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samtools · Oct 15, 2018 · 39c0997 · 39c0997
1 parent 4cf7ce9
commit 39c0997
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Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/src/main/java/htsjdk/samtools/CRAMIterator.java b/src/main/java/htsjdk/samtools/CRAMIterator.java
@@ -266,7 +266,7 @@ public boolean hasNext() {
 
     @Override
     public SAMRecord next() {
-        if(hasNext()) {
+        if (hasNext()) {
             return iterator.next();
         } else {
             throw new NoSuchElementException();

diff --git a/src/test/java/htsjdk/samtools/CRAMTestUtils.java b/src/test/java/htsjdk/samtools/CRAMTestUtils.java
@@ -14,6 +14,7 @@
 
 public final class CRAMTestUtils {
 
+    //private constructor since this is a utility class
     private CRAMTestUtils(){};
 
     /**
@@ -40,21 +41,22 @@ public static CRAMFileReader writeAndReadFromInMemoryCram(SAMRecordSetBuilder re
     }
 
     private static CRAMFileReader writeAndReadFromInMemoryCram(Collection<SAMRecord> records, CRAMReferenceSource source, SAMFileHeader header) throws IOException {
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-        CRAMFileWriter cramFileWriter = new CRAMFileWriter(baos, source, header, "whatever");
+        try(ByteArrayOutputStream baos = new ByteArrayOutputStream();
+            CRAMFileWriter cramFileWriter = new CRAMFileWriter(baos, source, header, "whatever")){
 
-        for (SAMRecord record : records) {
-            cramFileWriter.addAlignment(record);
-        }
-        cramFileWriter.close();
+            records.forEach(cramFileWriter::addAlignment);
+
+            //force a flush before reading from the buffer
+            cramFileWriter.close();
 
-        return new CRAMFileReader(new ByteArrayInputStream(baos.toByteArray()), (SeekableStream) null, source, ValidationStringency.SILENT);
+            return new CRAMFileReader(new ByteArrayInputStream(baos.toByteArray()), (SeekableStream) null, source, ValidationStringency.SILENT);
+        }
     }
 
     /**
      * return a CRAMReferenceSource that returns all A's for any sequence queried
      */
-    public static CRAMReferenceSource getFakeReferenceSource(){
+    public static CRAMReferenceSource getFakeReferenceSource() {
         return (sequenceRecord, tryNameVariants) -> {
             byte[] bases = new byte[sequenceRecord.getSequenceLength()];
             Arrays.fill(bases, (byte)'A');