Eric Banks 7c89fe01b3 Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.		2011-08-03 11:00:36 -04:00
..
R	Moved gsalib sources from private/ to public/	2011-07-27 12:29:43 -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	Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.	2011-08-03 11:00:36 -04:00
packages	Added edu.mit.broad.picard to Queue packaged jar.	2011-07-23 14:40:29 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Remove temporary index files (*.bai)	2011-07-30 02:05:22 -04:00
testdata	Testdata for diffObjects.	2011-07-18 10:47:03 -04:00