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  • 19a257a5c1 Multiple bugfixes Mark DePristo 2012-07-24 17:20:21 -0400
  • 3066894215 Bugfix for BCF2 Mark DePristo 2012-07-24 15:26:26 -0400
  • a99f3d6adf Don't use old CC and TR commands. Not fixing for now, just want to see whether I can get this to pass first. Eric Banks 2012-07-24 12:26:39 -0400
  • 055792d99c Merged bug fix from Stable into Unstable Guillermo del Angel 2012-07-24 20:33:34 -0400
  • 61ee7983d4 Don't use old CC and TR commands. Not fixing for now, just want to see whether I can get this to pass first. Eric Banks 2012-07-24 12:26:39 -0400
  • eb55061fd0 a) Document BEAGLE codec, b) Bug fix: inbreeding coefficient shouldn't be computed for non-diploid organisms in current implementaiton Guillermo del Angel 2012-07-24 12:16:15 -0400
  • c011837147 Merge remote-tracking branch 'unstable/master' Eric Banks 2012-07-24 11:15:31 -0400
  • 348e86159e Moving doclets to public Mauricio Carneiro 2012-07-23 23:50:24 -0400
  • 0cca75a290 Updated IWWW_DIR and WWW_DIR paths, and switch 'mv' to 'rsync' as requested by carneiro. Khalid Shakir 2012-07-23 23:29:00 -0400
  • 5cd98a36b9 Making ForumAPIUtils public Mauricio Carneiro 2012-07-23 17:44:24 -0400
  • 3d92f041f3 forgot to delete the merging line Mauricio Carneiro 2012-07-23 17:35:07 -0400
  • f3c504769b Added the ability to update the Forum Roger Zurawicki 2012-07-23 16:44:53 -0400
  • 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. Khalid Shakir 2012-07-23 16:32:31 -0400
  • a9ad9b3880 Inserted final paths for binaries. Khalid Shakir 2012-07-23 14:29:10 -0400
  • 41df9bd2a2 Moving BQSR plotting script to public so that it can be used with the substiution-model-only version. Ryan Poplin 2012-07-23 11:46:07 -0400
  • 2a14bbe4f0 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-07-23 11:28:26 -0400
  • 10d143c35c Adding error model header names in the BQSR recal plot. Making the downsampling of points look a little nicer. Ryan Poplin 2012-07-23 11:28:17 -0400
  • 675ccab2fa Renaming BQSR to BaseRecalibrator Eric Banks 2012-07-23 10:17:17 -0400
  • 2e486d83e2 Updating HaplotypeCaller docs and expanding integration tests. Ryan Poplin 2012-07-23 10:05:42 -0400
  • cd4b0dda71 Protect against the context covariate or any other covariate blowing up the recalibration report PDF file because of having too many possible values. Ryan Poplin 2012-07-22 19:20:19 -0400
  • 35415a523d Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-07-22 16:54:39 -0400
  • d38f3a071f fixing typo in comments Ryan Poplin 2012-07-22 16:54:19 -0400
  • 39f45127f3 Fix md5's broken by recent changes to FisherStrand calculation Guillermo del Angel 2012-07-21 14:41:38 -0400
  • df965d4a5a Fixing BQSR integration test Mauricio Carneiro 2012-07-21 10:52:59 -0400
  • d7bffb0024 Final final final version of the license. Mark DePristo 2012-07-20 17:59:26 -0400
  • 65f4b67b86 Fixing walker unit test with the new naming convention Mauricio Carneiro 2012-07-20 17:50:29 -0400
  • 921eaad33f Generalized the default platform parameter in BQSRv2 Mauricio Carneiro 2012-07-18 14:20:48 -0400
  • 5dc2143142 Removed support for walkers ending with "Walker" from the engine. Mauricio Carneiro 2012-07-20 17:26:28 -0400
  • d446d34227 GATK Error messages now point to the new website instead of GetSatisfaction. Mauricio Carneiro 2012-07-20 17:16:24 -0400
  • 116885a450 Removed the "Walker" suffix from all walkers that had it. Mauricio Carneiro 2012-07-20 16:33:29 -0400
  • dea049553a Adding missing testdata file Mark DePristo 2012-07-20 09:19:20 -0400
