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Added the "previous locus" to interesting sites VCF (locus with respect to which the site is phased) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4990 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-01-13 17:19:20 +00:00
parent e8f0ae4b09
commit b4a2112a0d
1 changed files with 8 additions and 7 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -141,7 +141,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
samplePrevGenotypes.put(samp, curLocus, compSampGt, evalSampGt);
if (prevCompAndEval != null) {
logger.debug("Potentially phaseable het locus: " + curLocus + " [relative to previous het locus: " + prevCompAndEval.getLocus() + "]");
GenomeLoc prevLocus = prevCompAndEval.getLocus();
logger.debug("Potentially phaseable het locus: " + curLocus + " [relative to previous het locus: " + prevLocus + "]");
PhaseStats ps = samplePhasingStatistics.ensureSampleStats(samp);
boolean compSampIsPhased = genotypesArePhasedAboveThreshold(compSampGt);
@ -149,11 +150,11 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
if (compSampIsPhased || evalSampIsPhased) {
if (!evalSampIsPhased) {
ps.onlyCompPhased++;
interesting.addReason("ONLY_COMP", samp, group, "");
interesting.addReason("ONLY_COMP", samp, group, prevLocus, "");
}
else if (!compSampIsPhased) {
ps.onlyEvalPhased++;
interesting.addReason("ONLY_EVAL", samp, group, "");
interesting.addReason("ONLY_EVAL", samp, group, prevLocus, "");
}
else { // both comp and eval are phased:
AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye());
@ -169,12 +170,12 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
Double compPQ = getPQ(compSampGt);
Double evalPQ = getPQ(evalSampGt);
if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0)
interesting.addReason("PQ_CHANGE", samp, group, compPQ + " -> " + evalPQ);
interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ);
}
else {
ps.phasesDisagree++;
logger.debug("SWITCHED locus: " + curLocus);
interesting.addReason("SWITCH", samp, group, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
interesting.addReason("SWITCH", samp, group, prevLocus, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
}
}
}
@ -243,8 +244,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
sb = new StringBuilder();
}
public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, String reason) {
sb.append(category + "(" + sample + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";");
public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, GenomeLoc prevLoc, String reason) {
sb.append(category + "(" + sample + ", previous= " + prevLoc + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";");
}
public String toString() {