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make AllelicVariant extend ReferenceOrderedDatum (not Comparable) since ROD itself is Comparable. Then we can generalize RMD tags. 

Blame Matt if this doesn't work - he said it wouldn't break anything.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1256 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-15 19:25:06 +00:00
parent 00d49976fb
commit 800f7e6360
2 changed files with 5 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
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@ -12,7 +12,7 @@ import java.util.List;
* Time: 11:02:03 AM * Time: 11:02:03 AM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public interface AllelicVariant extends Comparable<ReferenceOrderedDatum> { public interface AllelicVariant extends ReferenceOrderedDatum {
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
// //
// manipulating the SNP information // manipulating the SNP information

5
java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
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@ -37,7 +37,10 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
public double getMAF() { return 0.0; } public double getMAF() { return 0.0; }
public double getHeterozygosity() { return 0.0; } public double getHeterozygosity() { return 0.0; }
public boolean isGenotype() { return false; } public boolean isGenotype() { return false; }
public double getVariationConfidence() { return Double.parseDouble(this.get("6")); } public double getVariationConfidence() {
double value = Double.parseDouble(this.get("6"));
return (value > 0.0 ? value : 1.0);
}
public double getConsensusConfidence() { return -1; } public double getConsensusConfidence() { return -1; }
public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); } public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
public int getPloidy() throws IllegalStateException { return 2; } public int getPloidy() throws IllegalStateException { return 2; }