zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

convenience method to deal with genotypes that are unsorted (e.g. CA vs. AC) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-09 04:45:49 +00:00
parent 7fde6c0bf4
commit cff645e98b
1 changed files with 13 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
View File

@ -61,4 +61,17 @@ public enum DiploidGenotype {
public static DiploidGenotype createHomGenotype(char hom) { public static DiploidGenotype createHomGenotype(char hom) {
return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase()); return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());
} }
/**
* get the genotype, given a string of 2 chars which may not necessarily be ordered correctly
* @param genotype the string representation
* @return the diploid genotype
*/
public static DiploidGenotype unorderedValueOf(String genotype) {
if ( genotype == null || genotype.length() != 2 )
throw new IllegalArgumentException("Diploid genotypes are represented by 2 characters");
if ( genotype.charAt(0) > genotype.charAt(1) )
genotype = String.format("%c%c", genotype.charAt(1), genotype.charAt(0));
return valueOf(genotype);
}
} }