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Fixes for PooledConcordance bugs and lack of safety checking 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-11-07 01:54:10 +00:00
parent 7cb51dbc31
commit bf1bc94060
1 changed files with 26 additions and 16 deletions
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42
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -26,9 +26,9 @@ import java.util.*;
*
*/
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
//public class VariantEvalWalker extends RefWalker<Integer, Integer> {
public class VariantEvalWalker extends RodWalker<Integer, Integer> {
//@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
public class VariantEvalWalker extends RefWalker<Integer, Integer> {
//public class VariantEvalWalker extends RodWalker<Integer, Integer> {
@Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
public int minConfidenceScore = -1;
@ -129,10 +129,12 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
// Add new analyses here!
//
analyses.add(new ValidationDataAnalysis());
analyses.add(new PooledGenotypeConcordance(samplesFile));
// todo -- chris remove?
//analyses.add(new PooledGenotypeConcordance(samplesFile));
analyses.add(new VariantCounter());
analyses.add(new VariantDBCoverage(knownSNPDBName));
analyses.add(new PooledFrequencyAnalysis(numPeopleInPool,knownSNPDBName));
//analyses.add(new PooledFrequencyAnalysis(numPeopleInPool,knownSNPDBName));
if ( samplesFile == null )
analyses.add(new GenotypeConcordance(genotypeChipName, false));
else
@ -150,14 +152,22 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
Iterator<VariantAnalysis> iter = analyses.iterator();
while (iter.hasNext()) {
VariantAnalysis analysis = iter.next();
boolean disableForGenotyping = evalContainsGenotypes && !(analysis instanceof GenotypeAnalysis);
boolean disableForPopulation = !evalContainsGenotypes && !(analysis instanceof PopulationAnalysis);
boolean disableForPools = numPeopleInPool < 1 && analysis instanceof PoolAnalysis;
boolean disable = disableForGenotyping | disableForPopulation | disableForPools;
String causeName = disableForGenotyping ? "population" : (disableForPopulation ? "genotype" : (disableForPools ? "pool" : null));
if (disable) {
logger.info(String.format("Disabling %s-only analysis %s in set %s", causeName, analysis, setName));
VariantAnalysis removed = null;
if ( evalContainsGenotypes ) {
if ( ! (analysis instanceof GenotypeAnalysis ) ) {
removed = analysis;
iter.remove();
}
} else if ( ! (analysis instanceof PopulationAnalysis || analysis instanceof PoolAnalysis) ) {
removed = analysis;
iter.remove();
} else if ( numPeopleInPool > 1 && ! ( analysis instanceof PoolAnalysis ) ) {
removed = analysis;
iter.remove();
}
if ( removed != null ) {
logger.info(String.format("Disabling analysis %s in set %s", removed, setName));
}
}
@ -235,10 +245,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
if (eval != null)
if (eval.getNegLog10PError() < minConfidenceScore) eval = null;
if ( eval != null && (eval instanceof RodVCF) && ((RodVCF)eval).mCurrentRecord.isFiltered() ) {
//System.out.printf("Rejecting filtered record %s%n", eval);
eval = null;
}
if ( eval != null && (eval instanceof RodVCF) && ((RodVCF)eval).mCurrentRecord.isFiltered() ) {
//System.out.printf("Rejecting filtered record %s%n", eval);
eval = null;
}
// update stats about all of the SNPs
updateAnalysisSet(ANALYSIS_TYPE.ALL_SNPS, eval, tracker, ref.getBase(), context);