From 999424af1326f84536b7aa68aa1b60a1a073045e Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 29 Nov 2023 13:45:57 -0500 Subject: [PATCH] Report unfiltered variants in HTML output. --- .../svanna/cli/writer/html/HtmlResultWriter.java | 3 +-- .../svanna/cli/writer/vcf/VcfResultWriter.java | 6 +++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/html/HtmlResultWriter.java b/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/html/HtmlResultWriter.java index c015e337..366b8541 100644 --- a/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/html/HtmlResultWriter.java +++ b/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/html/HtmlResultWriter.java @@ -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 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()) diff --git a/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/vcf/VcfResultWriter.java b/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/vcf/VcfResultWriter.java index c3b42005..717fd6b5 100644 --- a/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/vcf/VcfResultWriter.java +++ b/svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/writer/vcf/VcfResultWriter.java @@ -77,15 +77,15 @@ private static Function> 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()); };