Removing IntervalListWriter toFile call

* fixes #1297 * nitpicky formatting and cleanup
samtools · Feb 26, 2019 · d6b44c6 · d6b44c6
1 parent a6c5837
commit d6b44c6
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Showing 3 changed files with 47 additions and 38 deletions.
diff --git a/src/main/java/htsjdk/samtools/util/IntervalListWriter.java b/src/main/java/htsjdk/samtools/util/IntervalListWriter.java
@@ -37,9 +37,9 @@
  * 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 +52,8 @@ 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 +67,19 @@ 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(TAB);
         out.write(interval.isPositiveStrand() ? '+' : '-');
-        out.write('\t');
-        if(interval.getName() != null){
-            out.write(interval.getName());
-        }
-        else{
-            out.write(".");
-        }
+        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 +59,26 @@ 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 {
-                actualList.add(interval);
+        try(final InputStream inputStream = new FileInputStream(tempFile)) {
+            readCodec.setInputStream(inputStream);
+            while (true) {
+                final Interval interval = readCodec.decode();
+                if (interval == null) {
+                    break;
+                } else {
+                    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 +32,18 @@ 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 {
+        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 +53,16 @@ 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());
     }
 }