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quick changes for G 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-08 16:33:27 +00:00
parent 907931c902
commit 4d1a6b3d99
1 changed files with 5 additions and 8 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
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@ -40,6 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader; import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
import java.io.PrintStream; import java.io.PrintStream;
@ -79,16 +80,12 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
if( tracker != null ) { if( tracker != null ) {
EnumSet<VariantContext.Type> vc = EnumSet.of(VariantContext.Type.SNP);
GenomeLoc loc = context.getLocation(); GenomeLoc loc = context.getLocation();
VariantContext vc_eval; VariantContext vc_eval;
vc_eval = tracker.getVariantContext(ref,"vcf", null, loc, false);
try { if ( vc_eval == null || vc_eval.isFiltered() )
vc_eval = tracker.getVariantContext(ref,"vcf", vc, loc, true);
} catch (java.util.NoSuchElementException e) {
return 0; return 0;
}
// output marker ID to Beagle input file // output marker ID to Beagle input file
beagleWriter.print(String.format("%s ",vc_eval.getLocation().toString())); beagleWriter.print(String.format("%s ",vc_eval.getLocation().toString()));
@ -105,7 +102,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
} }
if ( !vc_eval.hasGenotypes() ) if ( !vc_eval.hasGenotypes() )
return null; return 0;
Map<String, Genotype> genotypes = vc_eval.getGenotypes(); Map<String, Genotype> genotypes = vc_eval.getGenotypes();
for ( String sample : samples ) { for ( String sample : samples ) {
@ -123,7 +120,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
Double dg = Double.valueOf(gl); Double dg = Double.valueOf(gl);
if (dg> maxLikelihood) if (dg> maxLikelihood)
maxLikelihood = dg; maxLikelihood = dg;
likeArray.add(dg); likeArray.add(dg);
} }