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13 Commits (03294ae1c87821eeb91d675c934f80059a2347d2)

Author SHA1 Message Date
Eric Banks b6839b3049 Added checking in the GATK for mis-encoded quality scores. 
The check is performed by a Read Transformer that samples (currently set to once
every 1000 reads so that we don't hurt overall GATK performance) from the input
reads and checks to make sure that none of the base quals is too high (> Q60). If
we encounter such a base then we fail with a User Error.

* Can be over-ridden with --allow_potentially_misencoded_quality_scores.
* Also, the user can choose to fix his quals on the fly (presumably using PrintReads
  to write out a fixed bam) with the --fix_misencoded_quality_scores argument.

Added unit tests.
 2012-12-03 11:18:41 -05:00
Eric Banks 6030605242 Added quick check for creation of bad BAQ values associated with badly encoded base qualities; hopefully this can help us debug the non-reproducible issue seen by many users. 2012-11-28 13:26:31 -05:00
Mark DePristo 57b45bfb1e Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
Mauricio Carneiro e440d0ce69 BQSR triage #4 
* fixed queue script plot file names
   * updated the ReadGroupCovariate to use the platform unit instead of sample + lane.
   * fixed plotting of marginalized reported qualities
 2012-04-24 17:19:54 -04:00
Mauricio Carneiro 0f8c77391d BQSR bug triage #3 
* fixed context covariate famous "off by one" error
   * reduced maximum quality score to Q50 (following Eric/Ryan's suggestion)
   * remove context downsampling in BQSR R script
 2012-04-19 17:31:04 -04:00
Ryan Poplin 9e10779fa7 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. 2012-03-21 08:45:42 -04:00
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