Valentin Ruano-Rubio c5977e5c8f Correct wrong left-alignment of reads in HC bamout ... Story: ----- https://www.pivotaltracker.com/story/show/80684230 Changes: ------- - Corrected the bug: AlignmentUtils#createReadAlignedToRef was not realigning against the reference but the best haplotype for the read. Test: ---- - Added integration test in HaplotypeCallerIntegrationTest to check that the bug has been fixed. - Fixed md5s modified by this change; these are cause due to small changes in the state of the random-number generator and read vs variant site overlapping.		2014-11-10 10:09:58 -05:00
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src	Correct wrong left-alignment of reads in HC bamout	2014-11-10 10:09:58 -05:00
pom.xml	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00