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
e3f89fb054
Missing/malformed GATK report files are user errors
2012-08-02 11:33:21 -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
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
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
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
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
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
79195b97a3
Adding categories for the remaining uncategorized walkers
2012-07-30 11:35:08 -04:00
beb7610195
Resolving merge conflicts
2012-07-27 15:52:02 -04:00
27e7e11ec0
Allele refactoring checkpoint #3 : all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this.
2012-07-27 15:48:40 -04:00
a0890126a8
ActiveRegionWalker's isActive function returns a results object now instead of just a double.
2012-07-27 11:01:39 -04:00
ef335b6213
Several more walkers have been brought up to use the new Allele representation.
2012-07-27 02:14:25 -04:00
9e2209694a
Re-enable reverse trimming of alleles in UG engine when sub-selecting alleles after genotyping. UG integration tests now pass.
2012-07-27 00:47:15 -04:00
baf3e33730
Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass.
2012-07-26 23:27:11 -04:00
35e803e110
Merged bug fix from Stable into Unstable
2012-07-26 14:00:04 -04:00
4f741b4cd7
Smoothing in the BQSR bins should be one error observation and one non-error observation.
2012-07-26 13:59:02 -04:00
2ae890155c
Improvements to indel calling in pool caller: a) Compute per-read likelihoods in reference sample to determine wheter a read is informative or not. b) Fixed bugs in unit tests. c) Fixed padding-related bugs when computing matches/mismatches in ErrorModel, d) Added a couple of more integration tests to increase test coverage, including testing odd ploidy
2012-07-26 13:43:00 -04:00
a694d1b5de
Merge branch 'master' into allelePadding
2012-07-26 01:53:14 -04:00
32516a2f60
Initial checkpoint commit of VariantContext/Allele refactoring. There were just too many problems associated with the different representation of alleles in VCF (padded) vs. VariantContext (unpadded). We are moving VC to use the VCF representation. No more reference base for indels in VC and no more trimming and padding of alleles. Even reverse trimming has been stopped (the theory being that writers of VCF now know what they are doing and often want the reverse padding if they put it there; this has been requested on GetSatisfaction). Code compiles but presumably pretty much all tests with indels with fail at this point.
2012-07-26 01:50:39 -04:00
8c418a15da
Sorting out HMS error handling (fingers crossed)
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-- Check if a traversal error occurred in the last shard
-- Catch ExecutionException from the TreeReducer and throw as our HMS execption
-- ShardTraverser just throws the exception as formatted by the HMS, rather than wrapping it as a RuntimeException itself
-- EngineFeaturesIntegrationTests now uses public exampleFASTA (faster), and does 1000x iterations (slower)
2012-07-25 23:13:12 -04:00
9242f63a4d
On the way to really sorting out HMS error handling
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-- Better error message when a traveral error occurs (a real bug)
-- EngineFeaturesIntegrationTest runs the multi-threaded error testing routines 50x times
-- A bit of cleanup in WalkerTest
2012-07-25 22:11:10 -04:00
7eb3f54750
Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
2012-07-25 21:40:28 -04:00
2982b24c4b
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-07-25 20:36:53 -04:00
0a98a6aa8d
Adding extraDocs tag per Mauricio's request
2012-07-25 18:23:18 -04:00
fce5cb9f35
Few category changes
2012-07-25 17:23:02 -04:00
05fa377a8e
Adding GATK categories to standard walkers. Will add to remaining walkers after the next successful release (so that I can see which walkers are public and still need it).
2012-07-25 16:05:47 -04:00
d46cf47bd1
Updating Read Filter documentation
2012-07-25 15:05:47 -04:00
6a3bfa3811
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-07-25 14:11:11 -04:00
357e0b35af
Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error
2012-07-25 14:11:03 -04:00
5b74763096
Removed Categories.
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We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything.
Tools can be hidden from GATKdocs with the @Hidden annotation
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 13:46:24 -04:00
Joel Thibault
Eric Banks
Mark DePristo
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Roger Zurawicki