From a21c2a7e48f5c1e62a6cc8c6b8fe97c1df50232a Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 21 Jun 2009 04:51:42 +0000 Subject: [PATCH] don't make mapping quality too high git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1066 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IntervalCleanerWalker.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java index bf5ae5025..0a1cfb3ac 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java @@ -360,13 +360,13 @@ public class IntervalCleanerWalker extends LocusWindowWalker // however we don't have enough info to use the proper MAQ scoring system. // For now, we'll use a heuristic: // the mapping quality score is improved by the LOD difference in mismatching - // bases between the reference and alternate consensus + // bases between the reference and alternate consensus (divided by 10) // finish cleaning the appropriate reads for ( Pair indexPair : bestConsensus.readIndexes ) { AlignedRead aRead = altReads.get(indexPair.first); if ( aRead.finalizeUpdate() ) { - aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)improvement, 255)); + aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)(improvement/10.0), 255)); aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex)); } } @@ -393,7 +393,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker for ( AlignedRead aRec : leftMovedIndels ) aRec.finalizeUpdate(); for ( AlignedRead aRec : altReads ) { - if ( aRec.wasUpdated() ) + if ( !cleanedReadsOnly || aRec.wasUpdated() ) readsToWrite.add(new ComparableSAMRecord(aRec.getRead())); } }