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an attempt to bail out when unmapped reads are reached at the end of the file(s). still testing... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@973 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-10 19:53:50 +00:00
parent 030efc468f
commit 39dcd4f11f
1 changed files with 10 additions and 0 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -77,6 +77,12 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Override
public Integer map(char[] ref, SAMRecord read) {
if ( read.getReadUnmappedFlag() && read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX &&
read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) {
System.out.println("I think I reached unmapped reads at the end of the file(s) and I am done...");
return -1;
}
if ( read.getReadUnmappedFlag() ||
read.getDuplicateReadFlag() ||
read.getNotPrimaryAlignmentFlag() ||
@ -264,6 +270,10 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Override
public Integer reduce(Integer value, Integer sum) {
if ( value == -1 ) {
onTraversalDone(sum);
System.exit(1);
}
sum += value;
return sum;
}