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15 Commits (b316c9a5909bf29301e9d4643c97d86e80736a2a)

Author SHA1 Message Date
depristo 22ff2573d5 Removed MAG entirely 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5474 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-18 19:43:23 +00:00
kshakir b2b8a4f19f Re-un-final'ed BAQ.MAG as it was pre r5469. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5472 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-18 19:40:31 +00:00
depristo 7857cb5a22 Waiting to go to the hospital -- fixed a bug in the BAQ calculation where the BAQ would NPE if a read had no usable bases (all clipped, for example) but didn't fail the PF filter 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5469 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-18 17:45:21 +00:00
delangel 8c262eb605 Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties. 
Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet.

In detail:
a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils.
b) Refactored a couple of read utilities and moved from BAQ to ReadUtils.
c) New PairHMMIndelErrorModel class implementing new likelihood model
d) Several new hidden debug arguments in UAC.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 15:31:58 +00:00
hanna 7a22f19366 More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated 
case UserException.MalformedBAM to match case of UserExceptio.MissortedBAM for consistency and
ease-of-use.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5364 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-03 03:55:24 +00:00
depristo 2182b8c7e2 Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5108 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-28 15:08:21 +00:00
carneiro 9e93091e9a -baqGOP now takes phred scaled scores instead of probabilities in the command line. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-13 00:06:38 +00:00
ebanks f3ca2cc9de Add safety net to BAQ calculation: explicitly cast to byte/int and check for bad values 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4954 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 18:09:12 +00:00
depristo 5b46a900b3 Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4818 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-10 19:35:12 +00:00
depristo a63bbb2fec Optimized BAQ implementation. No longer does excessive amounts of copying of arrays. At this point I'm not 100% certain where additional performance improvements would come from 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4808 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-08 21:26:30 +00:00
depristo db55b2b0c6 Better testing of BAQ. Now really handles soft clipped reads properly by doing an expensive copy operation :-( will need to be transformed to a ByteBuffer in the near future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4807 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-08 17:37:00 +00:00
depristo 16e1bbd380 Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested. 
BAQ has generally useful improvements.  Refactor code to make it easier for BAQUnitTest to run.  minBaseQuality enforced on output, as well as input now.  Added BAQUnitTest that checks that the BAQ calculation is performing as expected.  Still needs to be expanded significantly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-08 01:01:39 +00:00
depristo bc885b7bd0 Don't print debugging output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4799 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-06 20:57:11 +00:00
depristo c91712bd59 BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker. 
SAMFileWriterStub now supports BAQ writing as an internal feature.  Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable.  Please look if you own these walkers, though

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-06 20:55:52 +00:00
depristo 5d2c2bd280 Just refactoring into utils/baq directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-06 17:43:43 +00:00