From 0dd5a0990d234f2f3111a2d1f1b4c1d62f41e843 Mon Sep 17 00:00:00 2001 From: kiran Date: Sat, 4 Sep 2010 00:36:55 +0000 Subject: [PATCH] Now annotates sites marked as filtered out (this is important if sites are in a lower-quality tranche). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4214 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/annotator/genomicannotator/GenomicAnnotator.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java index 8df744280..ce3d94f60 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java @@ -79,6 +79,9 @@ public class GenomicAnnotator extends RodWalker implements Tre @Argument(fullName="maxJoinTableSize", shortName="maxJoin", doc="The maximum allowed size (i.e. number of rows) for a table provided with the -J argument", required=false) protected Integer MAX_JOIN_TABLE_SIZE = 500000; + @Argument(fullName="ignoreFilteredSites", shortName="noFilt", doc="If specified, don't annotate sites marked as filtered out") + protected Boolean IGNORE_FILTERED_SITES = false; + private VariantAnnotatorEngine engine; /** @@ -240,7 +243,7 @@ public class GenomicAnnotator extends RodWalker implements Tre Set results = new LinkedHashSet(); for (VariantContext vc : tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false)) { - if ( vc.isFiltered() || + if ( (vc.isFiltered() && IGNORE_FILTERED_SITES) || (vc.isVariant() && !vc.isBiallelic()) ) { results.add(vc); } else {