From bbbad79f8c8464d9b044214f377429e595f3ba50 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 18 Feb 2010 18:12:58 +0000 Subject: [PATCH] Forgot to remove debugging code git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2854 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 62654509b..46d375b93 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -478,18 +478,12 @@ public class IndelRealigner extends ReadWalker { while ( iter.hasNext() ) { Consensus consensus = iter.next(); - int indelSize = 0; - for ( CigarElement ce : consensus.cigar.getCigarElements() ) - if ( ce.getOperator() == CigarOperator.I || ce.getOperator() == CigarOperator.D ) { - indelSize = ce.getLength(); - break; - } // if ( debugOn ) System.out.println("Consensus: "+consensus.str); for ( int j = 0; j < altReads.size(); j++ ) { AlignedRead toTest = altReads.get(j); - Pair altAlignment = findBestOffset(consensus.str, toTest, (int)leftmostIndex, indelSize); + Pair altAlignment = findBestOffset(consensus.str, toTest, (int)leftmostIndex); // the mismatch score is the min of its alignment vs. the reference and vs. the alternate int myScore = altAlignment.second; @@ -695,7 +689,7 @@ public class IndelRealigner extends ReadWalker { return new Consensus(altConsensus, cigar, indexOnRef); } - private Pair findBestOffset(final byte[] ref, final AlignedRead read, final int leftmostIndex, int indelSize) { + private Pair findBestOffset(final byte[] ref, final AlignedRead read, final int leftmostIndex) { // optimization: try the most likely alignment first (to get a low score to beat) int originalAlignment = read.getOriginalAlignmentStart() - leftmostIndex;