Commit Graph

7 Commits (3ba2e5667c30190096504ebe6d505c78d9eee3d9)

Author SHA1 Message Date
Mark DePristo 3ba2e5667c CalibrateGenotypesLikelihoods include pOfDGivenD now 2012-03-09 16:00:07 -05:00
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