cb8bc18aeb
Fix for error in HaplotypeCaller. HC has a UG argument collection for the UG engine but some of those arguments aren't appropriate to set.
2012-08-02 11:41:06 -04:00
9ac72dbd4d
Merged bug fix from Stable into Unstable
2012-08-01 10:56:45 -04:00
01265f78e6
Add sanity check and possible bug fix for forum user: if haplotypes cannot be created from given alleles when genotyping indels (e.g. too close to contig boundary, etc.) in pool mode, empty allele list, signifying site can't be genotyped
2012-08-01 10:50:00 -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
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
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
3dabb90eb0
Updating example active region walker integration test.
2012-07-30 21:26:16 -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
48b9495460
Fixes to the likelihood based LD calculation for deciding when to combine consecutive events.
2012-07-30 12:12:56 -04:00
9002758ede
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-30 12:10:00 -04:00
7a73042cd3
Bug fix for the case of merging two VCs when a deletion deletes the padding base for a consecutive indel. Added unit test to cover this case.
2012-07-30 12:09:23 -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
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
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
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
0a98a6aa8d
Adding extraDocs tag per Mauricio's request
2012-07-25 18:23:18 -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
2e486d83e2
Updating HaplotypeCaller docs and expanding integration tests.
2012-07-23 10:05:42 -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
1592841c93
New function for merging nearby events into MNPs or complex substitutions. Added extensive unit tests.
2012-07-19 13:16:33 -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
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
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
c55934043e
Moving HaplotypeCaller from private to protected
2012-07-17 14:41:19 -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
d5b3a2eabf
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 00:32:53 -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
6c6a324583
Loosen a restriction on isOriginalRead()
...
* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
2012-07-16 14:07:10 -04:00
d7bf74fb7e
Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.
2012-07-10 02:04:26 -04:00
6c17c50fa2
Updates to ReduceReads
...
* Added optional parameter to not hard clip on the interval border
* Made not clipping the default behavior (hence integration tests changed)
* Updated integration tests.
2012-07-09 13:46:51 -04:00
12d1c594df
Moving ReduceReads into protected
2012-06-25 17:01:33 -04:00
9c6bccfd8b
build system overhaul
...
* Added support for a protected directory whose contents are only made public in binary form
* Simplified and reorganized build.xml to improve readability and maintainability
* build.xml now autodetects most build properties:
-Includes private/protected if they exist
-No more STING_BUILD_TYPE or specialized targets for public-only, etc.
* Build targets have changed! There are now two main build options:
"ant" build everything (GATK and Queue)
"ant gatk" build just the GATK
It was too hard to build everything before -- now it is the default.
* To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line.
Much better than the old comment/uncomment method!
2012-05-17 15:16:29 -04:00
Ryan Poplin
Guillermo del Angel
Mark DePristo
Eric Banks
Mauricio Carneiro
Joel Thibault
David Roazen