Merge pull request #240 from TheJacksonLaboratory/report-unfiltered-v…

…ariants-in-html Report unfiltered variants in HTML output.
monarch-initiative · Feb 26, 2024 · 5c65e77 · 5c65e77
2 parents e153242 + 999424a
commit 5c65e77
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Showing 2 changed files with 4 additions and 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
@@ -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())

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
@@ -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());
         };