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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
This commit is contained in:
corin 2011-04-15 20:28:56 +00:00
parent 59215dab48
commit fce6d25075
1 changed files with 5 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
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@ -91,8 +91,9 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
if(each.getKey().equals("fileformat")) newlines.add(each); 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)); vcfWriter.writeHeader(new VCFHeader(newlines));
return 0; //To change body of implemented methods use File | Settings | File Templates. return 0; //To change body of implemented methods use File | Settings | File Templates.
@ -104,14 +105,12 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
public Map<String, Object> addValidation(int Validity, String Note, String Source, String Build){ public Map<String, Object> addValidation(int Validity, String Note, String Source){
HashMap<String, Object> validityAnnots = new HashMap<String, Object>(); HashMap<String, Object> validityAnnots = new HashMap<String, Object>();
validityAnnots.put("validity", Validity); validityAnnots.put("validity", Validity);
validityAnnots.put("user", System.getenv("USER")); validityAnnots.put("user", System.getenv("USER"));
if (Build.equals(".")) validityAnnots.put("build", getBuild());
else validityAnnots.put("build", Build);
validityAnnots.put("note", Note); validityAnnots.put("note", Note);
validityAnnots.put("Source", Source); validityAnnots.put("Source", Source);
@ -142,7 +141,7 @@ public class DeclareValidityWalker extends RodWalker<Integer, Integer>{
if (current == null) { if (current == null) {
return 0;} 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()); vcfWriter.add(declared, ref.getBase());
return 1; return 1;
} }