From f293eb7de1d831b3dcb10b4ec62a13130c07ae8b Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 16 Jul 2010 03:40:29 +0000 Subject: [PATCH] Fix for Kim: for some ungodly reason, I was initializing the bins that were maintaining counts to 1 instead of 0. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3801 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 4 ++-- 1 file changed, 2 insertions(+), 2 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 a715516af..ca7e343f2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -930,7 +930,7 @@ public class IndelRealigner extends ReadWalker { // set to 1 to prevent dividing by zero for ( int i=0; i < reference.length; i++ ) - originalMismatchBases[i] = totalOriginalBases[i] = cleanedMismatchBases[i] = totalCleanedBases[i] = 1; + originalMismatchBases[i] = totalOriginalBases[i] = cleanedMismatchBases[i] = totalCleanedBases[i] = 0; for (int i=0; i < reads.size(); i++) { final AlignedRead read = reads.get(i); @@ -991,7 +991,7 @@ public class IndelRealigner extends ReadWalker { if ( originalMismatchBases[i] > totalOriginalBases[i] * MISMATCH_THRESHOLD ) { didMismatch = true; originalMismatchColumns++; - if ( ((double)cleanedMismatchBases[i] / (double)totalCleanedBases[i]) > ((double)originalMismatchBases[i] / (double)totalOriginalBases[i]) * (1.0 - MISMATCH_COLUMN_CLEANED_FRACTION) ) { + if ( totalCleanedBases[i] > 0 && ((double)cleanedMismatchBases[i] / (double)totalCleanedBases[i]) > ((double)originalMismatchBases[i] / (double)totalOriginalBases[i]) * (1.0 - MISMATCH_COLUMN_CLEANED_FRACTION) ) { stillMismatches = true; cleanedMismatchColumns++; }