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Added isReference() to AllelicVariant and updated rodDbSNP accordingly 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@311 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-07 14:49:20 +00:00
parent 99579a1ef8
commit e95f427965
2 changed files with 8 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
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@ -53,6 +53,13 @@ public interface AllelicVariant extends Comparable<ReferenceOrderedDatum> {
* @return alternative allele base on the forward starnd
*/
char getAltSnpFWD() throws IllegalStateException;
/** Returns true if all observed alleles are reference alleles. All is<Variant> methods (where Variant=SNP,Insertion, etc) should
* return false at such site to ensure consistency. This method is included for use with genotyping calls (isGenotype()==true), it makes
* no sense for, e.g. dbSNP and should return false for the latter.
* @return
*/
boolean isReference();
/** Is this variant a SNP?
*

1
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -116,6 +116,7 @@ public class rodDbSNP extends ReferenceOrderedDatum implements AllelicVariant {
public boolean isInsertion() { return varType.contains("insertion"); }
public boolean isDeletion() { return varType.contains("deletion"); }
public boolean isIndel() { return isInsertion() || isDeletion() || varType.contains("in-del"); }
public boolean isReference() { return false; } // snp locations are never "reference", there's always a snp!!
public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
public boolean is2Hit2Allele() { return validationStatus.contains("by-2hit-2allele"); }