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updated interface 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-04-21 21:07:20 +00:00
parent 55ca272919
commit 521e202a10
1 changed files with 4 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
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@ -26,6 +26,10 @@ public interface Genotype extends Comparable<ReferenceOrderedDatum> {
GenomeLoc getLocation();
/** Returns actual observed alleles on the fwd strand. Allowed to return more than two alleles (@see #getPloidy()).
* For SNPs, the alleles are observed bases. For indels, the contract is that a no-event allele is represented by an empty string,
* while the event allele is represented by '+' (insertion) or '-' (deletion) followed by actual inserted or deleted bases. It
* is currently not specified how genotypes that report themselves as 'isReference()' should present their alleles: implementations
* can present reference bases (SNP-like) or empty strings (indel-like).
* @return list of alleles
*/
List<String> getFWDAlleles() ;