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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
This commit is contained in:
delangel 2011-06-08 11:28:17 +00:00
parent ad97099df6
commit d27800e07c
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -841,7 +841,7 @@ public class PairHMMIndelErrorModel {
numEndSoftClippedBases = read.getUnclippedEnd()- read.getAlignmentEnd(); numEndSoftClippedBases = read.getUnclippedEnd()- read.getAlignmentEnd();
// check for hard clips (never consider these bases): // check for hard clips (never consider these bases):
/* Cigar c = read.getCigar(); Cigar c = read.getCigar();
CigarElement first = c.getCigarElement(0); CigarElement first = c.getCigarElement(0);
CigarElement last = c.getCigarElement(c.numCigarElements()-1); CigarElement last = c.getCigarElement(c.numCigarElements()-1);
int numStartHardClippedBases = 0, numEndHardClippedBases = 0; int numStartHardClippedBases = 0, numEndHardClippedBases = 0;
@ -859,7 +859,7 @@ public class PairHMMIndelErrorModel {
numEndSoftClippedBases -= numEndHardClippedBases; numEndSoftClippedBases -= numEndHardClippedBases;
readStart += numStartHardClippedBases; readStart += numStartHardClippedBases;
readEnd -= numEndHardClippedBases; readEnd -= numEndHardClippedBases;
*/
// remove soft clips if necessary // remove soft clips if necessary
if ((read.getAlignmentStart()>=eventStartPos-eventLength && read.getAlignmentStart() <= eventStartPos+1) || if ((read.getAlignmentStart()>=eventStartPos-eventLength && read.getAlignmentStart() <= eventStartPos+1) ||
(read.getAlignmentEnd() >= eventStartPos && read.getAlignmentEnd() <= eventStartPos + eventLength)) { (read.getAlignmentEnd() >= eventStartPos && read.getAlignmentEnd() <= eventStartPos + eventLength)) {