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  • 17d1c9ed53 Updating NA12878 reviews with Mark. Ryan Poplin 2012-11-21 12:47:04 -0500
  • 4714ccc284 change the way CombineVariants check the priority arguments in order to throw error when the genotypeMergeOption argument is set to PRIORITIZE but PRIORITY_STRING is not provided Ami Levy-Moonshine 2012-11-21 10:47:35 -0500
  • d3817e789c made dedup setup not intermediate Douglas Voet 2012-11-21 09:07:08 -0500
  • 2e1a055aca Merged bug fix from Stable into Unstable Eric Banks 2012-11-20 23:20:33 -0500
  • c54fc94505 Protect against features that start off the end of the read (otherwise, Arrays.fill fails) Eric Banks 2012-11-20 23:19:59 -0500
  • c2efb04657 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Eric Banks 2012-11-20 22:43:15 -0500
  • 72e2d569c5 The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality. Eric Banks 2012-11-20 22:41:57 -0500
  • ff87642a91 Enable cycle covariate unit tests Eric Banks 2012-11-20 22:29:56 -0500
  • cc7680e601 NA12878 knowledge base backed by MongoDB Mark DePristo 2012-11-04 14:40:17 -0800
  • 7dadbae068 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Eric Banks 2012-11-20 16:13:34 -0500
  • 937ac7290f Lots more GGA fixes for the HC now that I understand what's going on internally. Integration tests pass except for the GGA test which I believe now produces better results. Eric Banks 2012-11-20 16:13:29 -0500
  • 8376c28728 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2012-11-20 12:35:39 -0500
  • d2a6e2526d Fixed Input vs. Argument Menachem Fromer 2012-11-20 12:34:47 -0500
  • 9111966261 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2012-11-20 12:19:58 -0500
  • e0e8b51906 Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Chris Hartl 2012-11-20 11:33:40 -0500
  • 5a97d03709 fix output names Douglas Voet 2012-11-20 11:27:53 -0500
  • 553e635415 Bring miscellaneous additional infrastructure scripts under version control David Roazen 2012-11-19 16:12:05 -0500
  • d07f3d4a5a Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2012-11-19 11:17:02 -0500
  • 3b78f3d982 fix hs metrics file name Douglas Voet 2012-11-19 10:38:10 -0500
  • 4f243acaa6 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Eric Banks 2012-11-19 10:34:44 -0500
  • 28b8401867 Checking in new git setup script David Roazen 2012-11-19 10:02:18 -0500
  • d46ffab0f2 added file1 and file2 parameters back for backwards compatibility Douglas Voet 2012-11-19 09:58:51 -0500
  • f0b8a0228f Quick fix for HC refactoring: when copying over Haplotype objects, make sure to copy over the artificial allele used to create it too. Eric Banks 2012-11-19 09:57:55 -0500
  • e68dc24aae Git infrastructure updates David Roazen 2012-11-19 09:45:54 -0500
  • e1a5c3ce7a Revert "Second test of new repos. Please ignore." David Roazen 2012-11-19 09:34:32 -0500
  • 9fc63efc30 Second test of new repos. Please ignore. David Roazen 2012-11-19 09:34:15 -0500
  • ff180a8e02 Significant refactoring of the Haplotype Caller to handle problems with GGA. The main fix is that we now maintain a mapping from 'original' allele to 'Smith-Waterman-based' allele so that we no longer need to do a (buggy) matching throughout the calling process. Eric Banks 2012-11-19 09:09:57 -0500
  • 78ce822b6f Protect against NPE when using non-GATK reports for inputs expecting valid GATK reports Eric Banks 2012-11-19 09:07:04 -0500
  • 2a16d6fa55 Revert "Testing out the new github-hosted repos. Please ignore." David Roazen 2012-11-19 08:07:19 -0500
  • 855a68ae39 Testing out the new github-hosted repos. Please ignore. David Roazen 2012-11-19 08:06:58 -0500
  • 918d83b5de added TrivialTask Q script Scott Frazer 2012-11-15 14:14:19 -0500
  • b70fd4a242 Initial testing of the Active Region Traversal contract Joel Thibault 2012-11-14 11:08:48 -0500
  • a68e6810c9 Back off experimental code that escaped last commit, not for general use yet Guillermo del Angel 2012-11-14 14:45:15 -0500
  • 89bbe73a43 Commenting out CMI pipeline test that wasn't meant to be in GATK repository (why was this merged??) Guillermo del Angel 2012-11-14 14:39:04 -0500
  • 3771d074dc Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-11-14 14:37:43 -0500
