8b83f4d6c7
Near final cleanup of PileupElement
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-- All functions documented and unit tested
-- New constructor interface
-- Cleanup some uses of old / removed functionality
2013-01-11 15:17:17 -05:00
fb9eb3d4ee
PileupElement and LIBS cleanup
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-- function to create pileup elements in AlignmentStateMachine and LIBS
-- Cleanup pileup element constructors, directing users to LIBS.createPileupFromRead() that really does the right thing
2013-01-11 15:17:17 -05:00
cc1d259cac
Implement get Length and Bases of OfImmediatelyFollowingIndel in PileupElement
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-- Added unit tests for this behavior. Updated users of this code
2013-01-11 15:17:17 -05:00
2c38310868
Create LIBS using new AlignmentStateMachine infrastructure
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-- Optimizations to AlignmentStateMachine
-- Properly count deletions. Added unit test for counting routines
-- AlignmentStateMachine.java is no longer recursive
-- Traversals now use new LIBS, not the old one
2013-01-11 15:17:17 -05:00
b53286cc3c
HaplotypeCaller mode to skip assembly and genotyping for performance testing
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-- Added HCPerformance evaluation Qscript
-- Added some docs about one of the HC integration tests
-- HaplotypeCaller / ART performance evaluation script
2013-01-11 15:17:16 -05:00
85baf71b39
Merged bug fix from Stable into Unstable
2013-01-11 11:05:27 -05:00
d78539774f
Another RR bug: off by one error led to ArrayIndexOutOfBoundsException when working with multiple samples and the variant region ended 1 base after the end of the last read for a given sample.
2013-01-11 11:05:09 -05:00
79b93f659c
Merged bug fix from Stable into Unstable
2013-01-11 09:20:13 -05:00
67fafbb625
Forgot an include
2013-01-11 09:19:46 -05:00
6bf0cc32f9
When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed.
2013-01-11 09:16:19 -05:00
e7906713d9
Moving some random walkers back to public as requested by Mark. Mauricio will the licenses get updated automatically?
2013-01-11 02:03:43 -05:00
3a51823c2a
Clean up imports
2013-01-10 23:35:01 -05:00
e4b7b1955c
Forgot to add the note about length normalization to the QD docs
2013-01-10 23:34:06 -05:00
ff5ac986d8
Fix docs for QD
2013-01-10 23:31:46 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
dd177b1714
Removing fully commented out varianteval evaluators
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- Files were completely commmented out, and were screwing up my license script. Dont like them. Removed them.
GSATDG-5
2013-01-10 17:06:12 -05:00
80dec72c53
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-10 14:35:59 -05:00
31a5f88c4f
Expanded unit tests to cover the Concordance Metrics class fairly uniformly.
2013-01-10 14:33:47 -05:00
1a18947abf
Adding new command line argument requested on the forum to control the maximum number of haplotypes that are sent forward for genotyping. In the presence of a large degree of heterozygosity the current algorithm breaks down and so this argument would need to be increased.
2013-01-09 15:54:02 -05:00
487fb2afb4
Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.
2013-01-09 15:30:46 -05:00
6787f86803
Eliminate the import of DiploidGenotype, which switched public/private underneath me but for some reason didn't stop me from compiling...
2013-01-09 13:23:24 -05:00
c1de92b511
Add in some todo items
2013-01-09 13:16:06 -05:00
8d126161e2
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-09 13:15:04 -05:00
3a0dd4b175
Oops, I broke the build. NOW we shouldn't have any more public->protected dependancies.
2013-01-09 11:12:28 -05:00
a921b06e02
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-09 11:06:17 -05:00
4fa439d89e
Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now
2013-01-09 11:06:10 -05:00
396bce1f28
Reverting this change until we can figure out the right thing to do here.
2013-01-09 10:51:30 -05:00
676e79542a
Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.
2013-01-09 10:39:48 -05:00
c87ad8c0ef
Bug fixes related to HC's GGA mode. Tracking just the artificial allele isn't sufficient when there are multiple GGA records that change the reference basis. Also, duplicated records screw up the tracking of merged alleles.
2013-01-09 10:00:46 -05:00
ad7c2a08d4
Normalize by the event type counts, not the total genotype counts: more useful normalization.
2013-01-09 09:12:41 -05:00
b56754606b
Initial break-out of GenotypeConcordance as a standalone walker. Some basic functionality testing. Currently performs only a pairwise comparison, but is very careful about proper tabulation through the GenotypeType enum.
2013-01-09 00:34:07 -05:00
264cc9e78d
Resolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class.
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Instead of the GATK Engine creating a new BaseRecalibrator (not clean), it just keeps track of the arguments (clean).
There are still some dependency issues, but it looks like they are related to Ami's code. Need to look into it further.
2013-01-08 16:23:29 -05:00
ee7d85c6e6
Move around the DiploidGenotype classes (so it can be used by the GATKPaperGenotyper)
2013-01-08 15:53:11 -05:00
0e2e672521
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-08 15:46:39 -05:00
f0bd1b5ae5
Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.
2013-01-08 15:46:32 -05:00
9cbb2b868f
ErrorRatePerCycleIntegrationTest fix
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-- sorting by row is required
2013-01-08 14:53:07 -05:00
b099e2b4ae
Moving integration tests to protected
2013-01-08 09:34:08 -05:00
dfe4cf1301
When merging the PerReadAlleleLikelihoodMap classes, I forgot to initialize the underlying objects. This was causing the LargeScaleTests to fail.
2013-01-08 09:24:12 -05:00
9e6c2afb28
Not sure why IntelliJ didn't add this for commit like the other dirs
2013-01-07 18:11:07 -05:00
3787ee6de7
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-07 17:07:29 -05:00
47d030a52d
Oops, move the covariates over too
2013-01-07 15:47:25 -05:00
35699a8376
Move bqsr utils to protected
2013-01-07 15:41:21 -05:00
a0219acfaa
Collapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone
2013-01-07 14:55:21 -05:00
35d9bd377c
Moved (nearly) all Walkers from public to protected and removed GATKLite utils
2013-01-07 14:42:40 -05:00
4f95f850b3
Bug fix in the HC's allele mapping for multi-allelic events. Using the allele alone as a key isn't sufficient because alleles change when the reference allele changes during VariantContextUtils.simpleMerge for multi-allelic events.
2013-01-07 11:05:44 -05:00
d3c2c97fb2
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-06 23:35:47 -05:00
81eef3aa37
merge development branchs of log-less HMM and FastGatherer to master
2013-01-06 23:01:58 -05:00
52067f0549
Handle merge conflicts
2013-01-06 12:29:12 -05:00
41bc416b65
Remove AAL and update MD5s.
2013-01-04 16:46:14 -05:00
bce6fce58d
Resolving merge conflicts after Mark's latest push
2013-01-04 14:46:39 -05:00
Mark DePristo
Eric Banks
Mauricio Carneiro
Chris Hartl
Ryan Poplin
Tad Jordan
Ami Levy-Moonshine