gatk-3.8

Author	SHA1	Message	Date
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
Khalid Shakir	8b81031bf8	Disabling tests for Lsf706 specific functionality.	2014-11-04 01:31:18 +08:00
Khalid Shakir	5c9fe1a06d	Split all imports of tools\|engine from utils, and all tools from engine. Second of two commits, modifying actual files.	2014-10-24 20:59:46 +08:00
Khalid Shakir	bb7151192a	Split all imports of tools\|engine from utils, and all tools from engine. First of two commits, renaming files only.	2014-10-24 20:59:45 +08:00