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Removing unnecessary printing routines 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-03-28 22:34:54 +00:00
parent b8ab74a6dc
commit a45ac220aa
1 changed files with 9 additions and 8 deletions
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17
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -19,9 +19,10 @@ import net.sf.samtools.SAMRecord;
public class HaplotypeScore implements InfoFieldAnnotation, WorkInProgressAnnotation { public class HaplotypeScore implements InfoFieldAnnotation, WorkInProgressAnnotation {
private final static boolean DEBUG = false;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
if ( !vc.isBiallelic() || !vc.isSNP() ) if ( !vc.isBiallelic() || !vc.isSNP() || stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
return null; return null;
AlignmentContext context = StratifiedAlignmentContext.joinContexts(stratifiedContexts.values(), StratifiedAlignmentContext.StratifiedContextType.COMPLETE); AlignmentContext context = StratifiedAlignmentContext.joinContexts(stratifiedContexts.values(), StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
@ -50,25 +51,25 @@ public class HaplotypeScore implements InfoFieldAnnotation, WorkInProgressAnnota
// calculate the haplotype scores by walking over all reads and comparing them to the haplotypes // calculate the haplotype scores by walking over all reads and comparing them to the haplotypes
private double scoreReadsAgainstHaplotypes(List<Consensus> haplotypes, ReadBackedPileup pileup, int contextSize) { private double scoreReadsAgainstHaplotypes(List<Consensus> haplotypes, ReadBackedPileup pileup, int contextSize) {
System.out.printf("REF: %s%n", haplotypes.get(0)); if ( DEBUG ) System.out.printf("REF: %s%n", haplotypes.get(0));
System.out.printf("ALT: %s%n", haplotypes.get(1)); if ( DEBUG ) System.out.printf("ALT: %s%n", haplotypes.get(1));
double[][] haplotypeScores = new double[pileup.size()][haplotypes.size()]; double[][] haplotypeScores = new double[pileup.size()][haplotypes.size()];
for ( ExtendedPileupElement p : pileup.extendedForeachIterator() ) { for ( ExtendedPileupElement p : pileup.extendedForeachIterator() ) {
SAMRecord read = p.getRead(); SAMRecord read = p.getRead();
int readOffsetFromPileup = p.getOffset(); int readOffsetFromPileup = p.getOffset();
System.out.printf("--------------------------------------------- Read %s%n", read.getReadName()); if ( DEBUG ) System.out.printf("--------------------------------------------- Read %s%n", read.getReadName());
double m = 10000000; double m = 10000000;
for ( int i = 0; i < haplotypes.size(); i++ ) { for ( int i = 0; i < haplotypes.size(); i++ ) {
Consensus haplotype = haplotypes.get(i); Consensus haplotype = haplotypes.get(i);
int start = readOffsetFromPileup - (contextSize - 1)/2; int start = readOffsetFromPileup - (contextSize - 1)/2;
double score = scoreReadAgainstHaplotype(read, start, contextSize, haplotype); double score = scoreReadAgainstHaplotype(read, start, contextSize, haplotype);
haplotypeScores[p.getPileupOffset()][i] = score; haplotypeScores[p.getPileupOffset()][i] = score;
System.out.printf(" vs. haplotype %d = %f%n", i, score); if ( DEBUG ) System.out.printf(" vs. haplotype %d = %f%n", i, score);
m = Math.min(score, m); m = Math.min(score, m);
} }
System.out.printf(" => best score was %f%n", m); if ( DEBUG ) System.out.printf(" => best score was %f%n", m);
} }
double overallScore = 0.0; double overallScore = 0.0;
@ -136,11 +137,11 @@ public class HaplotypeScore implements InfoFieldAnnotation, WorkInProgressAnnota
for ( int i = 0; i < contextSize; i++ ) { for ( int i = 0; i < contextSize; i++ ) {
int offsetFromPileup = i - pileupOffset; int offsetFromPileup = i - pileupOffset;
ReadBackedPileup offsetPileup = pileupAtOffset(pileup, offsetFromPileup); ReadBackedPileup offsetPileup = pileupAtOffset(pileup, offsetFromPileup);
System.out.printf("pileup is %s%n", offsetPileup); if ( DEBUG ) System.out.printf("pileup is %s%n", offsetPileup);
BaseQual bq = calcConsensusAtLocus(offsetPileup, FLAT_BASE_PRIORS); BaseQual bq = calcConsensusAtLocus(offsetPileup, FLAT_BASE_PRIORS);
this.bases[i] = bq.getBase(); this.bases[i] = bq.getBase();
this.quals[i] = bq.getQual(); this.quals[i] = bq.getQual();
System.out.printf(" At %d: offset %d bq = %c / %d%n", i, offsetFromPileup, (char)bq.getBase(), bq.getQual()); if ( DEBUG ) System.out.printf(" At %d: offset %d bq = %c / %d%n", i, offsetFromPileup, (char)bq.getBase(), bq.getQual());
} }
} }