1223d77546
Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events
2012-08-08 15:13:20 -04:00
0a2a646a52
Other random FindBugs fixes
2012-08-08 14:56:27 -04:00
4c84cc9486
Quick pass of FindBugs 'should be static inner class' fixes.
2012-08-08 14:42:06 -04:00
a0196c9f5b
Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.
2012-08-08 14:34:16 -04:00
4b2e3cec0b
Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools.
2012-08-08 14:29:41 -04:00
3e2752667c
Intermediate checkin for ReducedReads with HaplotypeCaller - change min read count over k-mer to average count over k-mer when doing assembly of a reduced read (not optimal, currently trying max and then will decide on best approach), fix merge conflicts
2012-08-08 12:07:33 -04:00
a7811d673f
Update URL for phone home / GATK key documentation output by the GATK upon error
2012-08-08 09:29:54 -04:00
cda8d944b7
Bugfixes for BCF with VQSR
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-- Old version converted doubles directly from strings. New version uses VariantContext getAttributeAsDouble() that looks at the values directly to determine how to convert from Object to Double (via Double.valueOf, (Double), or (Double)(Integer)).
-- getAttributeAsDouble() is now smart in converting integers to doubles as needed
-- Removed unnecessary logging info in BCF2Codec
-- Added integration tests to ensure that VQSR works end-to-end with BCF2 using sites version of the file khalid sent to me
-- Added vqsr.bcf_test.snps.unfiltered.bcf file for this integration test
2012-08-07 17:22:39 -04:00
80b94a4f9a
AdaptiveContexts implement pruning to a given chi2 p value
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-- Added bonferroni corrected p-value pruning, so you tell it how significant of a different you are willing to collapse in the tree, and it prunes the tree down to this maximum threshold
-- Penalty is now a phred-scaled p-value not the raw chi2 value
-- Split command line arguments in VisualizeContextTree into separate arguments for each type of pruning
2012-08-07 17:22:39 -04:00
982c735c76
VisualizeAdaptiveTree now considers only leaf nodes when computing max/min penalty
2012-08-07 17:22:39 -04:00
15085bf03e
The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads.
2012-08-07 13:58:22 -04:00
97c5ed4feb
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-06 20:22:31 -04:00
238d55cb61
Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead
2012-08-06 20:22:12 -04:00
00858f16a6
Deleting empty unit test for AdaptiveContexts
2012-08-06 12:58:13 -04:00
f1c30c3a59
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-06 12:02:26 -04:00
44f160f29f
indelGOP and indelGCP are now advanced, not hidden arguments
2012-08-06 11:42:55 -04:00
2f004665fb
Fixing public -> private dep
2012-08-06 11:42:55 -04:00
7bf5ca51ee
Major bugfix for adaptive contexts
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-- Basically I was treating the context history in the wrong direction, effectively predicting the further bases in the context based on the closer one. Totally backward. Updated the code to build the tree in the right direction.
-- Added a few more useful outputs for analysis (minPenalty and maxPenalty)
-- Misc. cleanup of the code
-- Overall I'm not 100% certain this is even the right way to think about the problem. Clearly this is producing a reasonable output but the sum of chi2 values over the entire tree is just enormous. Perhaps a MCMC convergence / sampling criterion would be a better way to think about this problem?
2012-08-06 11:42:55 -04:00
b4841548f1
Bug fixes and misc. improvements to running the adaptive context tools
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-- Better output file name defaults
-- Fixed nasty bug where I included non-existant quals in the contexts to process because they showed up in the Cycle covariate
-- Data is processed in qual order now, so it's easier to see progress
-- Logger messages explaining where we are in the process
-- When in UPDATE mode we still write out the information for an equivalent prune by depth for post analysis
2012-08-06 11:42:55 -04:00
b8709d8c67
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-06 11:41:28 -04:00
210db5ec27
Update -maxAlleles argument to -maxAltAlleles to make it more accurate. The hidden GSA production -capMaxAllelesForIndels argument also gets updated.
