e1bba91836
Ready for full-scale evaluation adaptive BQSR contexts
...
-- 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
...
* Add the RemoveProgramRecords annotation to LocusWalker
2012-08-03 09:54:16 -04:00
524d7ea306
Choose whether to keep program records based on Walker
...
* 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
...
-- 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
...
-- 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
...
-- 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
...
* 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
...
-- 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
...
-- Works according to visual inspection of output tree
2012-07-31 08:11:04 -04:00
315d25409f
Improvement to RecalDatum and VisualizeContextTree
...
-- 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
...
-- 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
...
-- 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)
...
-- 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
...
-- 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.
...
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
...
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:39 -04:00
fcefa61bce
Remove reference dependence in BCF2Codec
...
-- 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
...
-- 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
...
-- 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
...
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.
...
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
...
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.
...
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.
...
* 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
Mark DePristo
Guillermo del Angel
Ryan Poplin
Joel Thibault
Eric Banks
Mauricio Carneiro
Roger Zurawicki
Khalid Shakir
Christopher Hartl