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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
This commit is contained in:
ebanks 2010-07-16 03:40:29 +00:00
parent e7e58d7129
commit f293eb7de1
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -930,7 +930,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// 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<Integer, Integer> {
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++;
}