From b12cec4302843f9b17c1998a096e8fbdf3493976 Mon Sep 17 00:00:00 2001 From: fromer Date: Fri, 3 Dec 2010 20:34:17 +0000 Subject: [PATCH] Added emitOnlyMNPs flag git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4785 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/phasing/AnnotateMNPsWalker.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java index adf751bdc..089a7b52f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -61,6 +62,9 @@ public class AnnotateMNPsWalker extends RodWalker { protected VCFWriter writer = null; private ManualSortingVCFWriter sortingWriter = null; + @Argument(fullName = "emitOnlyMNPs", shortName = "emitOnlyMNPs", doc = "Only output MNP records; [default:false]", required = false) + protected boolean emitOnlyMNPs = false; + private LinkedList rodNames = null; private GenomeLocParser locParser = null; private TreeMap> MNPstartToStops = null; // Must be TreeMap sorted by START sites! @@ -203,7 +207,7 @@ public class AnnotateMNPsWalker extends RodWalker { } } } - else if (atStartOfVc) {// only want to write other VariantContexts records once (where they start): + else if (atStartOfVc && !emitOnlyMNPs) {// only want to write other VariantContexts records once (where they start): writeVCF(vc); } }