6 Commits (5343f8ba67cccb90fd91ad77e09f8bd9a2a2d7f5)

Author	SHA1	Message	Date
Ryan Poplin	5343f8ba67	Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv	2012-02-05 13:09:03 -05:00
Menachem Fromer	a9671b73ca	Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1)	2012-01-27 16:01:30 -05:00
Mark DePristo	048202d18e	Bugfix for cached quals	2011-09-02 21:13:28 -04:00
Mark DePristo	c3ea96d856	Removing many unused functions of unquestionable purpose	2011-09-02 08:42:01 -04:00
Eric Banks	a2597e7f00	This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.	2011-07-12 14:11:53 -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