Mauricio Carneiro 39b54211d0 Fixed hard clipping soft clipped bases after hard clips ... if soft clipped bases were after a hard clipped section of the read, the hard clip was clipping the left soft clip tail as if it were a right tail. Mayhem.		2011-09-22 15:46:55 -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	Fixed hard clipping soft clipped bases after hard clips	2011-09-22 15:46:55 -04:00
packages	Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.	2011-09-12 15:09:25 -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