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Completes #5260 on GitHub. #5464

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merged 4 commits into from
Nov 30, 2018
Merged

Completes #5260 on GitHub. #5464

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d22fe7e
Changed SelectVariants so that it van handle multiple rsIDs separated…
MartonKN Nov 29, 2018
203b739
The tests testKeepSelectionIDLiteral and testKeepSelectionIDFromFile …
MartonKN Nov 29, 2018
5083418
Changes due to review by David Benjamin and Phil Shapiro.
MartonKN Nov 30, 2018
eb246a2
Made the code in VariantIDsVariantFilter's test function more concise.
MartonKN Nov 30, 2018
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5 changes: 5 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@

import java.util.Set;
import java.util.LinkedHashSet;
import java.util.*;
import java.util.stream.*;

/**
* Keep only variants with any of these IDs.
Expand All @@ -22,6 +24,9 @@ public VariantIDsVariantFilter(Set<String> keepIDs) {

@Override
public boolean test(final VariantContext vc) {
if (vc.getID().indexOf(';') > 0) {
return Arrays.stream(vc.getID().split(";")).anyMatch(includeIDs::contains);
}
return includeIDs.contains(vc.getID());
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}
}
4 changes: 3 additions & 1 deletion ...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
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Expand Up @@ -138,6 +138,8 @@ public final class HaplotypeCallerEngine implements AssemblyRegionEvaluator {
private static final Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
private static final Allele FAKE_ALT_ALLELE = Allele.create("<FAKE_ALT>", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file

public static final int MINIMUM_READ_LENGTH = 10;
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/**
* Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header,
* and a reference file
Expand Down Expand Up @@ -523,7 +525,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur

final List<VariantContext> givenAlleles = new ArrayList<>();
if ( hcArgs.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES ) {
features.getValues(hcArgs.alleles).stream().filter(vc -> hcArgs.genotypeFilteredAlleles || vc.isNotFiltered()).forEach(givenAlleles::add);
features.getValues(hcArgs.alleles).stream().filter(vc -> (hcArgs.genotypeFilteredAlleles || vc.isNotFiltered()) && (vc.getEnd() - vc.getStart() + 1 >= MINIMUM_READ_LENGTH)).forEach(givenAlleles::add);

// No alleles found in this region so nothing to do!
if ( givenAlleles.isEmpty() ) {
Expand Down
1 change: 1 addition & 0 deletions ...g/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants/complexExample1.vcf
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Expand Up @@ -29,5 +29,6 @@
1 10044557 . C T 62.22 . AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0 GT:DP:GQ ./. ./. 0/1:31:15
1 10045603 . AAAA A 40.26 PASS AF=0.50 GT:DP:GQ 0/1:15:8 0/0:15:8 1/1:15:8
1 10045604 . A ACAT 41.26 PASS AF=0.50 GT:DP:GQ 1/1:14:7 0/0:15:8 1/0:15:8
1 10046982 testid0;testid1 C T 32.01 PASS AF=0.40;AlleleBalance=0.37;DoC=21;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=12.31;SB=-4.2;SpanningDeletions=0 GT:DP:GQ 1/0:3:49 ./. ./.
1 10048142 . A G 126.81 foo AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0 GT:DP:GQ 0/1:15:8 0/0:15:8 1/1:15:8
1 10048580 . T A 72.22 bar;baz AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0 GT:DP:GQ 0/1:15:8 0/0:15:8 1/1:15:8
1 change: 1 addition & 0 deletions ...tools/walkers/variantutils/SelectVariants/expected/testSelectVariants_KeepSelectionID.vcf
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Expand Up @@ -23,3 +23,4 @@
##source=ArbitrarySource
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
1 10001292 testid1 G A 12.22 PASS AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0 GT:DP:GQ 1/0:23:19 ./. ./.
1 10046982 testid0;testid1 C T 32.01 PASS AF=0.40;AlleleBalance=0.37;DoC=21;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=12.31;SB=-4.2;SpanningDeletions=0 GT:DP:GQ 1/0:3:49 ./. ./.