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Fix correctness issue when dynamically merging many files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5512 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-25 16:35:43 +00:00
parent c9283e6bc5
commit 8d8aed6a67
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
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@ -159,6 +159,9 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
final long readerStopOffset = position(); final long readerStopOffset = position();
scheduleIterators.add(new PeekableIterator<BAMScheduleEntry>(new BAMScheduleIterator(reader,readerStartOffset,readerStopOffset,maxChunkCount))); scheduleIterators.add(new PeekableIterator<BAMScheduleEntry>(new BAMScheduleIterator(reader,readerStartOffset,readerStopOffset,maxChunkCount)));
// Iterator initialization might move the file pointer. Make sure it gets reset back to where it was before iterator initialization.
position(readerStopOffset);
} }
advance(); advance();
@ -296,6 +299,8 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
private void write(final ByteBuffer buffer) { private void write(final ByteBuffer buffer) {
try { try {
scheduleFileChannel.write(buffer); scheduleFileChannel.write(buffer);
if(buffer.remaining() > 0)
throw new ReviewedStingException("Unable to write entire buffer to file.");
} }
catch(IOException ex) { catch(IOException ex) {
throw new ReviewedStingException("Unable to write data to BAM schedule file.",ex); throw new ReviewedStingException("Unable to write data to BAM schedule file.",ex);