genome/genome — pull request #349 by apregier (2014-12-18 22:29:41+00:00)
Title: Fix bam readcount

Previously, we were encoding one bam-readcount entry per sample in each vcf entry. This doesn't fully reflect the reality of the relationship between vcf entries and bam-readcount entries, since one vcf line might contain multiple alleles that are best represented by multiple bam-readcount entries (e.g. an insertion and a deletion on the same line).
Here, we change how bam-readcount lines are encoded in the vcf to accomodate per-allele bam-readcount entries.
When this goes live, we'll need to set test names on all software results of type Genome::VariantReporting::Suite::BamReadcount::AnnotateResult so that they are regenerated with the new encoding.