From 4623a34ad39628fd82781383b72cce2eb1f5a0a6 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 5 Jun 2009 18:46:41 +0000 Subject: [PATCH] Fix bug in realigning insertion cigar strings git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@914 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/indels/IntervalCleanerWalker.java | 4 ++-- .../gatk/walkers/indels/MismatchIntervalWalker.java | 2 +- 2 files 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 6f60b1162..b51bd0ee7 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 @@ -529,7 +529,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker } logger.debug("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns); - //out.println("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns); + //out.println("**** Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns); return (originalMismatchColumns == 0 || cleanedMismatchColumns < originalMismatchColumns); } @@ -551,7 +551,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker } difference = indelIndex - newIndex; } else if ( ce2.getOperator() == CigarOperator.I ) { - int indelIndex = ce1.getLength(); + int indelIndex = refIndex + ce1.getLength(); String indelString = readSeq.substring(indelIndex, indelIndex+ce2.getLength()); int newIndex = indelIndex; while ( newIndex > 0 ) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java index 8192643b5..1d5eb2639 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java @@ -16,7 +16,7 @@ public class MismatchIntervalWalker extends LocusWalker @Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false) public int windowSize = 10; @Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of mismatching base qualities threshold", required=false) - public double mismatchThreshold = 0.20; + public double mismatchThreshold = 0.15; private final int minReadsAtInterval = 4;