2012-08-06 11:31:18 -04:00
8f95a03bb6
Prevent NumberFormatExceptions when parsing the VCF POS field
2012-08-06 11:19:54 -04:00
b7eec2fd0e
Bug fixes related to the changes in allele padding. If a haplotype started with an insertion it led to array index out of bounds. Haplotype allele insert function is now very simple because all alleles are treated the same way. HaplotypeUnitTest now uses a variant context instead of creating Allele objects directly.
2012-08-05 12:29:10 -04:00
e1bba91836
Ready for full-scale evaluation adaptive BQSR contexts
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-- VisualizeContextTree now can write out an equivalent BQSR table determined after adaptive context merging of all RG x QUAL x CONTEXT trees
-- Docs, algorithm descriptions, etc so that it makes sense what's going on
-- VisualizeContextTree should really be simplified when into a single tool that just visualize the trees when / if we decide to make adaptive contexts standard part of BQSR
-- Misc. cleaning, organization of the code (recalibation tests were in private but corresponding actual files were public)
2012-08-03 16:02:53 -04:00
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
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
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
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
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
79195b97a3
Adding categories for the remaining uncategorized walkers
2012-07-30 11:35:08 -04:00
5b9a1af7fe
Intermediate fix for pool GL unit test: fix up artificial read pileup provider to give consistent data. b) Increase downsampling in pool integration tests with reference sample, and shorten MT tests so they don't last too long
2012-07-30 09:56:10 -04:00
7630c929a7
Re-enabling the unit tests for reverse allele clipping
2012-07-29 22:24:56 -04:00
b07bf1950b
Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now).
2012-07-29 22:19:49 -04:00
c4ae9c6cfb
With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.
2012-07-29 19:22:02 -04:00
99b15b2b3a
Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push.
2012-07-29 01:07:59 -04:00
2b1b00ade5
All integration tests and VC/Allele unit tests are passing
2012-07-27 17:03:49 -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
22bb4804f0
HaplotypeCaller now use an excessive number of high quality soft clips as a triggering signal in order to capture both end points of a large deletion in a single active region.
2012-07-27 12:44:02 -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
5671992db3
RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions
2012-07-25 22:05:04 -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
a5721a8846
Context covariate optimizations were not suited for multiple threads, so I removed them (since that ended up being much, much easier than trying to make the covariates thread local). Added -nt 2 layer to BQSR integration tests to confirm that it now works with multiple threads.
2012-07-25 13:38:07 -04:00
e0c07f5567
Reverting old commits that made error handling better because ultimately they made things worse.
2012-07-25 12:37:59 -04:00
16947e93f2
Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR
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Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:39 -04:00
fcefa61bce
Remove reference dependence in BCF2Codec
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-- Adding BCF2Codec to VCF.jar and associated unit tests
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
19a257a5c1
Multiple bugfixes
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-- VariantFiltration now properly sets passFilters in VC
-- BCF2 writer now properly decodes lazy BCF genotype data that it uses. Improper use generated a horrible subtle bug but the good news is that the extra checks I put in (unnecessarily a few days ago) caught the bug!
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
3066894215
Bugfix for BCF2
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-- Always decode genotypes block when writing out a BCF file. If the header changes (and we currently don't know this easily) then the dictionary keys used in the genotypes block may be invalid. Temporarily added a private static boolean that turns off writing of the blocks until Eric and his team rewrite the header.
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
eb55061fd0
a) Document BEAGLE codec, b) Bug fix: inbreeding coefficient shouldn't be computed for non-diploid organisms in current implementaiton
2012-07-24 12:16:15 -04:00
348e86159e
Moving doclets to public
2012-07-23 23:52:14 -04:00
5cd98a36b9
Making ForumAPIUtils public
2012-07-23 17:44:24 -04:00
3d92f041f3
forgot to delete the merging line
2012-07-23 17:35:07 -04:00
f3c504769b
Added the ability to update the Forum
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GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists.
More changes were made to the GATKDocs. Works nicely with bootstrap on and offline.
Cleaned up the code as well
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-23 17:17:33 -04:00
46ca49b63d
Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.
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Archived AnalyzeCovariates scripts and removed references in build packages / GATK extensions.
