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Change for lower-case references (always compare upper case bases) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1888 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-20 17:36:31 +00:00
parent 3b1fabeff0
commit b83df5616a
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -138,7 +138,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
public boolean useRead( SAMRecord read, int offset, ReferenceContext ref ) { public boolean useRead( SAMRecord read, int offset, ReferenceContext ref ) {
if ( Character.toUpperCase(read.getReadBases()[offset]) == ref.getBase() ) { if ( Character.toUpperCase(read.getReadBases()[offset]) == Character.toUpperCase(ref.getBase()) ) {
return false; return false;
} else if ( read.getMappingQuality() <= minMappingQuality ) { } else if ( read.getMappingQuality() <= minMappingQuality ) {
return false; return false;
@ -300,6 +300,9 @@ class BaseTransitionTable {
} }
public void update(char observedBase, char refBase ) { public void update(char observedBase, char refBase ) {
//if ( observedBase == refBase ) {
// throw new StingException("BaseTransitionTable received equal observed and reference bases, which should not happen.");
//}
table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)] ++; table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)] ++;
} }