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  • 0381fd7c83 Hmm, I thought I used the right md5s last time. Let's try again. Eric Banks 2012-08-02 11:25:10 -0400
  • 2f585b91be Update ex2.vcf and .bcf test files to new spec Mark DePristo 2012-08-01 17:10:35 -0400
  • c3c3d18611 Update BCF2 to put PASS as offset 0 not at the end Mark DePristo 2012-08-01 17:09:22 -0400
  • 25c773ef33 Adding VE integration test file to private/testdata Mark DePristo 2012-08-01 15:44:38 -0400
  • ccac77d888 Bugfix for incorrect allele counting in IndelSummary Mark DePristo 2012-08-01 11:57:16 -0400
  • 2b25df3d53 Add removeProgramRecords argument Joel Thibault 2012-07-30 10:19:57 -0400
  • d53105668b Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-01 14:53:06 -0400
  • fabca66d09 Another fix to VQSR docs Ryan Poplin 2012-08-01 14:52:49 -0400
  • 2be29ebd22 Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-01 14:35:30 -0400
  • 4093909a56 Updating VQSR docs. Removing references to old best practices pages. Ryan Poplin 2012-08-01 14:30:24 -0400
  • 52b93cab62 Merged bug fix from Stable into Unstable Eric Banks 2012-08-01 13:17:36 -0400
  • 22bf052828 Fixing BQSR GATK docs Eric Banks 2012-08-01 13:17:16 -0400
  • 9ac72dbd4d Merged bug fix from Stable into Unstable Guillermo del Angel 2012-08-01 10:56:45 -0400
  • 84cd23f891 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Guillermo del Angel 2012-08-01 10:55:37 -0400
  • 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 Guillermo del Angel 2012-08-01 10:50:00 -0400
  • 459832ee16 Fixed bug in FastaAlternateReferenceMaker when input VCF has overlapping deletions as reported a while back on GS Eric Banks 2012-08-01 10:45:04 -0400
  • a4a41458ef Update docs of FastaAlternateReferenceMaker as promised in older GS thread Eric Banks 2012-08-01 10:33:41 -0400
  • 687df2341d Merged bug fix from Stable into Unstable Eric Banks 2012-08-01 10:27:15 -0400
  • 05bf6e3726 Updating md5s in pipeline tests so that they finally pass Eric Banks 2012-08-01 10:27:00 -0400
  • 38e5419b11 Merged bug fix from Stable into Unstable Eric Banks 2012-08-01 09:50:31 -0400
  • 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. Eric Banks 2012-08-01 09:50:00 -0400
  • 7cf4b63d76 Disabling indel quals in BaseRecalibrator as it should be, not PrintReads. Eric Banks 2012-08-01 09:23:04 -0400
  • 0528337467 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-07-31 18:17:50 -0400
  • 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 Guillermo del Angel 2012-07-31 16:34:20 -0400
  • 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. Eric Banks 2012-07-31 16:00:36 -0400
  • ab53d73459 Quick fix to user error catching Eric Banks 2012-07-31 15:50:32 -0400
  • 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). Eric Banks 2012-07-31 15:37:22 -0400
  • fff78ab462 Archiving VQSRv3 Eric Banks 2012-07-31 14:34:42 -0400
  • 4f10386bd4 Del/Ins ratio should really be Ins/Del ratio on the summary page of the variant QC report. Ryan Poplin 2012-07-31 14:23:36 -0400
  • f7133ffc31 Cleanup syntax errors from BQSR reorganization Mark DePristo 2012-07-31 08:10:51 -0400
  • 762a3d9b50 Move BQSR.R to utils/recalibration in R Mark DePristo 2012-07-30 15:47:36 -0400
  • dad9bb1192 Changes order of writing BaseRecalibrator results so that if R blows up you still get a meaningful tree Mark DePristo 2012-07-30 15:46:00 -0400
  • 0c4e729e13 Working version of adaptive context calculations Mark DePristo 2012-07-30 15:44:33 -0400
