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PhasingEvaluator prints out interesting sites (only 1 phased, or phases disagree) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4233 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-09-08 18:21:21 +00:00
parent 40283f6456
commit ce031b2f05
1 changed files with 33 additions and 17 deletions
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50
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -42,8 +42,6 @@ import java.util.*;
public class GenotypePhasingEvaluator extends VariantEvaluator {
protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class);
private VariantEvalWalker.EvaluationContext group = null;
// a mapping from sample to stats
@DataPoint(name = "samples", description = "the phasing statistics for each sample")
SamplePhasingStatistics samplePhasingStatistics = null;
@ -73,11 +71,10 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
}
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
String interesting = null;
Reasons interesting = new Reasons();
if (ref == null)
return interesting;
return interesting.toString();
GenomeLoc curLocus = ref.getLocus();
this.group = group;
logger.debug("update2() locus: " + curLocus);
logger.debug("comp = " + comp + " eval = " + eval);
@ -136,23 +133,25 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
// Replace the previous with current:
samplePrevGenotypes.put(samp, curLocus, compSampGt, evalSampGt);
if (prevCompAndEval != null) {
logger.debug("Potentially phaseable locus: " + curLocus);
Genotype prevCompSampGt = prevCompAndEval.getCompGenotpye();
Genotype prevEvalSampGt = prevCompAndEval.getEvalGenotype();
PhaseStats ps = samplePhasingStatistics.ensureSampleStats(samp);
boolean compSampIsPhased = genotypesArePhasedAboveThreshold(compSampGt);
boolean evalSampIsPhased = genotypesArePhasedAboveThreshold(evalSampGt);
if (compSampIsPhased || evalSampIsPhased) {
if (!evalSampIsPhased)
if (!evalSampIsPhased) {
ps.onlyCompPhased++;
else if (!compSampIsPhased)
interesting.addReason("ONLY_COMP", samp, group, "");
}
else if (!compSampIsPhased) {
ps.onlyEvalPhased++;
else {
Biallele prevCompBiallele = new Biallele(prevCompSampGt);
Biallele prevEvalBiallele = new Biallele(prevEvalSampGt);
interesting.addReason("ONLY_EVAL", samp, group, "");
}
else {
Biallele prevCompBiallele = new Biallele(prevCompAndEval.getCompGenotpye());
Biallele prevEvalBiallele = new Biallele(prevCompAndEval.getEvalGenotype());
// Sufficient to check only the top of comp, since we ensured that comp and eval have the same diploid genotypes for this sample:
boolean topsMatch = (topMatchesTop(prevCompBiallele, prevEvalBiallele) && topMatchesTop(compBiallele, evalBiallele));
@ -164,9 +163,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
else {
ps.phasesDisagree++;
logger.debug("SWITCHED locus: " + curLocus);
if (interesting == null)
interesting = "SWITCH=";
interesting += samp + ": " + toString(prevCompBiallele, compBiallele) + " -> " + toString(prevEvalBiallele, evalBiallele) + ";";
interesting.addReason("SWITCH", samp, group, toString(prevCompBiallele, compBiallele) + " -> " + toString(prevEvalBiallele, evalBiallele));
}
}
}
@ -179,7 +176,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
}
logger.debug("\n" + samplePhasingStatistics + "\n");
return interesting;
return interesting.toString();
}
public static boolean isRelevantToPhasing(VariantContext vc) {
@ -220,6 +217,25 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
public void finalizeEvaluation() {
}
private static class Reasons {
private StringBuilder sb;
public Reasons() {
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 String toString() {
if (sb.length() == 0)
return null;
return "reasons=" + sb.toString();
}
}
}