From fce6d250755207223c5d1170c6f061204943c381 Mon Sep 17 00:00:00 2001 From: corin Date: Fri, 15 Apr 2011 20:28:56 +0000 Subject: [PATCH] Moved the reference ID to a meta data field for validity declaration. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5650 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/validation/DeclareValidityWalker.java | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java index 04f2e6b2f..6d4c5fbe2 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java @@ -91,8 +91,9 @@ public class DeclareValidityWalker extends RodWalker{ if(each.getKey().equals("fileformat")) newlines.add(each); } - - + if (build.equals(".")) build=getBuild(); + VCFHeaderLine ref = new VCFHeaderLine("reference", build); + newlines.add(ref); vcfWriter.writeHeader(new VCFHeader(newlines)); return 0; //To change body of implemented methods use File | Settings | File Templates. @@ -104,14 +105,12 @@ public class DeclareValidityWalker extends RodWalker{ - public Map addValidation(int Validity, String Note, String Source, String Build){ + public Map addValidation(int Validity, String Note, String Source){ HashMap validityAnnots = new HashMap(); validityAnnots.put("validity", Validity); validityAnnots.put("user", System.getenv("USER")); - if (Build.equals(".")) validityAnnots.put("build", getBuild()); - else validityAnnots.put("build", Build); validityAnnots.put("note", Note); validityAnnots.put("Source", Source); @@ -142,7 +141,7 @@ public class DeclareValidityWalker extends RodWalker{ if (current == null) { return 0;} - VariantContext declared = VariantContext.modifyAttributes( current, addValidation(validity, note, source, build)); + VariantContext declared = VariantContext.modifyAttributes( current, addValidation(validity, note, source)); vcfWriter.add(declared, ref.getBase()); return 1; }