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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
This commit is contained in:
kiran 2010-09-04 00:36:55 +00:00
parent e9af893bf4
commit 0dd5a0990d
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
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@ -79,6 +79,9 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> 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<Integer, Integer> implements Tre
Set<VariantContext> results = new LinkedHashSet<VariantContext>();
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 {