  • 3ee46cced2 Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-07-19 21:25:40 -0400
  • af383c30b5 Ensure that the gene summary has a header line Christopher Hartl 2012-07-19 21:24:04 -0400
  • 2ca5fc62a2 Support for MISSING BCF2 type Mark DePristo 2012-07-19 16:14:11 -0400
  • 50365d01c4 Updated HSPTest expected values due to variant eval changes in earlier commit. Khalid Shakir 2012-07-19 15:24:53 -0400
  • 1592841c93 New function for merging nearby events into MNPs or complex substitutions. Added extensive unit tests. Ryan Poplin 2012-07-19 13:16:33 -0400
  • a4884f82cd Final final version of GATK beta license Mark DePristo 2012-07-19 10:35:54 -0400
  • 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 Guillermo del Angel 2012-07-19 10:24:08 -0400
  • 5f5edeca63 Reverting move of BQSR tests to public, as per DR's email Eric Banks 2012-07-19 10:02:05 -0400
  • 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. Eric Banks 2012-07-18 22:44:37 -0400
  • 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. Eric Banks 2012-07-18 21:48:58 -0400
  • 9c1ab1b0c0 Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency. Eric Banks 2012-07-18 21:11:33 -0400
  • 0b87b0ead8 Use lazy evaluation to initialize MongoDB Joel Thibault 2012-07-09 14:05:08 -0400
  • 994c5c31c1 Enabling VariantEval integration tests for ValidationReport Mark DePristo 2012-07-18 16:07:21 -0400
  • 74e153ff4a FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing Mark DePristo 2012-07-18 16:06:59 -0400
  • 30f441d385 Finalizing GATK2 license text Mark DePristo 2012-07-18 11:11:28 -0400
  • dede3a30e9 Improvements to the validation report of VariantEval Mark DePristo 2012-07-10 18:00:16 -0700
  • 559a4826be Improvements to the validation report of VariantEval Mark DePristo 2012-07-10 17:45:06 -0700
  • dc292c0317 FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations Mark DePristo 2012-07-09 14:27:01 -0700
  • bd799fc989 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-18 16:01:20 -0400
  • 2c0f073ab1 Make -qq arg hidden for now since it's still very experimental Eric Banks 2012-07-18 15:43:25 -0400
  • b46c85e8b4 More bad BAM file catching Eric Banks 2012-07-18 15:26:31 -0400
  • 659eee13a6 Handle NPE generated in UG when non-standard reference bases are present in the fasta Eric Banks 2012-07-18 15:16:27 -0400
  • 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. Eric Banks 2012-07-18 15:11:38 -0400
  • 4c730542f0 Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later. Eric Banks 2012-07-18 13:56:35 -0400
  • 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). Eric Banks 2012-07-18 12:57:34 -0400
  • fd0c2d269e Change committest target to allow inheritance of properties David Roazen 2012-07-18 12:37:04 -0400
  • 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. Eric Banks 2012-07-18 12:31:59 -0400
  • 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! Eric Banks 2012-07-17 23:36:43 -0400
  • a8d08ea18d As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0. Eric Banks 2012-07-17 22:18:43 -0400
  • 7e2c830636 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-17 21:54:56 -0400
  • a9f27e5b02 Updated md5s for DPP test Eric Banks 2012-07-17 21:54:46 -0400
  • 29273abab7 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-07-17 16:58:12 -0400
  • 731bbba2e6 Bug fixes for integration test, use correct new UG syntax Guillermo del Angel 2012-07-17 16:57:59 -0400
  • 33be41ecf5 Cleaning up integration test Eric Banks 2012-07-17 16:06:04 -0400
  • 8dbc9cb29c Add the ability to emit the original quals in the OQ tag Eric Banks 2012-07-17 15:52:56 -0400
  • 4e3780fd4f Updated md5 for PBPP Eric Banks 2012-07-17 15:47:43 -0400
  • 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. Guillermo del Angel 2012-07-17 15:27:04 -0400
  • 68d0e4dd6d - Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE Laurent Francioli 2012-07-17 16:28:11 +0200
  • 863eb5b5c0 Use Context not Dinuc covariate Eric Banks 2012-07-17 15:18:11 -0400
  • b0d99fd10d Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-17 15:12:28 -0400
  • 305db8c0d1 Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us. Eric Banks 2012-07-17 15:11:03 -0400
  • bf2d5efe4d Moving HaplotypeCaller integration and unit tests over to protected as well. Ryan Poplin 2012-07-17 14:51:26 -0400
  • c55934043e Moving HaplotypeCaller from private to protected Ryan Poplin 2012-07-17 14:41:19 -0400
  • 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. Ryan Poplin 2012-07-17 14:38:36 -0400
  • 110886e8b9 Oops, got the logic wrong. Eric Banks 2012-07-17 13:37:11 -0400
  • 836f882c30 Forgot to escape fallback text in email script; fixed TERRIBLE sed-related bug David Roazen 2012-07-17 13:14:12 -0400
  • a963b37424 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-17 13:15:37 -0400
  • 17d627b86d Update the DPP and PBPP to use the BQSRv2 walkers Eric Banks 2012-07-17 13:15:32 -0400
  • 3a64398d07 Cleaned up the isGATKLite check Eric Banks 2012-07-17 12:46:16 -0400
  • 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. Eric Banks 2012-07-17 12:23:40 -0400
  • 1913d1bbd0 Put RunReport S3 upload on timeout thread Chris Saunders 2012-05-31 18:16:54 -0700
  • beacdf66c5 Bringing the git email scripts under version control David Roazen 2012-07-17 11:24:30 -0400
  • d4f55f5376 Revert "Email script test: test "no net change" detection" David Roazen 2012-07-17 11:16:42 -0400
  • a5548d1592 Email script test: test "no net change" detection David Roazen 2012-07-17 11:16:23 -0400
  • 251f141e22 Revert "Email script test: added an under-limit file" David Roazen 2012-07-17 11:12:56 -0400
  • 7cfc6968fc Email script test: added an under-limit file David Roazen 2012-07-17 11:11:12 -0400
  • 159439aa7d Revert "Email script test: added a file with a number of lines equal to the line limit" David Roazen 2012-07-17 11:08:52 -0400
  • 207e42a5a3 Email script test: added a file with a number of lines equal to the line limit David Roazen 2012-07-17 11:06:00 -0400
  • 385fff595c Revert "Email script test: added a file over the new line limit" David Roazen 2012-07-17 11:04:17 -0400
  • b4afa60d7f Email script test: added a file over the new line limit David Roazen 2012-07-17 11:02:17 -0400
  • 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). Eric Banks 2012-07-17 10:52:43 -0400
  • d5b3a2eabf Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-17 00:32:53 -0400
  • 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. Eric Banks 2012-07-17 00:32:34 -0400
  • a003148d50 Move AnalyzeCovariates over too. Eric Banks 2012-07-16 16:11:56 -0400
  • 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). Eric Banks 2012-07-16 15:34:50 -0400
  • 52baac1e16 Move BQSRv2 into public and v1 into the archive. Eric Banks 2012-07-16 14:23:38 -0400
  • 6c6a324583 Loosen a restriction on isOriginalRead() Joel Thibault 2012-07-13 15:24:46 -0400
  • 07822d6c0f Fixed input annotations for master/test files on DiffObjectsWalker. Khalid Shakir 2012-07-16 13:32:54 -0400
  • 2a830939df Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-07-14 23:49:59 -0400