  • 93640b382e Preliminary version of adaptive context covariate algorithm Mark DePristo 2012-07-30 08:31:38 -0400
  • 315d25409f Improvement to RecalDatum and VisualizeContextTree Mark DePristo 2012-07-29 13:13:13 -0400
  • 57b45bfb1e Extensive unit tests, contacts, and documentation for RecalDatum Mark DePristo 2012-07-27 14:34:13 -0400
  • e00ed8bc5e Cleanup BQSR classes Mark DePristo 2012-07-27 12:25:06 -0400
  • 191294eedc Initial cleanup of RecalDatum for move and further refactoring Mark DePristo 2012-07-27 09:39:16 -0400
  • 0670316288 Be clearer that dcov 50 is good for 4x, should use 200 for >30x Mark DePristo 2012-07-26 16:51:17 -0400
  • 8db4e787b1 V1 of tool to visualize the quality score information in the context covariates Mark DePristo 2012-07-26 13:56:06 -0400
  • 874dbf5b58 Maximum wait for GATK run report upload reduced to 10 seconds Mark DePristo 2012-07-26 09:46:56 -0400
  • e6b326c189 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-07-30 21:32:19 -0400
  • 6c9d3ec155 Remerge after changes to allele construction code. More cleanups/fixes to artificial read pileup provider Guillermo del Angel 2012-07-30 21:32:03 -0400
  • 3dabb90eb0 Updating example active region walker integration test. Ryan Poplin 2012-07-30 21:26:16 -0400
  • c2b57ee444 updating HC integration tests after these changes. Ryan Poplin 2012-07-30 12:41:40 -0400
  • 7ed06ee7b9 Updating FindCoveredIntervals to use the changes to the ActiveRegionWalker. Ryan Poplin 2012-07-30 12:16:27 -0400
  • 13591b169f Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-07-30 12:13:24 -0400
  • 48b9495460 Fixes to the likelihood based LD calculation for deciding when to combine consecutive events. Ryan Poplin 2012-07-30 12:12:56 -0400
  • 9002758ede Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-07-30 12:10:00 -0400
  • 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. Ryan Poplin 2012-07-30 12:09:23 -0400
  • 0b30588d67 Catch yet another class of User Errors Eric Banks 2012-07-30 11:59:56 -0400
  • 5743694196 Merged bug fix from Stable into Unstable Eric Banks 2012-07-30 11:35:28 -0400
  • 79195b97a3 Adding categories for the remaining uncategorized walkers Eric Banks 2012-07-30 11:35:08 -0400
  • 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 Guillermo del Angel 2012-07-30 09:56:10 -0400
  • 7630c929a7 Re-enabling the unit tests for reverse allele clipping Eric Banks 2012-07-29 22:24:56 -0400
  • 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). Eric Banks 2012-07-29 22:19:49 -0400
  • 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. Eric Banks 2012-07-29 19:22:02 -0400
  • 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. Eric Banks 2012-07-29 01:07:59 -0400
  • 2b1b00ade5 All integration tests and VC/Allele unit tests are passing Eric Banks 2012-07-27 17:03:49 -0400
  • beb7610195 Resolving merge conflicts Eric Banks 2012-07-27 15:52:02 -0400
  • 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. Eric Banks 2012-07-27 15:48:40 -0400
  • 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. Ryan Poplin 2012-07-27 12:44:02 -0400
  • a0890126a8 ActiveRegionWalker's isActive function returns a results object now instead of just a double. Ryan Poplin 2012-07-27 11:01:39 -0400
  • ef335b6213 Several more walkers have been brought up to use the new Allele representation. Eric Banks 2012-07-27 02:14:25 -0400
  • 9e2209694a Re-enable reverse trimming of alleles in UG engine when sub-selecting alleles after genotyping. UG integration tests now pass. Eric Banks 2012-07-27 00:47:15 -0400
