Eric Banks 445735a4a5 There was no reason to be sharing the Haplotype infrastructure between the HaplotypeCaller and the HaplotypeScore annotation since they were really looking for different things. ... Separated them out, adding efficiencies for the HaplotypeScore version.		2013-01-16 11:10:13 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	There was no reason to be sharing the Haplotype infrastructure between the HaplotypeCaller and the HaplotypeScore annotation since they were really looking for different things.	2013-01-16 11:10:13 -05:00
test	The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases.	2013-01-16 10:22:43 -05:00