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12 Commits (3a64398d07cefa346c5081a79b936fa71e1dda1f)

Author SHA1 Message Date
Eric Banks 3a64398d07 Cleaned up the isGATKLite check 2012-07-17 12:46:16 -04:00
Eric Banks 62c5228048 1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method. 2012-07-17 12:23:40 -04:00
Eric Banks 40618ac471 A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots). 2012-07-17 10:52:43 -04:00
Eric Banks d5b3a2eabf Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2012-07-17 00:32:53 -04:00
Eric Banks f657b8bda8 Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow. 2012-07-17 00:32:34 -04:00
Eric Banks 0a89adbcdb Add utility decorators so that classes can tell you which package source they come from if they want to (suggested by Khalid). Using those decorators, we can easily pull out the BQSR updateDataForPileupElement() method into a standard RecalibrationEngine and an AdvancedRecalibrationEngine and use the protected one (AdvancedRE) if available (otherwise, the public one). 2012-07-16 15:34:50 -04:00
Eric Banks 52baac1e16 Move BQSRv2 into public and v1 into the archive. 2012-07-16 14:23:38 -04:00
Joel Thibault 6c6a324583 Loosen a restriction on isOriginalRead() 
* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
 2012-07-16 14:07:10 -04:00
Eric Banks d7bf74fb7e Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests. 2012-07-10 02:04:26 -04:00
Mauricio Carneiro 6c17c50fa2 Updates to ReduceReads 
* Added optional parameter to not hard clip on the interval border
   * Made not clipping the default behavior (hence integration tests changed)
   * Updated integration tests.
 2012-07-09 13:46:51 -04:00
Mauricio Carneiro 12d1c594df Moving ReduceReads into protected 2012-06-25 17:01:33 -04:00
David Roazen 9c6bccfd8b build system overhaul 
* Added support for a protected directory whose contents are only made public in binary form

* Simplified and reorganized build.xml to improve readability and maintainability

* build.xml now autodetects most build properties:
    -Includes private/protected if they exist
    -No more STING_BUILD_TYPE or specialized targets for public-only, etc.

* Build targets have changed! There are now two main build options:

"ant"       build everything (GATK and Queue)
"ant gatk"  build just the GATK

It was too hard to build everything before -- now it is the default.

* To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line.
  Much better than the old comment/uncomment method!
 2012-05-17 15:16:29 -04:00