2012-07-23 16:32:31 -04:00
2a14bbe4f0
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-23 11:28:26 -04:00
10d143c35c
Adding error model header names in the BQSR recal plot. Making the downsampling of points look a little nicer.
2012-07-23 11:28:17 -04:00
675ccab2fa
Renaming BQSR to BaseRecalibrator
2012-07-23 10:17:17 -04:00
2e486d83e2
Updating HaplotypeCaller docs and expanding integration tests.
2012-07-23 10:05:42 -04:00
39f45127f3
Fix md5's broken by recent changes to FisherStrand calculation
2012-07-21 14:41:38 -04:00
65f4b67b86
Fixing walker unit test with the new naming convention
2012-07-20 17:50:29 -04:00
921eaad33f
Generalized the default platform parameter in BQSRv2
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Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform.
2012-07-20 17:29:13 -04:00
5dc2143142
Removed support for walkers ending with "Walker" from the engine.
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If your walker has "Walker" in the name, you will have to use "Walker" on the -T to access it.
2012-07-20 17:27:11 -04:00
d446d34227
GATK Error messages now point to the new website instead of GetSatisfaction.
2012-07-20 17:27:11 -04:00
116885a450
Removed the "Walker" suffix from all walkers that had it.
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* Did not touch archived walkers... those can be named whatever.
* Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
* Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-20 17:27:11 -04:00
3ee46cced2
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-19 21:25:40 -04:00
af383c30b5
Ensure that the gene summary has a header line
2012-07-19 21:24:04 -04:00
2ca5fc62a2
Support for MISSING BCF2 type
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-- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference.
-- Enabled integration test reading Heng's ex2.bcf file
-- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length
-- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X
-- Added integration test reading 1000G SV chr1 calls (from Chris)
2012-07-19 16:14:26 -04:00
c16f9f2f15
a) Use new method to check for GATK Like, b) minor improvements to indel pool caller (more to come): brain-dead, quick way to limit number of alt alleles to genotype. We can't process too many alt alleles because of the combinatorial explosion of GL values with high ploidy, and some STR validation targets had up to 12 alt alleles, resulting of GL vectors of > 1e8 elements. Can't use pileup elements since typically not many alleles will be in one pileup, and different alleles will appear in different samples, TBD a nicer solution. c) Commit to posterity scala script for large scale validation calling, still work in progress
2012-07-19 10:24:08 -04:00
5f5edeca63
Reverting move of BQSR tests to public, as per DR's email
2012-07-19 10:02:05 -04:00
e370030e6c
As requested by Mark, I've broken out the code to pull out the protected subclass when available (and otherwise use the public version) into the GATKLiteUtils class. People should use this code instead of reimplementing all of the java reflection on their own.
2012-07-18 22:44:37 -04:00
d46ccec04e
Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.
2012-07-18 21:48:58 -04:00
9c1ab1b0c0
Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency.
2012-07-18 21:11:33 -04:00
994c5c31c1
Enabling VariantEval integration tests for ValidationReport
2012-07-18 16:07:47 -04:00
74e153ff4a
FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing
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-- Previously used hardcoded MAPQ > 20 && QUAL > 20 but now uses isUsableBase
-- Updating MD5s as appropriate
2012-07-18 16:07:47 -04:00
dede3a30e9
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
2012-07-18 16:07:47 -04:00
559a4826be
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
2012-07-18 16:07:46 -04:00
dc292c0317
FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations
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-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.
2012-07-18 16:07:46 -04:00
2c0f073ab1
Make -qq arg hidden for now since it's still very experimental
2012-07-18 15:43:25 -04:00
b46c85e8b4
More bad BAM file catching
2012-07-18 15:26:31 -04:00
659eee13a6
Handle NPE generated in UG when non-standard reference bases are present in the fasta
2012-07-18 15:16:27 -04:00
9af2cfe283
Catch underlying file system problems that get masked as Tribble index errors. There's also a quick patch to the HMS that isn't really the ultimate fix needed; Mark and I will review at a later point.
2012-07-18 15:11:38 -04:00
4c730542f0
Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.
2012-07-18 13:56:35 -04:00
ae08d35138
Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).
