Christopher Hartl f9cdc119af Added a method to ReadUtils that converts reads of the form 10S20M10S to 40M (just unclips the soft-clips). ... Be careful when using this - if you're writing a bam file it will be potentially written out of order (since the previous alignment start was at the M, not the S).		2011-09-21 18:16:42 -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 a method to ReadUtils that converts reads of the form 10S20M10S to 40M (just unclips the soft-clips).	2011-09-21 18:16:42 -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	Bringing latest updates of ReduceReads to the master repository	2011-09-20 16:35:09 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00