
         }
         return new Interval(
-            this.dict.getSequence(sequenceIndex).getSequenceName(),
-            this.binaryCodec.readInt(),
-            this.binaryCodec.readInt(),
-            this.binaryCodec.readBoolean(),
-             (this.binaryCodec.readBoolean()) ? this.binaryCodec.readNullTerminatedString() : null
+            dict.getSequence(sequenceIndex).getSequenceName(),
+            binaryCodec.readInt(),
+            binaryCodec.readInt(),
+            binaryCodec.readBoolean(),
+             (binaryCodec.readBoolean()) ? binaryCodec.readNullTerminatedString() : null
         );
     }
 }
diff --git a/src/main/java/htsjdk/samtools/util/IntervalListWriter.java b/src/main/java/htsjdk/samtools/util/IntervalListWriter.java
@@ -25,6 +25,7 @@
 
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMTextHeaderCodec;
+import htsjdk.tribble.annotation.Strand;
 
 import java.io.BufferedWriter;
 import java.io.Closeable;
@@ -37,9 +38,9 @@
  * to write, such that they all cannot be held in memory, for example in an {@link IntervalList}.
  */
 public class IntervalListWriter implements Closeable {
+    private static final char TAB = '\t';
 
     private final BufferedWriter out;
-    private final FormatUtil format = new FormatUtil();
 
     /** Creates a new writer, writing a header to the file.
      * @param path a path to write to.  If exists it will be overwritten.
@@ -52,8 +53,8 @@ public IntervalListWriter(final Path path) {
      * @param path a file to write to.  If exists it will be overwritten.
      * @param header the header to write.
      */
-    public IntervalListWriter(final  Path path, final SAMFileHeader header) {
-        out = IOUtil.openFileForBufferedWriting(path.toFile());
+    public IntervalListWriter(final Path path, final SAMFileHeader header) {
+        out = IOUtil.openFileForBufferedWriting(path);
 
         // Write out the header
         if (header != null) {
@@ -67,23 +68,19 @@ public IntervalListWriter(final  Path path, final SAMFileHeader header) {
      */
     public void write(final Interval interval) throws IOException {
         out.write(interval.getContig());
-        out.write('\t');
+        out.write(TAB);
         out.write(Integer.toString(interval.getStart()));
-        out.write('\t');
+        out.write(TAB);
         out.write(Integer.toString(interval.getEnd()));
-        out.write('\t');
-        out.write(interval.isPositiveStrand() ? '+' : '-');
-        out.write('\t');
-        if(interval.getName() != null){
-            out.write(interval.getName());
-        }
-        else{
-            out.write(".");
-        }
+        out.write(TAB);
+        out.write(interval.getStrand().encode());
+        out.write(TAB);
+        out.write(interval.getName() != null ? interval.getName() : ".");
         out.newLine();
     }
 
     /** Closes the writer. */
+    @Override
     public void close() throws IOException {
         out.flush();
         out.close();

diff --git a/src/test/java/htsjdk/samtools/util/IntervalCodecTest.java b/src/test/java/htsjdk/samtools/util/IntervalCodecTest.java
@@ -59,27 +59,25 @@ public void testEndToEnd() throws IOException  {
         expectedList.add(new Interval("chr1", 50, 150, true, "number-5"));
         expectedList.add(new Interval("chr1", 150, 250, false, "number-6"));
 
-        final OutputStream outputStream = new FileOutputStream(tempFile);
-        final IntervalCodec writeCodec = new IntervalCodec(this.dict);
-        writeCodec.setOutputStream(outputStream);
-        for (final Interval interval : expectedList.getIntervals()) {
-            writeCodec.encode(interval);
+        try (final OutputStream outputStream = new FileOutputStream(tempFile)) {
+            final IntervalCodec writeCodec = new IntervalCodec(this.dict);
+            writeCodec.setOutputStream(outputStream);
+            for (final Interval interval : expectedList.getIntervals()) {
+                writeCodec.encode(interval);
+            }
         }
-        outputStream.close();
 
         final IntervalCodec readCodec = new IntervalCodec(this.dict);
-        final InputStream inputStream = new FileInputStream(tempFile);
-        readCodec.setInputStream(inputStream);
-        while (true) {
-            final Interval interval = readCodec.decode();
-            if (interval == null) {
-                break;
-            }
-            else {
+        try (final InputStream inputStream = new FileInputStream(tempFile)) {
+            readCodec.setInputStream(inputStream);
+            while (true) {
+                final Interval interval = readCodec.decode();
+                if (interval == null) {
+                    break;
+                }
                 actualList.add(interval);
             }
         }
-        inputStream.close();
 