2012-07-18 12:57:34 -04:00
f2fe59a9d4
Wow, there are a ton of errors captured having to do with being unable to merge the temp Tribble output. I'm expanding the error message a bit to help see if we can do anything going forward.
2012-07-18 12:31:59 -04:00
e4db8dde91
Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!
2012-07-17 23:36:43 -04:00
a8d08ea18d
As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.
2012-07-17 22:18:43 -04:00
29273abab7
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 16:58:12 -04:00
731bbba2e6
Bug fixes for integration test, use correct new UG syntax
2012-07-17 16:57:59 -04:00
33be41ecf5
Cleaning up integration test
2012-07-17 16:06:04 -04:00
8dbc9cb29c
Add the ability to emit the original quals in the OQ tag
2012-07-17 15:52:56 -04:00
40b8c7172c
Pool Caller refactoring in preparation of GATK 2.0: a) PoolCallerUnifiedArgumentCollection disappeared, and arguments moved to UnifiedArgumentCollection. b) PoolCallerWalker is no longer needed and redundant, all functionality subsumed by UG. UG now checks if GATK is lite - if so, don't allow ploidy > 2. c) Moved pool classes from private to protected. d) Changed the way to specify ploidy. Instead of specifying samples per pool and having ploidy = 2*samplesPerPool, have user specify ploidy directly, which is cleaner. Update tests accordingly. We can now call triploid seedless grape genotypes correctly in theory. e) Renamed argument -reference to -reference_sample_calls since the former is ambiguous and it's not clear what it refers to.
2012-07-17 15:27:04 -04:00
68d0e4dd6d
- Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE
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-Updated integrationtests to reflect changes in MVF file output
Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-07-17 15:21:10 -04:00
b0d99fd10d
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 15:12:28 -04:00
305db8c0d1
Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us.
2012-07-17 15:11:03 -04:00
6efbcd99f1
HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.
2012-07-17 14:38:36 -04:00
110886e8b9
Oops, got the logic wrong.
2012-07-17 13:37:11 -04:00
a963b37424
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 13:15:37 -04:00
3a64398d07
Cleaned up the isGATKLite check
2012-07-17 12:46:16 -04:00
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
1913d1bbd0
Put RunReport S3 upload on timeout thread
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Move the RunReport S3 upload process onto a separate thread with a timeout allowing the parent to continue.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
2012-07-17 12:19:39 -04:00
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
d5b3a2eabf
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 00:32:53 -04:00
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
a003148d50
Move AnalyzeCovariates over too.
2012-07-16 16:11:56 -04:00
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
52baac1e16
Move BQSRv2 into public and v1 into the archive.
2012-07-16 14:23:38 -04:00
07822d6c0f
Fixed input annotations for master/test files on DiffObjectsWalker.
2012-07-16 13:33:11 -04:00
2a830939df
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-14 23:49:59 -04:00
f29cadd7e2
By default, don't quantize quals in BQSRv2
2012-07-14 23:49:48 -04:00
75543a3f22
ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.
2012-07-13 18:50:27 -04:00
443f02ffc2
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-13 16:09:24 -04:00
6dfcc486e8
In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
2012-07-13 15:40:56 -04:00
5d0a7335ea
remove unnecessary use in the PRIORITY list
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remove unneeded imports
2012-07-13 15:27:08 -04:00
d70bb59182
HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.
2012-07-10 14:22:23 -06:00
279dff9f81
Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants
2012-07-10 13:59:00 -04:00
7eb45b4038
Fixed BQSR IntegrationTests
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* BinaryTag covariate is Experimental, not Standard (this was breaking integration tests)
* New parameter in the Recalibration report requires new MD5 for one of the integration tests.
2012-07-09 13:55:12 -04:00
dd0c47ab7e
Don't cast to a specific walker type since any walker can use the VA engine
2012-07-09 10:25:58 -04:00
5b0ade67c8
Updates to VCF processing for better BCF processing
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-- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order]. Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy
-- Updating GATK code to use the appropriate header function (this is why so many files have changed)
-- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this)
-- Bugfix for adding contig lines to BCF2 header dictionary
-- VCFHeader metaData no longer sorted internally. The system now maintains the data in header order, and only sorts output as requested in API
-- VCFWriter and BCF2Writer now explictly sort their header lines
-- Don't allow filters to be added that are PASS in the contract
2012-07-08 15:44:33 -07:00
63f5262e45
mergeInfoWithMaxAC is no longer hidden in CombineVariants
2012-07-08 15:44:32 -07:00
66aee613e2
Bugfix for set key in mergeInfoWithMaxAC.
