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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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12 changes: 11 additions & 1 deletion 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 @@ -22,6 +22,16 @@ public VariantIDsVariantFilter(Set<String> keepIDs) {

@Override
public boolean test(final VariantContext vc) {
return includeIDs.contains(vc.getID());
if (vc.getID().indexOf(';') > 0) {
String[] vc_ids = vc.getID().split(";");
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for (String vc_id : vc_ids) {
if (includeIDs.contains(vc_id)) {
return true;
}
}
return false;
} else {
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return includeIDs.contains(vc.getID());
}
}
}
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 ./. ./.