Eric Banks f0b8a0228f Quick fix for HC refactoring: when copying over Haplotype objects, make sure to copy over the artificial allele used to create it too.		2012-11-19 09:57:55 -05:00
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src/org/broadinstitute/sting	Quick fix for HC refactoring: when copying over Haplotype objects, make sure to copy over the artificial allele used to create it too.	2012-11-19 09:57:55 -05:00
test/org/broadinstitute/sting	Significant refactoring of the Haplotype Caller to handle problems with GGA. The main fix is that we now maintain a mapping from 'original' allele to 'Smith-Waterman-based' allele so that we no longer need to do a (buggy) matching throughout the calling process.	2012-11-19 09:09:57 -05:00