Slight reorganization of genotype interface

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java

@@ -1,26 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.ReadBackedPileup;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class GenotypeFactory
- *
- * Create genotypes, given certain pileup information
- */
-public interface GenotypeGenerator {
-
-    /**
-     * given all the data associated with a locus, make a genotypeLocus object containing the likelihoods and posterior probs
-     * 
-     * @param tracker contains the reference meta data for this location, which may contain relevent information like dpSNP or hapmap information
-     * @param ref the reference base
-     * @param pileup a pileup of the reads, containing the reads and their offsets
-     * @return a GenotypeLocus, containing each of the genotypes and their associated likelihood and posterior prob values
-     */
-    public org.broadinstitute.sting.utils.genotype.calls.GenotypeCall callGenotypes(RefMetaDataTracker tracker, char ref, ReadBackedPileup pileup);
-}