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don't crash when an unmapped read is encountered, just write it into the output file, it should be ok 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1111 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-26 15:33:59 +00:00
parent da1f168a3e
commit 1a97c86f95
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjector.java
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@ -95,6 +95,12 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
*/ */
@Override @Override
public Integer map(char[] ref, SAMRecord read) { public Integer map(char[] ref, SAMRecord read) {
if( read.getReadUnmappedFlag() ) {
outputBAM.addAlignment(read);
return 0;
}
GenomeLoc loc = GenomeLocParser.createGenomeLoc(read); GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
while( loc.isPast(interval) && intervals.size() > 0 ) { while( loc.isPast(interval) && intervals.size() > 0 ) {