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Output indels in the format appropriate for low-coverage indel submission 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@832 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-27 17:32:15 +00:00
parent 3098ed091c
commit 9bd6489f8e
1 changed files with 9 additions and 3 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -270,12 +270,18 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( bestConsensus != null && ((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0 >= LOD_THRESHOLD ) { if ( bestConsensus != null && ((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0 >= LOD_THRESHOLD ) {
logger.debug("CLEAN: " + bestConsensus.str ); logger.debug("CLEAN: " + bestConsensus.str );
if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) { if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
// NOTE: indels are printed out in the format specified for the low-coverage pilot1
// indel calls (tab-delimited): chr position size type sequence
StringBuffer str = new StringBuffer(); StringBuffer str = new StringBuffer();
str.append(reads.get(0).getReferenceName()); str.append(reads.get(0).getReferenceName());
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength() - 1; int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength();
str.append(":" + (leftmostIndex + position)); str.append("\t" + (leftmostIndex + position - 1));
CigarElement ce = bestConsensus.cigar.getCigarElement(1); CigarElement ce = bestConsensus.cigar.getCigarElement(1);
str.append("\t" + ce.getLength() + ce.getOperator()); str.append("\t" + ce.getLength() + "\t" + ce.getOperator() + "\t");
if ( ce.getOperator() == CigarOperator.D )
str.append(reference.substring(position, position+ce.getLength()));
else
str.append(bestConsensus.str.substring(position, position+ce.getLength()));
str.append("\t" + (((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0) + "\n"); str.append("\t" + (((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0) + "\n");
try { try {
indelOutput.write(str.toString()); indelOutput.write(str.toString());