Eric Banks d3baa4b8ca Have Haplotype extend the Allele class. ... This way, we don't need to create a new Allele for every read/Haplotype pair to be placed in the PerReadAlleleLikelihoodMap (very inefficient). Also, now we can easily get the Haplotype associated with the best allele for a given read.		2013-01-15 11:36:20 -05:00
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src/org/broadinstitute/sting	Have Haplotype extend the Allele class.	2013-01-15 11:36:20 -05:00
test/org/broadinstitute/sting	1. Initial implementation of bam writing for the HaplotypeCaller with -bam argument; currently only assembled haplotypes are emitted.	2013-01-15 10:19:18 -05:00