From d27800e07caa203e904724f1ab821507745f5778 Mon Sep 17 00:00:00 2001 From: delangel Date: Wed, 8 Jun 2011 11:28:17 +0000 Subject: [PATCH] a) Forgot to commit this ages ago: uncomment code to ignore hard clipped bases when computing indel likelihoods. b) First part of fix for correctly processing mixed multi-allelic records: correctly compute start/stop of vc when there are no null alleles (i.e. record is not a simple indel). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5957 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 6def5c3ac..56e2ab6b3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -841,7 +841,7 @@ public class PairHMMIndelErrorModel { numEndSoftClippedBases = read.getUnclippedEnd()- read.getAlignmentEnd(); // check for hard clips (never consider these bases): - /* Cigar c = read.getCigar(); + Cigar c = read.getCigar(); CigarElement first = c.getCigarElement(0); CigarElement last = c.getCigarElement(c.numCigarElements()-1); int numStartHardClippedBases = 0, numEndHardClippedBases = 0; @@ -859,7 +859,7 @@ public class PairHMMIndelErrorModel { numEndSoftClippedBases -= numEndHardClippedBases; readStart += numStartHardClippedBases; readEnd -= numEndHardClippedBases; - */ + // remove soft clips if necessary if ((read.getAlignmentStart()>=eventStartPos-eventLength && read.getAlignmentStart() <= eventStartPos+1) || (read.getAlignmentEnd() >= eventStartPos && read.getAlignmentEnd() <= eventStartPos + eventLength)) {