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Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3620 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-23 17:49:14 +00:00
parent b6bceb39b0
commit f0fc34bb8e
1 changed files with 7 additions and 3 deletions
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10
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
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@ -123,6 +123,7 @@ public class Allele implements Comparable<Allele> {
private final static Allele ALT_G = new Allele("G", false);
private final static Allele REF_T = new Allele("T", true);
private final static Allele ALT_T = new Allele("T", false);
private final static Allele REF_N = new Allele("N", true);
private final static Allele REF_NULL = new Allele("-", true);
private final static Allele ALT_NULL = new Allele("-", false);
public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false);
@ -156,7 +157,8 @@ public class Allele implements Comparable<Allele> {
case 'C': return isRef ? REF_C : ALT_C;
case 'G': return isRef ? REF_G : ALT_G;
case 'T': return isRef ? REF_T : ALT_T;
default: throw new IllegalArgumentException("Illegal lower-case base: " + (char)bases[0]);
case 'N': if (isRef) return REF_N;
default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]);
}
} else {
return new Allele(bases, isRef);
@ -205,8 +207,10 @@ public class Allele implements Comparable<Allele> {
for ( int i = 0; i < bases.length; i++ ) {
switch (bases[i]) {
case 'A': case 'C': case 'G': case 'T': break;
case 'N': if(!reference)
return false; break;
case 'N':
if (!reference)
return false;
break;
default:
return false;
}