         Assert.assertEquals(
                 actualList.getIntervals(),

diff --git a/src/test/java/htsjdk/samtools/util/IntervalListWriterTest.java b/src/test/java/htsjdk/samtools/util/IntervalListWriterTest.java
@@ -1,5 +1,8 @@
 package htsjdk.samtools.util;
 
+import com.google.common.jimfs.Configuration;
+import com.google.common.jimfs.Jimfs;
+import com.google.common.jimfs.SystemJimfsFileSystemProvider;
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -10,6 +13,9 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.FileSystem;
+import java.nio.file.Files;
+import java.nio.file.Path;
 
 public class IntervalListWriterTest extends HtsjdkTest {
     private SAMSequenceDictionary dict;
@@ -26,7 +32,19 @@ void setup() {
     public void testEndToEnd() throws IOException {
         final File tempFile = File.createTempFile("IntervalListWriterTest.", ".interval_list");
         tempFile.deleteOnExit();
+        testEndToEnd(tempFile.toPath());
+    }
+
+    @Test
+    public void testEndToEndOnPath() throws IOException {
+        //create an in memory file system that mimics a unix one
+        try (FileSystem jimfs = Jimfs.newFileSystem(Configuration.unix())) {
+            final Path tempFile = Files.createTempFile(jimfs.getRootDirectories().iterator().next(), "IntervalListWriterTest.", ".interval_list");
+            testEndToEnd(tempFile);
+        }
+    }
 
+    private void testEndToEnd(Path tempFile) throws IOException {
         final IntervalList expectedList = new IntervalList(this.dict);
 
         expectedList.add(new Interval("chr1", 50, 150));
@@ -36,19 +54,16 @@ public void testEndToEnd() throws IOException {
         expectedList.add(new Interval("chr1", 50, 150, true, "number-5"));
         expectedList.add(new Interval("chr1", 150, 250, false, "number-6"));
 
-        final IntervalListWriter writer = new IntervalListWriter(tempFile.toPath(), new SAMFileHeader(this.dict));
-        for (final Interval interval : expectedList.getIntervals()) {
-            writer.write(interval);
+        try (final IntervalListWriter writer = new IntervalListWriter(tempFile, new SAMFileHeader(this.dict))) {
+            for (final Interval interval : expectedList.getIntervals()) {
+                writer.write(interval);
+            }
         }
-        writer.close();
 
-        final IntervalList actualList = IntervalList.fromFile(tempFile);
+        final IntervalList actualList = IntervalList.fromPath(tempFile);
         final SAMSequenceDictionary actualDict = actualList.getHeader().getSequenceDictionary();
         final SAMSequenceDictionary expectedDict = expectedList.getHeader().getSequenceDictionary();
         Assert.assertTrue(actualDict.isSameDictionary(expectedDict));
-        Assert.assertEquals(
-                actualList.getIntervals(),
-                expectedList.getIntervals()
-        );
+        Assert.assertEquals(actualList.getIntervals(), expectedList.getIntervals());
     }
 }
diff --git a/src/test/java/htsjdk/samtools/util/IntervalTest.java b/src/test/java/htsjdk/samtools/util/IntervalTest.java
@@ -0,0 +1,22 @@
+package htsjdk.samtools.util;
+
+import htsjdk.HtsjdkTest;
+import htsjdk.tribble.annotation.Strand;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class IntervalTest extends HtsjdkTest {
+    @DataProvider
+    public Object[][] booleanProvider(){
+        return new Object[][]{{true}, {false}};
+    }
+
+    @Test(dataProvider = "booleanProvider")
+    public void testGetStrand(boolean isNegativeStrand){
+        final Interval interval = new Interval("chr1", 1, 100, isNegativeStrand, "name");
+        Assert.assertEquals(isNegativeStrand, interval.isNegativeStrand());
+        Assert.assertNotEquals(isNegativeStrand, interval.isPositiveStrand());
+        Assert.assertEquals(isNegativeStrand, interval.getStrand() == Strand.NEGATIVE);
+    }
+}