  • 8b749673bc centralize header element removal in reduce reads Mauricio Carneiro 2012-11-14 13:59:34 -0500
  • 843384e435 Rename hg19 files in bundle to b37 since that's what they are Eric Banks 2012-11-14 11:47:09 -0500
  • e35fd1c717 Merging CMI-0.5.0 and GATK-2.2 together. Mauricio Carneiro 2012-11-14 10:42:03 -0500
  • a079d8d0d1 Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters Mauricio Carneiro 2012-11-13 15:21:57 -0500
  • dba31018f4 Implementation of BySampleSAMFileWriter ReduceReads now works with the n-way-out capability, splitting by sample. DEV-27 #resolve #time 3m Mauricio Carneiro 2012-11-13 01:18:37 -0500
  • 8503db6e87 moving cancer pipeline qscript over to cmi-cancer Kristian Cibulskis 2012-11-09 10:18:22 -0500
  • de53c32361 moving to cmi-cancer Kristian Cibulskis 2012-11-09 10:01:02 -0500
  • ff63c53961 Increase bwa mem limit by 1 Gb - see if we can avoid random job failures that way Guillermo del Angel 2012-11-07 06:45:59 -0800
  • a17cd54b68 Co-Reduction implementation in ReduceReads Mauricio Carneiro 2012-10-24 16:57:08 -0400
  • f4511c0d6f made parameters not required, fixed some null file names Douglas Voet 2012-11-06 14:43:15 -0500
  • 1bfe73397f made parameters not required, switched date sequenced format, bug fixes in pulling remote files Douglas Voet 2012-11-06 14:00:36 -0500
  • f9cc68ce17 pull metadata from metadata service Scott Frazer 2012-11-05 22:45:46 -0500
  • 6d59dd3455 Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass. Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass. QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]]. Added an QCommandPlugin.initScript utility method for handling specialized script types. kshakir 2012-11-04 23:42:02 -0500
  • 42ddf51156 Merged bug fix from Stable into Unstable Eric Banks 2012-11-14 10:29:09 -0500
  • 49869344b8 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-11-14 09:42:35 -0500
  • 040a27d2d2 minor typo in SortROD; Few changes in the CatVariants (still under development) Ami Levy Moonshine 2012-11-14 09:36:32 -0500
  • cab8ba7c75 Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters Mauricio Carneiro 2012-11-13 15:21:57 -0500
  • ba41f65759 Protect against NPEs in SelectVariants by checking for missing Genotypes Eric Banks 2012-11-13 11:53:39 -0500
  • c7335c9902 Having a malformed GATK report is a User Error Eric Banks 2012-11-13 11:53:12 -0500
  • 525cf331f4 Don't catch a User Error and re-throw as a Reviewed Exception. That makes Eric unhappy. Eric Banks 2012-11-13 11:52:47 -0500
  • 95a4ba57bf Implementation of BySampleSAMFileWriter ReduceReads now works with the n-way-out capability, splitting by sample. DEV-27 #resolve #time 3m Mauricio Carneiro 2012-11-13 01:18:37 -0500
  • 1f23a82aa4 moving cancer pipeline qscript over to cmi-cancer Kristian Cibulskis 2012-11-09 10:18:22 -0500
  • d3f9465307 moving to cmi-cancer Kristian Cibulskis 2012-11-09 10:01:02 -0500
  • e93d461910 Adding integration test to BQSR for the csv file Eric Banks 2012-11-09 09:11:04 -0500
  • ee776e996a Merged bug fix from Stable into Unstable Eric Banks 2012-11-09 08:35:51 -0500
  • 66cbaaee31 Fixed nasty bug in BQSR csv file creation: numbers larger than 999 in the Errors column were printed out with commas (which looks like a separate column). Eric Banks 2012-11-09 08:33:55 -0500
  • e9183d9fe0 Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec. Eric Banks 2012-11-08 15:07:47 -0500
  • 17ab3a39d5 Make the --intermediate_csv_file argument un-hidden. Eric Banks 2012-11-08 14:35:23 -0500
  • 28c7492b98 Increase bwa mem limit by 1 Gb - see if we can avoid random job failures that way Guillermo del Angel 2012-11-07 06:45:59 -0800
  • 2da76db945 Updating integration tests Eric Banks 2012-11-06 22:23:05 -0800
  • e6f33a2e34 Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-11-06 20:55:34 -0800
  • f4d4846435 Merged bug fix from Stable into Unstable Eric Banks 2012-11-06 20:53:54 -0800
  • 15b8c08132 Apparently CIGAR elements can have 0 length according to the spec, but 0Ms were causing left alignment of indels to fail. Fixed. Eric Banks 2012-11-06 20:53:33 -0800
  • 0a2dded093 Fixes for bugs uncovered by unit tests Eric Banks 2012-11-06 16:07:40 -0800
