6f8e7692d4
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-03 12:24:37 -04:00
9e25b209e0
First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller
2012-08-03 12:24:23 -04:00
8817fc70d1
Merged bug fix from Stable into Unstable
2012-08-03 10:45:01 -04:00
f40d0a0a28
Updating VQSR to work with the MNP and symbolic variants that are coming out of the HaplotypeCaller. Integration tests change because of the MNPs in dbSNP.
2012-08-03 10:44:36 -04:00
51bd03cc36
Add RemoveProgramRecords annotation to ActiveRegionWalker
2012-08-03 09:54:16 -04:00
addbfd6437
Add a RemoveProgramRecords annotation
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* Add the RemoveProgramRecords annotation to LocusWalker
2012-08-03 09:54:16 -04:00
524d7ea306
Choose whether to keep program records based on Walker
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* Add keepProgramRecords argument
* Make removeProgramRecords / keepProgramRecords override default
2012-08-03 09:54:16 -04:00
e04989f76d
Bugfix for new PASS position in dictionary in BCF2
2012-08-03 09:42:21 -04:00
fb5dabce18
Update BCF2 to include a minor version number so we can rev (and report errors) with BCF2
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-- We are no likely to fail with an error when reading old BCF files, rather than just giving bad results
-- Added new class BCFVersion that consolidates all of the version management of BCF
2012-08-02 17:30:30 -04:00
e3f89fb054
Missing/malformed GATK report files are user errors
2012-08-02 11:33:21 -04:00
cc01f844d4
Merged bug fix from Stable into Unstable
2012-08-02 11:25:28 -04:00
0381fd7c83
Hmm, I thought I used the right md5s last time. Let's try again.
2012-08-02 11:25:10 -04:00
c3c3d18611
Update BCF2 to put PASS as offset 0 not at the end
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-- Unfortunately this commit breaks backward compatibility with all existing BCF2 files...
2012-08-01 17:09:22 -04:00
ccac77d888
Bugfix for incorrect allele counting in IndelSummary
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-- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs
-- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles
-- Update a few pieces of code to get previous correct behavior
-- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct)
-- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default
2012-08-01 15:45:12 -04:00
2b25df3d53
Add removeProgramRecords argument
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* Add unit test for the removeProgramRecords
2012-08-01 15:33:05 -04:00
d53105668b
Merged bug fix from Stable into Unstable
2012-08-01 14:53:06 -04:00
fabca66d09
Another fix to VQSR docs
2012-08-01 14:52:49 -04:00
2be29ebd22
Merged bug fix from Stable into Unstable
2012-08-01 14:35:30 -04:00
4093909a56
Updating VQSR docs. Removing references to old best practices pages.
2012-08-01 14:30:24 -04:00
52b93cab62
Merged bug fix from Stable into Unstable
2012-08-01 13:17:36 -04:00
22bf052828
Fixing BQSR GATK docs
2012-08-01 13:17:16 -04:00
459832ee16
Fixed bug in FastaAlternateReferenceMaker when input VCF has overlapping deletions as reported a while back on GS
2012-08-01 10:45:04 -04:00
a4a41458ef
Update docs of FastaAlternateReferenceMaker as promised in older GS thread
2012-08-01 10:33:41 -04:00
687df2341d
Merged bug fix from Stable into Unstable
2012-08-01 10:27:15 -04:00
05bf6e3726
Updating md5s in pipeline tests so that they finally pass
2012-08-01 10:27:00 -04:00
38e5419b11
Merged bug fix from Stable into Unstable
2012-08-01 09:50:31 -04:00
56f8afab97
Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.
2012-08-01 09:50:00 -04:00
7cf4b63d76
Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.
2012-08-01 09:23:04 -04:00
0528337467
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-31 18:17:50 -04:00
4a23f3cd11
Simple cleanup of pool caller code - since usage is much more general than just calling pools, AF calculation models and GL calculation models are renamed from Pool -> GeneralPloidy. Also, don't have users specify special arguments for -glm and -pnrm. Instead, when running UG with sample ploidy != 2, the correct general ploidy modules are automatically detected and loaded. -glm now reverts to old [SNP|INDEL|BOTH] usage
2012-07-31 16:34:20 -04:00
6cb10cef96
Fixed older GS reported bug. Actually, the problem really lies in Picard (can't set max records in RAM without it throwing an exception, reported on their JIRA) so I just masked out the problem by removing this never-used argument from this rarely-used tool.
