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Allowing N's in ALT field 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3650 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-28 11:41:32 +00:00
parent 3a9d426ca8
commit 464ac63a22
1 changed files with 3 additions and 12 deletions
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15
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
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@ -1,8 +1,5 @@
package org.broadinstitute.sting.gatk.contexts.variantcontext; package org.broadinstitute.sting.gatk.contexts.variantcontext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.ArrayList; import java.util.ArrayList;
@ -124,6 +121,7 @@ public class Allele implements Comparable<Allele> {
private final static Allele REF_T = new Allele("T", true); private final static Allele REF_T = new Allele("T", true);
private final static Allele ALT_T = new Allele("T", false); 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_N = new Allele("N", true);
private final static Allele ALT_N = new Allele("N", false);
private final static Allele REF_NULL = new Allele("-", true); private final static Allele REF_NULL = new Allele("-", true);
private final static Allele ALT_NULL = new Allele("-", false); private final static Allele ALT_NULL = new Allele("-", false);
public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false); public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false);
@ -157,7 +155,7 @@ public class Allele implements Comparable<Allele> {
case 'C': return isRef ? REF_C : ALT_C; case 'C': return isRef ? REF_C : ALT_C;
case 'G': return isRef ? REF_G : ALT_G; case 'G': return isRef ? REF_G : ALT_G;
case 'T': return isRef ? REF_T : ALT_T; case 'T': return isRef ? REF_T : ALT_T;
case 'N': if (isRef) return REF_N; case 'N': return isRef ? REF_N : ALT_N;
default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]); default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]);
} }
} else { } else {
@ -206,17 +204,10 @@ public class Allele implements Comparable<Allele> {
for ( int i = 0; i < bases.length; i++ ) { for ( int i = 0; i < bases.length; i++ ) {
switch (bases[i]) { switch (bases[i]) {
case 'A': case 'C': case 'G': case 'T': break; case 'A': case 'C': case 'G': case 'T': case 'N' : break;
case 'N':
if (!reference)
return false;
break;
default: default:
return false; return false;
} }
// if ( ! BaseUtils.isRegularBase(bases[i]) ) {
// return false;
// }
} }
return true; return true;