  • b07106b3a7 Reimplement the allele biased downsampling to be smarter. Now we don't blindly pull n% of reads off of each allele. Instead, we try all possible genotype conformations for the contaminating sample and choose the one that provides the best genotype for the target sample (based heuristically on allele balance). This method allows us to save some of the reads that belong to the target sample, which should make Daniel M happy. Added unit tests to test the biased downsampling functionality. Eric Banks 2012-11-06 14:39:58 -0800
  • 6f6106d50c Merge branch 'develop' of https://github.com/broadinstitute/cmi-gatk into develop Scott Frazer 2012-11-06 14:44:00 -0500
  • 9ecd73ec7d made parameters not required, fixed some null file names Douglas Voet 2012-11-06 14:43:15 -0500
  • 4a2ffd7c8d made parameters not required, switched date sequenced format, bug fixes in pulling remote files Douglas Voet 2012-11-06 14:00:36 -0500
  • 2c0bf89961 Co-Reduction implementation in ReduceReads Mauricio Carneiro 2012-10-24 16:57:08 -0400
  • f78d8fa157 Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2012-11-06 10:21:17 -0500
  • 48112c9337 pull metadata from metadata service Scott Frazer 2012-11-05 22:45:46 -0500
  • bff7803f3a update the Mills_and_1000G_gold_standard file Ami Levy Moonshine 2012-11-05 13:00:40 -0500
  • 659ec4b6b7 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-11-05 11:43:57 -0500
  • fca6321be2 update the dbSNP file Ami Levy Moonshine 2012-11-05 11:43:36 -0500
  • 2ec3852acd Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass. Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass. QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]]. Added an QCommandPlugin.initScript utility method for handling specialized script types. kshakir 2012-11-04 23:42:02 -0500
  • bf7c832d25 Merged bug fix from Stable into Unstable David Roazen 2012-11-02 19:23:11 -0400
  • eae2d019cf Refuse to package the GATK from a non-clean working directory David Roazen 2012-11-02 19:01:59 -0400
  • 0ab4022f23 Final r119 tribble jar Mark DePristo 2012-11-02 14:30:20 -0400
  • 73157ae3d3 Allow each pipeline test the max of 10 hours to run David Roazen 2012-11-02 12:02:59 -0400
  • f8a0a947e3 Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging Mark DePristo 2012-11-02 09:09:32 -0400
  • c0db3fe8f8 Merge branch 'develop' Guillermo del Angel 2012-11-02 06:58:42 -0400
  • 52c635b551 Merge branch 'master' of github.com:broadinstitute/cmi-gatk Guillermo del Angel 2012-11-02 06:58:21 -0400
  • 6185e8c432 Allow large-scale tests 5 hours each to run David Roazen 2012-11-01 17:48:58 -0400
  • e03c9269ad Damned if I do damned if I don't: SGE doesn't like more than 1 thread and BQSR scatter-gather is broken, so disable for now. Pipeline will still take forever for now Guillermo del Angel 2012-11-01 15:57:45 -0400
  • 386b45e94d This VE eval module isn't useful anymore. Ryan Poplin 2012-11-01 15:44:41 -0400
  • 872abddfce Add custom TestNGTestTransformer that adds a maximum test runtime of 10 minutes to all testng tests Mark DePristo 2012-10-31 19:52:25 -0400
  • 7dd7afe739 Use BQSR in SingleExomeCalling evaluation Mark DePristo 2012-10-31 15:10:21 -0400
  • 1444cd753b Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome Mark DePristo 2012-10-30 16:58:55 -0400
  • 9cd04c335c Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data Mark DePristo 2012-10-29 19:06:05 -0400
  • b9d796f502 More memory/parallelization tweaks: BQSR scatter-gather broken in latest GATK, so disabled. Used multithreading with bigger memory instead Guillermo del Angel 2012-11-01 12:55:00 -0400
  • 94a13c05ed Merged bug fix from Stable into Unstable Eric Banks 2012-10-31 22:57:26 -0400
  • 47a0f5859e Don't run these tests if not GAKT lite Eric Banks 2012-10-31 22:56:38 -0400
  • 2db2747723 More tweaks in pipeline parameters Guillermo del Angel 2012-10-31 21:32:19 -0400
  • 881c843307 Merged bug fix from Stable into Unstable Eric Banks 2012-10-31 21:28:27 -0400
  • f8af8a2355 Moving UG integration tests to protected since they use protected-only contamination filtering. Adding a new UGLite integration test to confirm that contamination filtering is ignored in lite. Eric Banks 2012-10-31 21:28:07 -0400