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-- Previous version was always setting set=source of info with highest AC. Should actually have been set to the set annotation value itself.
2012-07-08 15:44:32 -07:00
91f0ed8059
Fixed nasty Rscript typo in VariantRecalibrator when compactPDF is available
2012-07-08 15:44:32 -07:00
87b090c362
Update VariantRecalibator error message to use -resource not old -B syntax
2012-07-08 15:44:31 -07:00
125e6c1a47
added BinaryTagCovariate for ancient dna analysis
2012-07-06 15:03:20 -04:00
e93b025b39
Fixing unit test
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with the new clipping behavior for weird cigars, we no longer can assert the final number of bases in the unit test, so I'm taking this bit off the unit test.
2012-07-06 12:08:09 -04:00
f603d4c48c
Fixing PairHMMIndelErrorModel boundary issue
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When checking the limits of a read to clip, it wasn't considering reads that may already been clipped before.
2012-07-06 11:48:04 -04:00
dd571d9aa0
Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.
2012-07-04 01:22:20 -04:00
33306d2e20
Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.
2012-07-04 00:21:21 -04:00
7d30558e6f
Only 'pad' the cycle covariate for indels, not substitutions
2012-07-03 23:47:01 -04:00
17efbbf8b1
Fixed ReadClipperUnitTest
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The behavior of the clipping on weird cigar strings such as 1I1S1H and 9S56H has changed, and the test has to change accordingly.
2012-07-03 16:38:51 -04:00
22f1afddaa
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-03 14:55:59 -04:00
617eebd204
More misc cleanup
2012-07-03 14:55:37 -04:00
344c3aeb1d
Cleanup from previous commit
2012-07-03 14:42:44 -04:00
9e8e78de15
Adding the model name to the VQSR filter lines so that they don't get clobbered with consecutive VQSR runs for SNPs and then indels.
2012-07-03 14:30:37 -04:00
0b37d44b0d
Optimizations for the RecalDatum to make BQSR (Count Covariates) much faster. Needs some cleanup.
2012-07-03 13:05:11 -04:00
031322ff00
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-03 00:12:59 -04:00
a4670113bd
Refactored/renamed the nested integer array; cleaned up code a bit.
2012-07-03 00:12:33 -04:00
f92139dd82
Ooops, UG VA path for rank sum tests aren't happy with empty lists. Disabling clipping rank sum test for now.
2012-07-02 21:12:42 -04:00
7e7b4cd1b9
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-02 16:37:54 -04:00
b807ff63ef
HaplotypeCaller now creates MNP and complex substitutions by using LD information to decide if events segregate together on haplotypes. Added unit test.
2012-07-02 16:37:39 -04:00
3cea080aa8
Cache SoftStart() and SoftEnd() in the GATKSAMRecord
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these are costly operations when done repeatedly on the same read.
2012-07-02 16:22:00 -04:00
88a02fa2cb
Fixing but for reads with cigars like 9S54H
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When hard-clipping predict when the read is going to be fully hard clipped to the point where only soft/hard-clips are left in the read and preemptively eliminate the read before the SAMRecord mathematics on malformed cigars kills the GATK.
2012-07-02 16:22:00 -04:00
1b0a775773
Disabling bcf2 reading from samtools because it's 1 basis; updating select variants integrationtest
2012-07-02 15:55:42 -04:00
cac72bce91
Initial version of int indexed mapping for BQSR. Will be cleaned up in a bit.
2012-07-02 14:33:33 -04:00
Ryan Poplin
Eric Banks
Guillermo del Angel
David Roazen
Mark DePristo
Joel Thibault
Mauricio Carneiro
Roger Zurawicki
Khalid Shakir
Christopher Hartl
Laurent Francioli
Chris Saunders
Ami Levy Moonshine