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Cleanup for new SampleUtils function 

-- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase
This commit is contained in:
Mark DePristo 2011-11-10 13:27:13 -05:00
parent 35fe9c8a06
commit 67b022c34b
5 changed files with 11 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -41,6 +41,9 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
public long nDeletions = 0; public long nDeletions = 0;
@DataPoint(description = "Number of complex indels") @DataPoint(description = "Number of complex indels")
public long nComplex = 0; public long nComplex = 0;
@DataPoint(description = "Number of symbolic events")
public long nSymbolic = 0;
@DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)") @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
public long nMixed = 0; public long nMixed = 0;
@ -131,8 +134,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
nMixed++; nMixed++;
break; break;
case SYMBOLIC: case SYMBOLIC:
// ignore symbolic alleles, but don't fail nSymbolic++;
// todo - consistent way of treating symbolic alleles thgoughout codebase?
break; break;
default: default:
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType()); throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
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@ -103,7 +103,7 @@ public class G1KPhaseITable extends VariantEvaluator {
} }
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( eval == null ) return null; if ( eval == null || eval.isMonomorphic() ) return null;
switch (eval.getType()) { switch (eval.getType()) {
// case NO_VARIATION: // case NO_VARIATION:

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -162,7 +162,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
private boolean sitesOnlyVCF = false; private boolean sitesOnlyVCF = false;
public void initialize() { public void initialize() {
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null); Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
if ( PRIORITY_STRING == null ) { if ( PRIORITY_STRING == null ) {
PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); PRIORITY_STRING = Utils.join(",", vcfRods.keySet());

2
public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
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@ -150,7 +150,7 @@ public class SampleUtils {
// iterate to get all of the sample names // iterate to get all of the sample names
for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit, null).entrySet() ) { for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
Set<String> vcfSamples = pair.getValue().getGenotypeSamples(); Set<String> vcfSamples = pair.getValue().getGenotypeSamples();
for ( String sample : vcfSamples ) for ( String sample : vcfSamples )
addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey()); addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey());

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
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@ -51,6 +51,10 @@ public class VCFUtils {
return getVCFHeadersFromRods(toolkit, names); return getVCFHeadersFromRods(toolkit, names);
} }
public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
}
public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) { public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
Map<String, VCFHeader> data = new HashMap<String, VCFHeader>(); Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();