Eric Banks a694d1b5de Merge branch 'master' into allelePadding		2012-07-26 01:53:14 -04:00
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src/org/broadinstitute/sting	Merge branch 'master' into allelePadding	2012-07-26 01:53:14 -04:00
test/org/broadinstitute/sting/gatk/walkers	Initial checkpoint commit of VariantContext/Allele refactoring. There were just too many problems associated with the different representation of alleles in VCF (padded) vs. VariantContext (unpadded). We are moving VC to use the VCF representation. No more reference base for indels in VC and no more trimming and padding of alleles. Even reverse trimming has been stopped (the theory being that writers of VCF now know what they are doing and often want the reverse padding if they put it there; this has been requested on GetSatisfaction). Code compiles but presumably pretty much all tests with indels with fail at this point.	2012-07-26 01:50:39 -04:00