From e6200fe5b51b13a077e2adee55a4a1d8079bc8e9 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 21 May 2009 19:24:10 +0000 Subject: [PATCH] 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 --- .../sting/playground/gatk/walkers/IntervalCleanerWalker.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java index 1cd6824b7..708edb3f2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java @@ -65,7 +65,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker List reads = context.getReads(); ArrayList goodReads = new ArrayList(); for ( SAMRecord read : reads ) { - if ( read.getReadLength() <= maxReadLength && + if ( (maxReadLength < 0 || read.getReadLength() <= maxReadLength) && !read.getReadUnmappedFlag() && !read.getNotPrimaryAlignmentFlag() && !read.getDuplicateReadFlag() && @@ -259,7 +259,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength(); str.append(":" + (leftmostIndex + position)); 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 { indelOutput.write(str.toString()); } catch (Exception e) {}