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read.getReadString().charAt(offset) --> read.getReadBases()[offset] 

[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-24 04:25:19 +00:00
parent ec321abd7b
commit c90bea39a1
8 changed files with 10 additions and 10 deletions
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2
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -193,7 +193,7 @@ public class LocusIteratorByState extends LocusIterator {
logger.debug(String.format("printState():")); logger.debug(String.format("printState():"));
SAMRecord read = state.getRead(); SAMRecord read = state.getRead();
int offset = state.getReadOffset(); int offset = state.getReadOffset();
logger.debug(String.format(" read: %s(%d)=%s, cigar=%s", read.getReadName(), offset, read.getReadString().charAt(offset), read.getCigarString())); logger.debug(String.format(" read: %s(%d)=%s, cigar=%s", read.getReadName(), offset, (char)read.getReadBases()[offset], read.getCigarString()));
} }
} }

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -163,7 +163,7 @@ public class FisherStrand extends StandardVariantAnnotation {
if ( offset == -1 ) if ( offset == -1 )
continue; continue;
int readAllele = BaseUtils.simpleBaseToBaseIndex(read.getReadString().charAt(offset)); int readAllele = BaseUtils.simpleBaseToBaseIndex((char)read.getReadBases()[offset]);
boolean isFW = !read.getReadNegativeStrandFlag(); boolean isFW = !read.getReadNegativeStrandFlag();
if (readAllele == allele1 || readAllele == allele2) { if (readAllele == allele1 || readAllele == allele2) {

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
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@ -281,7 +281,7 @@ public class GenotypeLikelihoods implements Cloneable {
continue; continue;
SAMRecord read = pileup.getReads().get(i); SAMRecord read = pileup.getReads().get(i);
char base = read.getReadString().charAt(offset); char base = (char)read.getReadBases()[offset];
byte qual = read.getBaseQualities()[offset]; byte qual = read.getBaseQualities()[offset];
if ( ! ignoreBadBases || ! badBase(base) ) { if ( ! ignoreBadBases || ! badBase(base) ) {
n += add(base, qual, read, offset); n += add(base, qual, read, offset);

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
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@ -126,7 +126,7 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
for (int i = 0; i < reads.size(); i++) { for (int i = 0; i < reads.size(); i++) {
read = reads.get(i); read = reads.get(i);
offset = offsets.get(i); offset = offsets.get(i);
base = read.getReadString().charAt(offset); base = (char)read.getReadBases()[offset];
qual = read.getBaseQualities()[offset]; qual = read.getBaseQualities()[offset];
//mapquality = read.getMappingQuality(); //mapquality = read.getMappingQuality();
if (!ReadsToDiscard.contains(read.getReadName()) && BaseUtils.simpleBaseToBaseIndex(base) != -1) { if (!ReadsToDiscard.contains(read.getReadName()) && BaseUtils.simpleBaseToBaseIndex(base) != -1) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
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@ -341,7 +341,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
for (int i = 0; i < reads.size(); i++) { for (int i = 0; i < reads.size(); i++) {
read = reads.get(i); read = reads.get(i);
offset = offsets.get(i); offset = offsets.get(i);
base = read.getReadString().charAt(offset); base = (char)read.getReadBases()[offset];
qual = read.getBaseQualities()[offset]; qual = read.getBaseQualities()[offset];
mapquality = read.getMappingQuality(); mapquality = read.getMappingQuality();
if (mapquality >= 5 && BaseUtils.simpleBaseToBaseIndex(base) != -1) { if (mapquality >= 5 && BaseUtils.simpleBaseToBaseIndex(base) != -1) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
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@ -138,7 +138,7 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
} }
int offset = offsets.get(i); int offset = offsets.get(i);
char base = read.getReadString().charAt(offset); char base = (char)read.getReadBases()[offset];
byte qual = read.getBaseQualities()[offset]; byte qual = read.getBaseQualities()[offset];
if (qual == 0) { continue; } if (qual == 0) { continue; }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
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@ -44,7 +44,7 @@ public class PrintCoverageWalker extends LocusWalker<Integer, Integer> {
} }
int offset = context.getOffsets().get(i); int offset = context.getOffsets().get(i);
char base = read.getReadString().charAt(offset); char base = (char)read.getReadBases()[offset];
if (base == 'a' || base == 'A') { aCount++; } if (base == 'a' || base == 'A') { aCount++; }
if (base == 'c' || base == 'C') { cCount++; } if (base == 'c' || base == 'C') { cCount++; }
if (base == 'g' || base == 'G') { gCount++; } if (base == 'g' || base == 'G') { gCount++; }

6
java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
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@ -41,7 +41,7 @@ public class AlignmentUtils {
case M: case M:
for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) { for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
char refChr = (char)ref[i_ref]; char refChr = (char)ref[i_ref];
char readChr = r.getReadString().charAt(i_read); char readChr = (char)r.getReadBases()[i_read];
if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 || if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
BaseUtils.simpleBaseToBaseIndex(refChr) == -1 ) BaseUtils.simpleBaseToBaseIndex(refChr) == -1 )
continue; // do not count Ns/Xs/etc ? continue; // do not count Ns/Xs/etc ?
@ -77,8 +77,8 @@ public class AlignmentUtils {
switch( ce.getOperator() ) { switch( ce.getOperator() ) {
case M: case M:
for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) { for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
char refChr = (char)ref[i_ref]; char refChr = ref[i_ref];
char readChr = r.getReadString().charAt(i_read); char readChr = (char)r.getReadBases()[i_read];
if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 || if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
BaseUtils.simpleBaseToBaseIndex(refChr) == -1 ) BaseUtils.simpleBaseToBaseIndex(refChr) == -1 )
continue; // do not count Ns/Xs/etc ? continue; // do not count Ns/Xs/etc ?