Mark DePristo 4f09453470 Refactored reduced read utilities ... -- UnitTests for key functions on reduced reads -- PileupElement calls static functions in ReadUtils -- Simple routine that takes a reduced read and fills in its quals with its reduced qual		2011-09-26 12:58:31 -04:00
..
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	Refactored reduced read utilities	2011-09-26 12:58:31 -04:00
packages	Fix the AnalayzeCovariates packaging.	2011-09-22 11:55:40 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Updating the MDCP	2011-09-22 11:27:40 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00