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Added minimum phasing quality for phasing evaluation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4219 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-09-07 14:29:11 +00:00
parent 5d0d9c7dce
commit 754c2c761e
2 changed files with 14 additions and 14 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -42,13 +42,6 @@ import java.util.*;
public class GenotypePhasingEvaluator extends VariantEvaluator { public class GenotypePhasingEvaluator extends VariantEvaluator {
protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class); protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class);
//
//@Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to consider eval track phasing; [default:20.0]", required = false)
//
protected Double phaseQualityThresh = 20.0; // PQ = 20.0 <=> P(error) = 10^(-20/10) = 0.01, P(correct) = 0.99
//
//
private VariantEvalWalker.EvaluationContext group = null; private VariantEvalWalker.EvaluationContext group = null;
// a mapping from sample to stats // a mapping from sample to stats
@ -68,7 +61,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
public GenotypePhasingEvaluator(VariantEvalWalker parent) { public GenotypePhasingEvaluator(VariantEvalWalker parent) {
super(parent); super(parent);
this.samplePhasingStatistics = new SamplePhasingStatistics(phaseQualityThresh); this.samplePhasingStatistics = new SamplePhasingStatistics(getVEWalker().minPhaseQuality);
this.samplePrevGenotypes = new SamplePreviousGenotypes(); this.samplePrevGenotypes = new SamplePreviousGenotypes();
} }
@ -98,7 +91,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
logger.debug("update2() locus: " + curLocus); logger.debug("update2() locus: " + curLocus);
logger.debug("comp = " + comp + " eval = " + eval); logger.debug("comp = " + comp + " eval = " + eval);
if (comp == null || eval == null || comp.isFiltered()) // ignore existence of filtered variants in comp [NOTE that eval will be checked BOTH filtered and unfiltered (by VariantEvalWalker)] if (!isUsable(comp) || !isUsable(eval))
return interesting; return interesting;
if (!comp.isBiallelic() || !eval.isBiallelic() || !comp.getAlternateAllele(0).equals(eval.getAlternateAllele(0))) // these are not the same biallelic variants if (!comp.isBiallelic() || !eval.isBiallelic() || !comp.getAlternateAllele(0).equals(eval.getAlternateAllele(0))) // these are not the same biallelic variants
@ -169,12 +162,16 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
return interesting; return interesting;
} }
public static boolean isUsable(VariantContext vc) {
return (vc != null && !vc.isFiltered());
}
public boolean genotypesArePhasedAboveThreshold(Genotype gt) { public boolean genotypesArePhasedAboveThreshold(Genotype gt) {
if (!gt.genotypesArePhased()) if (!gt.genotypesArePhased())
return false; return false;
Object pq = gt.getAttributes().get("PQ"); Object pq = gt.getAttributes().get("PQ");
return (pq == null || (new Double(pq.toString()) >= phaseQualityThresh)); return (pq == null || (new Double(pq.toString()) >= getVEWalker().minPhaseQuality));
} }
// //
@ -370,11 +367,11 @@ class PhaseStats {
*/ */
class SamplePhasingStatistics implements TableType { class SamplePhasingStatistics implements TableType {
private HashMap<String, PhaseStats> sampleStats = null; private HashMap<String, PhaseStats> sampleStats = null;
private double phaseQualityThresh; private double minPhaseQuality;
public SamplePhasingStatistics(double phaseQualityThresh) { public SamplePhasingStatistics(double minPhaseQuality) {
this.sampleStats = new HashMap<String, PhaseStats>(); this.sampleStats = new HashMap<String, PhaseStats>();
this.phaseQualityThresh = phaseQualityThresh; this.minPhaseQuality = minPhaseQuality;
} }
public PhaseStats ensureSampleStats(String samp) { public PhaseStats ensureSampleStats(String samp) {
@ -409,7 +406,7 @@ class SamplePhasingStatistics implements TableType {
} }
public String getName() { public String getName() {
return "Sample Phasing Statistics (for PQ >= " + phaseQualityThresh + ")"; return "Sample Phasing Statistics (for PQ >= " + minPhaseQuality + ")";
} }
public String toString() { public String toString() {

3
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -210,6 +210,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false) @Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false)
private String TRANCHE_FILENAME = null; private String TRANCHE_FILENAME = null;
// For GenotypePhasingEvaluator:
@Argument(fullName = "minPhaseQuality", shortName = "minPQ", doc = "The minimum phasing quality (PQ) score required to consider phasing; [default:20.0]", required = false)
protected Double minPhaseQuality = 20.0; // PQ = 20.0 <=> P(error) = 10^(-20/10) = 0.01, P(correct) = 0.99
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //