zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Commit Graph

  • 016b25be87 Update annoying md5s in unit tests, also failing because of header fixing Mark DePristo 2012-06-26 17:30:48 -0400
  • cd32b6ae54 CombineVariantsUnitTest was failing because the header repair was fixing the problem it wanted to detect Mark DePristo 2012-06-26 17:30:30 -0400
  • bbd46690e6 fixing conflicts Mauricio Carneiro 2012-06-26 17:12:24 -0400
  • 91f02dfd85 fixing pipeline tests (sorry, my bad) Mauricio Carneiro 2012-06-26 17:10:58 -0400
  • 1f45551a15 Bugfixes to G count types in VCF header Mark DePristo 2012-06-26 15:28:17 -0400
  • 7ef5ce28cc VariantRecalibrator test currently doesn't work with shadowBCF Mark DePristo 2012-06-25 20:56:00 -0400
  • 5f5885ec78 Updating many MD5s to reflect correct fixed headers Mark DePristo 2012-06-25 13:16:18 -0400
  • 39c849aced Bugfix to ensure the DB=1 old files decode properly Mark DePristo 2012-06-25 13:14:55 -0400
  • c1ac0e2760 BCF2 cleanup Mark DePristo 2012-06-25 10:27:37 -0400
  • 0b5980d7b3 Added Heng's nasty ex2.vcf to standard tests Mark DePristo 2012-06-22 17:25:44 -0400
  • 11dbfc92a7 Horrible bugfix to decodeLoc() in BCF2Codec Mark DePristo 2012-06-22 17:03:59 -0400
  • 896df0d6b0 vcf4.1.example.vcf must have a well-formed header Mark DePristo 2012-06-22 13:06:39 -0400
  • fb26c0f054 Update integration tests to reflect header changes Mark DePristo 2012-06-22 13:06:24 -0400
  • 7b96263f8b Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet Mark DePristo 2012-06-22 13:05:59 -0400
  • 61f0c46423 Rev tribble to 110. Log is: Mark DePristo 2012-06-22 13:03:53 -0400
  • 7dbba465ee Bugfix for shadow BCFs to not attempt to write to /dev/null.bcf Mark DePristo 2012-06-22 11:32:18 -0400
  • 6e9a81aabe Minor bugfix -- now that the testfile is in our testdata regenerate the idx file as needed to pass tests Mark DePristo 2012-06-21 16:56:56 -0400
  • 9346c5b37a Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-06-26 14:55:41 -0400
  • 334d66f2b1 Updating validation parameter in the DPP Mauricio Carneiro 2012-06-26 14:54:37 -0400
  • 7eb3e4da41 Added integration Tests for DiagnoseTargets Roger Zurawicki 2012-06-15 12:11:13 -0400
  • 12d1c594df Moving ReduceReads into protected Mauricio Carneiro 2012-06-25 17:00:56 -0400
  • 2d6511b9ac Fixing ReduceReads integration tests Mauricio Carneiro 2012-06-25 16:27:50 -0400
  • f0c54d99ed Account for a null attributes object Joel Thibault 2012-06-22 16:56:04 -0400
  • d0cf8bcc80 Add unit tests for VariantContextBuilder.rmAttribute() and .attribute() Joel Thibault 2012-06-22 16:01:15 -0400
  • fd9effbfe2 Fix Exception typo Joel Thibault 2012-06-22 16:05:52 -0400
  • 48987830c4 Bug fix in HC GGA mode for not considering haplotypes which have an event at the location of interest that isn't the allele of interest Ryan Poplin 2012-06-25 11:39:57 -0400
  • 429ad44421 Bug fix for read pos rank sum test annotation. Shouldn't be using the un-hardclipped start as the alignment start. Ryan Poplin 2012-06-22 14:53:29 -0400
  • 735b59d942 Bug fix in MLEAC calculation for when the exact model says the greedy AC of the alternate allele is zero. Ryan Poplin 2012-06-22 12:38:48 -0400
  • 457d781029 Adding VCF header lines for the experimental HaplotypeCaller specific annotations Ryan Poplin 2012-06-22 10:51:59 -0400
  • 0650b349d7 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-22 10:42:49 -0400
  • f0d05429eb Being more strict in which kmers are allowed to make up the assembly graph. More unit tests for pruning in the assembly graph. Ryan Poplin 2012-06-22 10:42:43 -0400
  • eed32df30d a) Sanity check in PoolCaller: if user didn't specify correct -glm or -pnrm models then error out with useful message, b) Have VariantsToTable deal with case where sample namess have spaces: technically they're allowed (or at least not explicitly forbidden) but they'll produce R-incompatible tables. TBD which other tools have issues, or whether there's a generic fix for this Guillermo del Angel 2012-06-21 21:19:55 -0400
  • d17369e0ac A few misc. residual errors in last commit Mark DePristo 2012-06-21 16:04:25 -0400
  • 734756d6b2 Final fixes before BCF2 mark III push Mark DePristo 2012-06-21 15:14:06 -0400
  • 31ee8aa01a JEXL update Mark DePristo 2012-06-21 09:54:36 -0400
  • 24dd8ee51b Header fixes for testdata Mark DePristo 2012-06-20 20:00:24 -0400
  • 549293b6f7 Bugfixes towards final BCF2 implementation Mark DePristo 2012-06-20 20:00:17 -0400
  • 66337a9899 Moved most testdata from public to private Mark DePristo 2012-06-20 15:36:23 -0400
  • 567dba0f76 Cleanup of VCF header lines and constants, BCF2 bugfixes Mark DePristo 2012-06-20 15:35:36 -0400
  • c4e0233ba3 Updating testdata to have proper VCF headers Mark DePristo 2012-06-19 09:47:38 -0400
  • fba7dafa0e Finalizing BCF2 mark III commit Mark DePristo 2012-06-19 09:46:26 -0400
  • 0c8b830db7 Updating MD5s for inclusion of RPA field header Mark DePristo 2012-06-15 15:53:54 -0400
  • d015a5738d Bugfixes for VCFWriterUnitTest and TestProvider to deal with stricter VCFWriter behavior Mark DePristo 2012-06-15 15:14:36 -0400
  • 9c81f45c9f Phase I commit to get shadowBCFs passing tests Mark DePristo 2012-06-15 14:25:00 -0400
  • ab53220635 Refactor on how RR treats soft clips Mauricio Carneiro 2012-06-19 13:26:43 -0400
  • aa0a4bbe78 Bug fixes for pool GL unit test: a) test-only ErrorModel constructor wasn't setting the hasData flag properly, b) GL log-error probabiliy cache was filled but never used (duh), c) restore high depth unit test since it's back to taking a couple of minutes Guillermo del Angel 2012-06-20 17:04:45 -0400
  • 769e190202 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-20 09:59:55 -0400
  • c5b1615bb9 tmp: disable pool GL unit tests with depth=10,000 because they're too long. For some reason last commit made GL computation too slow and now takes orders of magnitude more than before, cause TBD. This allows test to run in a bit more reasonable amounts of time Guillermo del Angel 2012-06-19 20:04:41 -0400
  • fe1d6e3953 Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-06-19 08:02:00 -0400
  • 79ef3325bd Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations. Christopher Hartl 2012-06-19 07:50:13 -0400
  • 15ae906f32 Once I was playing with integration tests it was simple to fix the ones I left broken from earlier today. Eric Banks 2012-06-18 21:54:58 -0400
  • 62cee2fb5b Feature request from Tim that could be useful to all: there's now an --interval_padding argument that specifies how many basepairs to add to each of the intervals provided with -L (on both ends). This is particularly useful when trying to run over the exome plus flanks and don't want to have to pre-compute the flanks (just use e.g. --interval_padding 50). Added integration test to cover this feature. Eric Banks 2012-06-18 21:36:27 -0400
  • 4393adf9e7 If present, VE's AlleleCount stratification uses the MLE AC by default (and otherwise drops down to use the greedy AC). Added integration test to cover it. Eric Banks 2012-06-18 13:36:14 -0400
  • 707151f0a4 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-18 12:55:58 -0400
  • 82a2c40338 Emit the MLE AC and AF in the INFO field of the UG output Eric Banks 2012-06-18 12:19:36 -0400
  • dc039b965e misc minor cleanup Ryan Poplin 2012-06-18 08:59:50 -0400
  • 5ec737f008 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-18 08:51:48 -0400
  • e3147969d9 Smith Waterman parameters have somehow gotten too diverged from what it is used in the indel realigner. Results are very dependent on these params. Changes to the assembly to not create long haplotypes out of only small pieces that were properly assembled. Ryan Poplin 2012-06-18 08:51:41 -0400
  • 677babf546 Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort. Eric Banks 2012-06-15 15:55:03 -0400
  • 783b7f6899 Misc cleanup Eric Banks 2012-06-15 10:39:19 -0400
  • 0c218e4822 Refactoring mostly for readability (and small performance improvement) Eric Banks 2012-06-15 10:36:41 -0400
  • c54e84e739 Ryan confirmed that we don't need separate arguments to control the context size for insertions and deletions, which allows us to cut down the expensive context calculations. Eric Banks 2012-06-15 09:28:56 -0400
  • 61fcbcb190 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-06-15 02:45:57 -0400
  • 6431078eff The previous commit had a minor bug fix that required updating an md5: previously, an extra cycle at the end of the read was being 'padded' out so cycle 72 wasn't making it into the table. Ryan, probably not worth rerunning your analysis for this. Eric Banks 2012-06-15 02:45:44 -0400
  • 4895fe2289 No more extraneous array creation in BQSR covariate classes; now covariates push their data directly to the ReadCovariates class as it's calculated (no more going through CovariateValues.java) Eric Banks 2012-06-15 02:32:00 -0400
  • 66cff7da6e Yet another intermediate pool caller commit - just minor bug fixes/cleanups this time, allow working functionality when reference sample data is not available for eval/comparison purposes Guillermo del Angel 2012-06-14 20:37:45 -0400
  • 5c23ab0817 Final cleanup of VCFWriterUnitTest Mark DePristo 2012-06-14 16:42:07 -0400
  • 0384ce5d34 Simple optimizations for BCF2Encoder Mark DePristo 2012-06-14 16:40:00 -0400
  • 68eed7b313 Optimizations for VCF and BCF2 Mark DePristo 2012-06-14 13:22:31 -0400
  • 09df584788 Fixed nasty bug where we weren't closing the underlying PositionalOutputStream in IndexingVariantContextWriter Mark DePristo 2012-06-14 09:42:11 -0400
  • fbc45e14d3 Cleanup formatting of VCF floats Mark DePristo 2012-06-13 21:57:47 -0400
  • 8b01969762 More code cleanup and optimizations to BCF2 writer Mark DePristo 2012-06-13 21:49:22 -0400
  • e34ca0acb1 Passing all unittests Mark DePristo 2012-06-13 20:28:23 -0400
  • a19ae9434e updateMD5s allows you to specify only select tests to update Mark DePristo 2012-06-13 17:50:55 -0400
  • 71da76039e Final support for variable length lists of strings in BCF2 Mark DePristo 2012-06-13 17:50:21 -0400
  • bd9d40fb84 Code cleanup and more documentation for BCFFieldWriters Mark DePristo 2012-06-13 17:07:19 -0400
  • dc07067265 Fix bug in incorrectly reporting relative paths in log Mark DePristo 2012-06-13 17:06:08 -0400
  • 856905ee5b Cleanup Genotypes Mark DePristo 2012-06-13 14:01:35 -0400
  • aa2178cc68 Updating MD5s to latest version to reflect inclusion of contigs in headers Mark DePristo 2012-06-13 13:32:28 -0400
  • 0e81484f0f More testdata test files Mark DePristo 2012-06-13 13:30:45 -0400
  • 7a8e2a8ada updateMD5s allows multiple MD5 matches across files now Mark DePristo 2012-06-13 13:30:13 -0400
  • 6a0e0951af In upgrade to VCF4 replace 0 with PASS Mark DePristo 2012-06-13 13:29:51 -0400
  • 31997f8092 Bugfixes on the way to passing integration tests Mark DePristo 2012-06-13 13:29:17 -0400
  • ea1b699778 Cleanup the interface for BCF2FieldEncoder Mark DePristo 2012-06-13 10:17:10 -0400
  • dd6aee347a Genotype encoding uses the BCF2FieldEncoder system Mark DePristo 2012-06-12 15:44:12 -0400
  • 9ac4203254 GenotypeAnnotations now accept a GenotypeBuilder and directly update the builder with their value Mark DePristo 2012-06-11 13:57:48 -0400
  • 7506994d09 Nearing final BCF commit Mark DePristo 2012-06-11 12:43:11 -0400
  • 6272612808 Testing utility to perform diffs N times Mark DePristo 2012-06-11 12:03:57 -0400
  • 8014178f2f Algorithmically faster version of DiffEngine Mark DePristo 2012-06-10 20:13:18 -0400
  • 2a86b81a3f Initial version of clean, fast formatting routines built dynamically from a VCF header Mark DePristo 2012-06-10 10:53:51 -0400
  • 51a3b6e25e No more makePrecisionFormatStringFromDenominatorValue Mark DePristo 2012-06-10 08:55:23 -0400
  • a822087f11 Bugfix for R 2.15 not including reshape Mark DePristo 2012-06-09 10:10:30 -0400
  • 43ad890fcc Finalizing BCF2 v2 Mark DePristo 2012-06-07 08:34:25 -0400
  • 938d3ada32 Working version Mark DePristo 2012-06-06 15:01:02 -0400
  • 37e5d32019 Remove logger.info statement Mark DePristo 2012-06-06 15:00:35 -0400
  • 6cfb2d1393 Restoring SelectVariantsIntegrationTest Mark DePristo 2012-06-06 14:10:35 -0400
  • 01ddf9555a Performance optimizations for Genotype field decoding for GT field Mark DePristo 2012-06-06 14:10:05 -0400
  • 7fbca7013e Don't add missing value binding from field to Genotype object in VCF3Codec Mark DePristo 2012-06-06 14:08:15 -0400
  • cfd1e50068 Minor updates to test code Mark DePristo 2012-06-06 14:07:07 -0400
  • 54817f8d16 VCFHeaderUnitTest needed to be updated to reflect that we are doing VCF4.1 not VCF4.0 Mark DePristo 2012-06-06 14:06:13 -0400