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Need to return real values for some of the AllelicVariant methods 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1264 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-16 02:31:10 +00:00
parent 045d74d09c
commit 88ffb08af4
1 changed files with 10 additions and 3 deletions
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13
java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
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@ -148,9 +148,16 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
return new String( b ); return new String( b );
} }
public char getRefSnpFWD() throws IllegalStateException { return 0; } public char getRefSnpFWD() throws IllegalStateException { return getReferenceBase(); }
public String getAltBasesFWD() { return null; } public String getAltBasesFWD() { return getBestGenotype(); }
public char getAltSnpFWD() throws IllegalStateException { return 0; } public char getAltSnpFWD() throws IllegalStateException {
String bases = getBestGenotype();
if ( bases.charAt(0) != getRefSnpFWD() )
return bases.charAt(0);
else
return bases.charAt(1);
}
public boolean isReference() { return ! isSNP(); } public boolean isReference() { return ! isSNP(); }
public boolean isSNP() { return getLodBtr() > 5; } public boolean isSNP() { return getLodBtr() > 5; }
public boolean isInsertion() { return false; } public boolean isInsertion() { return false; }