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Fixed bug where new sharding system wasn't grabbing the reads that start at the end of a bin. Caused by what I currently believe to be a bug in Picard -- will verify with Alec. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2826 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-11 17:00:04 +00:00
parent 96fee7cf7a
commit 34e566c90d
1 changed files with 1 additions and 3 deletions
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4
java/src/net/sf/samtools/BAMFileReader2.java
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@ -399,8 +399,6 @@ class BAMFileReader2
public SAMRecord next() { public SAMRecord next() {
final SAMRecord result = mNextRecord; final SAMRecord result = mNextRecord;
if(result.getAlignmentStart() <= 11632602 && result.getAlignmentEnd() >= 11632602)
System.out.printf("11632602: %s%n", result.getReadName());
advance(); advance();
return result; return result;
} }
@ -495,7 +493,7 @@ class BAMFileReader2
throws IOException { throws IOException {
while (true) { while (true) {
// Advance to next file block if necessary // Advance to next file block if necessary
while (mCompressedInputStream.getFilePointer() >= mFilePointerLimit) { while (mCompressedInputStream.getFilePointer() > mFilePointerLimit) {
if (mFilePointers == null || if (mFilePointers == null ||
mFilePointerIndex >= mFilePointers.length) { mFilePointerIndex >= mFilePointers.length) {
return null; return null;