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Variant fixes #16

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Merged
akmorrow13 merged 2 commits into from
Jun 12, 2017
Merged

Variant fixes #16

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3f9f209
Fixed overlap issue for Variants and Coverage display
Jun 12, 2017
dfd1638
Fixed off by 1 error for Variant display
Jun 12, 2017
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2 changes: 1 addition & 1 deletion src/main/sources/CoverageDataSource.js
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ function keyFunction(p: PositionCount): string {
}

function filterFunction(range: ContigInterval<string>, p: PositionCount): boolean {
return range.chrContainsLocus(p.contig, p.start);
return range.chrIntersects(new ContigInterval(p.contig, p.start, p.end));
}

function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource {
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10 changes: 9 additions & 1 deletion src/main/sources/VariantDataSource.js
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ function keyFunction(vc: VariantContext): string {
}

function filterFunction(range: ContigInterval<string>, vc: VariantContext): boolean {
return range.chrContainsLocus(vc.variant.contig, vc.variant.position);
return range.chrIntersects(new ContigInterval(vc.variant.contig, vc.variant.position, vc.variant.end));
}

function createFromVariantUrl(remoteSource: RemoteRequest,
Expand Down Expand Up @@ -79,6 +79,14 @@ function createFromVariantUrl(remoteSource: RemoteRequest,
if (response !== null) {
// parse VariantContexts
var variants = _.map(response, v => JSON.parse(v));

// GA4GH schemas are 0-based, so we adjust the variant position
// by 1 to display correctly
variants = _.map(variants, v => {
v.variant.position += 1;
v.variant.end += 1;
return v;
});
variants.forEach(v => cache.put(v, resolution));
}
console.info(`Fetched variants from server:", ${new Date().getTime() - startTimeMilliseconds}`);
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