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don't ignore reads when maxReadLength isn't set 

also, print out LOD score for cleaning


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-21 19:24:10 +00:00
parent 0219d33e10
commit e6200fe5b5
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -65,7 +65,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
List<SAMRecord> reads = context.getReads(); List<SAMRecord> reads = context.getReads();
ArrayList<SAMRecord> goodReads = new ArrayList<SAMRecord>(); ArrayList<SAMRecord> goodReads = new ArrayList<SAMRecord>();
for ( SAMRecord read : reads ) { for ( SAMRecord read : reads ) {
if ( read.getReadLength() <= maxReadLength && if ( (maxReadLength < 0 || read.getReadLength() <= maxReadLength) &&
!read.getReadUnmappedFlag() && !read.getReadUnmappedFlag() &&
!read.getNotPrimaryAlignmentFlag() && !read.getNotPrimaryAlignmentFlag() &&
!read.getDuplicateReadFlag() && !read.getDuplicateReadFlag() &&
@ -259,7 +259,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength(); int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength();
str.append(":" + (leftmostIndex + position)); str.append(":" + (leftmostIndex + position));
CigarElement ce = bestConsensus.cigar.getCigarElement(1); CigarElement ce = bestConsensus.cigar.getCigarElement(1);
str.append(" " + ce.getLength() + ce.getOperator() + "\n"); str.append("\t" + ce.getLength() + ce.getOperator());
str.append("\t" + (((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0) + "\n");
try { try {
indelOutput.write(str.toString()); indelOutput.write(str.toString());
} catch (Exception e) {} } catch (Exception e) {}