Ryan Poplin
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9e10779fa7
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Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests.
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2012-03-21 08:45:42 -04:00 |
Mark DePristo
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3ba2e5667c
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CalibrateGenotypesLikelihoods include pOfDGivenD now
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2012-03-09 16:00:07 -05:00 |
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Ryan Poplin
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5343f8ba67
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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
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2012-02-05 13:09:03 -05:00 |
Menachem Fromer
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a9671b73ca
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Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1)
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2012-01-27 16:01:30 -05:00 |
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Mark DePristo
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048202d18e
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Bugfix for cached quals
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2011-09-02 21:13:28 -04:00 |
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Mark DePristo
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c3ea96d856
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Removing many unused functions of unquestionable purpose
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2011-09-02 08:42:01 -04:00 |
Eric Banks
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a2597e7f00
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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.
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2011-07-12 14:11:53 -04:00 |
David Roazen
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3c9497788e
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Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
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2011-06-28 06:55:19 -04:00 |