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Wasn't always returning the correct alt base 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-30 03:08:04 +00:00
parent 5429b4d4a8
commit feb7238f10
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java
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@ -24,7 +24,11 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
public String getRefBasesFWD() { return this.get("2"); }
public char getRefSnpFWD() throws IllegalStateException { return getRefBasesFWD().charAt(0); }
public String getAltBasesFWD() { return this.get("3"); }
public char getAltSnpFWD() throws IllegalStateException { return getAltBasesFWD().charAt(0); }
public char getAltSnpFWD() throws IllegalStateException {
if ( getAltBasesFWD().charAt(0) != getRefSnpFWD() )
return getAltBasesFWD().charAt(0);
return getAltBasesFWD().charAt(1);
}
public boolean isReference() { return getVariationConfidence() < 0.01; }
public boolean isSNP() { return ! isReference(); }
public boolean isInsertion() { return false; }