Mark DePristo 034a997d07 Generalized Reads -> Fragment calculation ... -- Supports ReadBackedPileup -> FragmentCollection as before -- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller -- General cleanup, renaming, move to separate package, more extensive unit tests, etc. -- Added toFragment() function to ReadBackedPileup interface		2011-10-26 15:54:38 -04:00
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R	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -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	Generalized Reads -> Fragment calculation	2011-10-26 15:54:38 -04:00
packages	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00