From 521e202a10fe94c3c0f221dc3e87310fb6fcc4cb Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 21 Apr 2009 21:07:20 +0000 Subject: [PATCH] updated interface git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java index 43780a1b2..a4a1eb2f3 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java @@ -26,6 +26,10 @@ public interface Genotype extends Comparable { 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 getFWDAlleles() ;