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Report unfiltered variants in HTML output. #240

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merged 1 commit into from
Feb 26, 2024
Merged

Report unfiltered variants in HTML output. #240

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3 changes: 1 addition & 2 deletions svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/html/HtmlResultWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,7 @@ public void write(AnalysisResults results, OutputOptions outputOptions) {
// Limit performing of the expensive DB lookups to several dozens of variants that will be reported
// in the report, and not to the entire variant corpus
List<String> visualizations = variantLandscapes.stream()
.filter(s -> s.variant().numberOfAltReads() >= analysisParameters.minAltReadSupport()
&& s.variant().passedFilters()
.filter(s -> s.variant().passedFilters()
&& !Double.isNaN(s.variant().svPriority().getPriority()))
.filter(v -> !(v.variant() instanceof GenomicBreakendVariant) || !doNotReportBreakends)
.limit(outputOptions.nVariantsToReport())
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6 changes: 3 additions & 3 deletions svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/vcf/VcfResultWriter.java
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Expand Up @@ -77,15 +77,15 @@ private static Function<FullSvannaVariant, Optional<VariantContext>> addInfoFiel
VariantContext vc = sv.variantContext();
if (vc == null) {
GenomicVariant gv = sv.genomicVariant();
LogUtils.logDebug(LOGGER, "Cannot write VCF line for variant '{}' because variant context is missing. {}:{}{}>{}",
LOGGER.debug("Cannot write VCF line for variant '{}' because variant context is missing. {}:{}{}>{}",
gv.id(), gv.contig().name(), gv.startOnStrandWithCoordinateSystem(gv.strand(), CoordinateSystem.oneBased()), gv.ref(), gv.alt());
return Optional.empty();
}

VariantContextBuilder builder = new VariantContextBuilder(vc);
if (svPriority == null || Double.isNaN(svPriority.getPriority()))
return Optional.of(builder.make());
return Optional.of(vc);

VariantContextBuilder builder = new VariantContextBuilder(vc);
return Optional.of(builder.attribute(SVANNA_PSV_FIELD_NAME, svPriority.getPriority())
.make());
};
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