Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Retain all source IDs on VariantContext merge #8750

Closed
wants to merge 1 commit into from
Closed

Retain all source IDs on VariantContext merge #8750

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1217,7 +1217,10 @@ public static VariantContext simpleMerge(final Collection<VariantContext> unsort

final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);

final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID);
// This preserves the GATK3-like behavior of reporting all sources, delimited with hyphen:
final String allSources = variantSources.isEmpty() ? name : variantSources.stream().sorted().collect(Collectors.joining("-"));

final VariantContextBuilder builder = new VariantContextBuilder().source(allSources).id(ID);
builder.loc(longestVC.getContig(), longestVC.getStart(), longestVC.getEnd());
builder.alleles(alleles);
builder.genotypes(genotypes);
Expand Down
Loading