  • baf3e33730 Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass. Eric Banks 2012-07-26 23:27:11 -0400
  • 35e803e110 Merged bug fix from Stable into Unstable Ryan Poplin 2012-07-26 14:00:04 -0400
  • 4f741b4cd7 Smoothing in the BQSR bins should be one error observation and one non-error observation. Ryan Poplin 2012-07-26 13:59:02 -0400
  • 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 Guillermo del Angel 2012-07-26 13:43:00 -0400
  • a694d1b5de Merge branch 'master' into allelePadding Eric Banks 2012-07-26 01:53:14 -0400
  • 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. Eric Banks 2012-07-26 01:50:39 -0400
  • 1e8610b2c6 Merged bug fix from Stable into Unstable Mark DePristo 2012-07-25 23:14:15 -0400
  • 8c418a15da Sorting out HMS error handling (fingers crossed) Mark DePristo 2012-07-25 23:13:12 -0400
  • 5e9e1101a3 Merged bug fix from Stable into Unstable Mark DePristo 2012-07-25 22:11:35 -0400
  • 9242f63a4d On the way to really sorting out HMS error handling Mark DePristo 2012-07-25 22:11:10 -0400
  • 5671992db3 RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions Mark DePristo 2012-07-25 22:05:04 -0400
  • 2949ecab40 Merged bug fix from Stable into Unstable Eric Banks 2012-07-25 21:41:09 -0400
  • 7eb3f54750 Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers. Eric Banks 2012-07-25 21:40:28 -0400
  • 2982b24c4b Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Eric Banks 2012-07-25 20:36:53 -0400
  • 0a98a6aa8d Adding extraDocs tag per Mauricio's request Eric Banks 2012-07-25 18:23:18 -0400
  • 6857b91aec Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-07-25 17:23:15 -0400
  • fce5cb9f35 Few category changes Mauricio Carneiro 2012-07-25 17:23:02 -0400
  • 68193ecf2e Merged bug fix from Stable into Unstable Eric Banks 2012-07-25 16:06:09 -0400
  • 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). Eric Banks 2012-07-25 16:05:47 -0400
  • c85a557311 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-07-25 15:25:34 -0400
  • d46cf47bd1 Updating Read Filter documentation Mauricio Carneiro 2012-07-25 15:04:30 -0400
  • 304c3e9802 Merged bug fix from Stable into Unstable Eric Banks 2012-07-25 14:12:00 -0400
  • 6a3bfa3811 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Eric Banks 2012-07-25 14:11:11 -0400
  • 357e0b35af Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error Eric Banks 2012-07-25 14:11:03 -0400
  • 1e4816e150 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-07-25 13:47:07 -0400
  • 5b74763096 Removed Categories. Roger Zurawicki 2012-07-24 16:52:06 -0400
  • 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. Eric Banks 2012-07-25 13:38:07 -0400
  • e0c07f5567 Reverting old commits that made error handling better because ultimately they made things worse. Eric Banks 2012-07-25 12:37:59 -0400
  • 0285c1fe9e Ensure that PrintReads has enough RAM Joel Thibault 2012-07-24 13:56:33 -0400
  • aef77e96d8 Combine BAMs using PrintReads Joel Thibault 2012-07-24 10:44:25 -0400
  • 3df058a8f3 Test for processing many BAMs at once Joel Thibault 2012-07-06 16:38:53 -0400
  • f5f61d28b7 Merged bug fix from Stable into Unstable Mark DePristo 2012-07-25 09:01:21 -0400
  • 66b409921a Testfile for VF integration test Mark DePristo 2012-07-25 09:00:55 -0400
  • 16947e93f2 Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR Mark DePristo 2012-07-25 08:53:22 -0400
  • fcefa61bce Remove reference dependence in BCF2Codec Mark DePristo 2012-07-24 17:22:40 -0400