2012-07-31 16:00:36 -04:00
ab53d73459
Quick fix to user error catching
2012-07-31 15:50:32 -04:00
10111450aa
Fixed AlignmentUtils bug for handling Ns in the CIGAR string. Added a UG integration test that calls a BAM with such reads (provided by a user on GetSatisfaction).
2012-07-31 15:37:22 -04:00
f7133ffc31
Cleanup syntax errors from BQSR reorganization
2012-07-31 08:11:05 -04:00
762a3d9b50
Move BQSR.R to utils/recalibration in R
2012-07-31 08:11:04 -04:00
dad9bb1192
Changes order of writing BaseRecalibrator results so that if R blows up you still get a meaningful tree
2012-07-31 08:11:04 -04:00
0c4e729e13
Working version of adaptive context calculations
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-- Uses chi2 test for independences to determine if subcontext is worth representing. Give excellent visual results
-- Writes out analysis output file producing excellent results in R
-- Trivial reformatting of MathUtils
2012-07-31 08:11:04 -04:00
93640b382e
Preliminary version of adaptive context covariate algorithm
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-- Works according to visual inspection of output tree
2012-07-31 08:11:04 -04:00
315d25409f
Improvement to RecalDatum and VisualizeContextTree
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-- Reorganize functions in RecalDatum so that error rate can be computed indepentently. Added unit tests. Removed equals() method, which is a buggy without it's associated implementation for hashcode
-- New class RecalDatumTree based on QualIntervals that inherits from RecalDatum but includes the concept of sub data
-- VisualizeContextTree now uses RecalDatumTree and can trivially compute the penalty function for merging nodes, which it displays in the graph
2012-07-31 08:11:04 -04:00
57b45bfb1e
Extensive unit tests, contacts, and documentation for RecalDatum
2012-07-31 08:11:03 -04:00
e00ed8bc5e
Cleanup BQSR classes
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-- Moved most of BQSR classes (which are used throughout the codebase) to utils.recalibration. It's better in my opinion to keep commonly used code in utils, and only specialized code in walkers. As code becomes embedded throughout GATK its should be refactored to live in utils
-- Removed unncessary imports of BQSR in VQSR v3
-- Now ready to refactor QualQuantizer and unit test into a subclass of RecalDatum, refactor unit tests into RecalDatum unit tests, and generalize into hierarchical recal datum that can be used in QualQuantizer and the analysis of adaptive context covariate
-- Update PluginManager to sort the plugins and interfaces. This allows us to have a deterministic order in which the plugin classes come back, which caused BQSR integration tests to temporarily change because I moved my classes around a bit.
2012-07-31 08:11:03 -04:00
191294eedc
Initial cleanup of RecalDatum for move and further refactoring
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-- Moved Datum, the now unnecessary superclass, into RecalDatum
-- Fixed some obviously dangerous synchronization errors in RecalDatum, though these may not have caused problems because they may not have been called in parallel mode
2012-07-31 08:11:03 -04:00
0670316288
Be clearer that dcov 50 is good for 4x, should use 200 for >30x
2012-07-31 08:11:02 -04:00
874dbf5b58
Maximum wait for GATK run report upload reduced to 10 seconds
2012-07-31 08:11:02 -04:00
e6b326c189
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-30 21:32:19 -04:00
6c9d3ec155
Remerge after changes to allele construction code. More cleanups/fixes to artificial read pileup provider
2012-07-30 21:32:03 -04:00
7ed06ee7b9
Updating FindCoveredIntervals to use the changes to the ActiveRegionWalker.
2012-07-30 12:16:27 -04:00
13591b169f
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-30 12:13:24 -04:00
0b30588d67
Catch yet another class of User Errors
2012-07-30 11:59:56 -04:00
5743694196
Merged bug fix from Stable into Unstable
2012-07-30 11:35:28 -04:00
Guillermo del Angel
Ryan Poplin
Joel Thibault
Mark DePristo
Eric Banks