Roger Zurawicki 4fd5630f6a Added ReadClipper Unit Test ... * Includes tests that include HardClip to Read and Reference Coords. * Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing		2011-09-28 23:13:50 -04:00
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R	Merge branch 'master' into sgintervals	2011-09-19 09:50:19 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Added ReadClipper Unit Test	2011-09-28 23:13:50 -04:00
packages	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merged bug fix from Stable into Unstable	2011-09-27 14:34:39 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00