gatk-3.8

Author	SHA1	Message	Date
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
Mark DePristo	eacf205f40	Tests needed to be updated to reflect the code reorg of tribble.	2011-07-16 09:22:34 -04:00
Eric Banks	6a431da554	Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.	2011-07-13 14:40:01 -04:00
David Roazen	f18fffd625	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00