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Removing more toUpperCase sanity checks 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-02 14:38:39 +00:00
parent 56e504789a
commit 4a555827aa
5 changed files with 5 additions and 9 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -63,7 +63,7 @@ public class AlleleBalance implements InfoFieldAnnotation, StandardAnnotation {
continue; continue;
if ( vc.isSNP() ) { if ( vc.isSNP() ) {
final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases()).toUpperCase(); final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases());
if ( bases.length() == 0 ) if ( bases.length() == 0 )
return null; return null;
char refChr = vc.getReference().toString().charAt(0); char refChr = vc.getReference().toString().charAt(0);

4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -55,14 +55,14 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
int leftRun = 0; int leftRun = 0;
for ( int i = refBasePos - 1; i >= 0; i--) { for ( int i = refBasePos - 1; i >= 0; i--) {
if ( Character.toUpperCase(bases[i]) != altAllele ) if ( bases[i] != altAllele )
break; break;
leftRun++; leftRun++;
} }
int rightRun = 0; int rightRun = 0;
for ( int i = refBasePos + 1; i < bases.length; i++) { for ( int i = refBasePos + 1; i < bases.length; i++) {
if ( Character.toUpperCase(bases[i]) != altAllele ) if ( bases[i] != altAllele )
break; break;
rightRun++; rightRun++;
} }

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -115,7 +115,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
if ( verboseWriter != null ) { if ( verboseWriter != null ) {
StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t"); StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
for ( byte altAllele : BaseUtils.BASES ) { for ( byte altAllele : BaseUtils.BASES ) {
//char base = Character.toUpperCase(altAllele);
header.append("POfDGivenAFFor" + (char)altAllele + "\t"); header.append("POfDGivenAFFor" + (char)altAllele + "\t");
header.append("PosteriorAFFor" + (char)altAllele + "\t"); header.append("PosteriorAFFor" + (char)altAllele + "\t");
} }

4
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -123,7 +123,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
if ( pileup != null ) { if ( pileup != null ) {
int mismatchQualities = 0, totalQualities = 0; int mismatchQualities = 0, totalQualities = 0;
char refBase = (char)ref.getBase(); byte refBase = ref.getBase();
for (PileupElement p : pileup ) { for (PileupElement p : pileup ) {
// check the ends of the reads to see how far they extend // check the ends of the reads to see how far they extend
SAMRecord read = p.getRead(); SAMRecord read = p.getRead();
@ -136,7 +136,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
// look for mismatches // look for mismatches
else { else {
if ( Character.toUpperCase(p.getBase()) != refBase ) if ( p.getBase() != refBase )
mismatchQualities += p.getQual(); mismatchQualities += p.getQual();
totalQualities += p.getQual(); totalQualities += p.getQual();
} }

3
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -195,9 +195,6 @@ public class AlignmentUtils {
byte readChr = readBases[readIndex]; byte readChr = readBases[readIndex];
if ( readChr != refChr ) if ( readChr != refChr )
sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1; sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
// char readChr = (char)readBases[readIndex];
// if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
// sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
} }
break; break;
case I: case I: