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  • ecf66b93ec ILSS now outputs proper quality strings (should be phred-Q + 64, and capped at [2,40]) Chris Hartl 2011-08-17 22:23:21 -0400
  • cc3df8f11a Moving GAV walker to public Mauricio Carneiro 2011-08-17 21:54:40 -0400
  • a9df365364 GenotypeAndValidate walker updated Mauricio Carneiro 2011-08-17 17:48:04 -0400
  • fa1db3913b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-17 21:49:25 -0400
  • 8e83b6646b Bug fix for Chris: don't validate ref base for complex events. Eric Banks 2011-08-17 21:49:14 -0400
  • 2bbf29b07a Merged bug fix from Stable into Unstable Matt Hanna 2011-08-17 17:01:36 -0400
  • c104dd7a09 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-08-17 16:59:12 -0400
  • 81a792afeb Reverting optimization disable in unstable. Matt Hanna 2011-08-17 16:58:24 -0400
  • 2e35592295 GATKDocs for CallableLoci Mark DePristo 2011-08-17 16:32:01 -0400
  • c193f52e5d Fixed up examples: pasting from wiki still had old rod syntax Guillermo del Angel 2011-08-17 16:29:45 -0400
  • 2b2a4e0795 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable Matt Hanna 2011-08-17 16:26:45 -0400
  • 297c9e513c Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable into unstable Matt Hanna 2011-08-17 16:24:02 -0400
  • a210a62ab9 Merged bug fix from Stable into Unstable Matt Hanna 2011-08-17 16:23:31 -0400
  • fdd46a5e99 License automatically added. Mark DePristo 2011-08-17 16:22:37 -0400
  • d59e6ed274 Fix for RefSeqCodec bug and better error messages Mark DePristo 2011-08-17 16:22:07 -0400
  • d170187896 Disable optimization that increases marginal speed of the GATK slightly but can produce data loss in a narrow corner case where the BGZF block(s) locations and offsets in the last index bucket of contig n overlap exactly with the BGZF block locations and offset in the last index bucket of contig n+1. Matt Hanna 2011-08-17 16:16:05 -0400
  • 53006da9a5 Improved descriptions for the SnpEff annotations in the VCF header (based on Eric's feedback). David Roazen 2011-08-17 14:55:32 -0400
  • 784fb148b9 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-17 15:47:01 -0400
  • 671330950d Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden Guillermo del Angel 2011-08-17 15:46:31 -0400
  • 0af68e052a Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable Andrey Sivachenko 2011-08-17 15:17:47 -0400
  • a423546cdd fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once) Andrey Sivachenko 2011-08-17 15:17:31 -0400
  • 710d34633e now the reads that are too long are truly ignored (fix of the fix) Andrey Sivachenko 2011-08-17 15:16:23 -0400
  • 40f64a27be Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-17 14:21:55 -0400
  • 2f19046f0c Adding docs to the 2 beasts. Saved the worst for last. Eric Banks 2011-08-17 14:19:14 -0400
  • 8a92143938 Change @argument to @input Chris Hartl 2011-08-17 14:18:34 -0400
  • 4dab59bfb5 Added: a simulator for intron loss reads. Chris Hartl 2011-08-17 14:14:31 -0400
  • eea8087c73 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-17 14:06:25 -0400
  • 069554efe5 somatic indel detector does not die on reads that are too long (likely contain a huge deletion) anymore; instead print a warning and ignore the read Andrey Sivachenko 2011-08-17 14:05:19 -0400
  • c405a75f54 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-17 13:28:25 -0400
  • 575303ae6b Renaming for consistency and bringing up to speed with new rod system Eric Banks 2011-08-17 13:28:19 -0400
  • 6d629c176c Adding docs Eric Banks 2011-08-17 13:27:36 -0400
  • a21e193a9e Adding docs to 3 more walkers Eric Banks 2011-08-17 12:35:08 -0400
  • 98acb546a9 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2011-08-17 12:22:29 -0400
  • d1bb302d12 Added GatkDocs documentation Menachem Fromer 2011-08-17 12:21:37 -0400
  • 3da71a9bb6 Clean up summary Mark DePristo 2011-08-17 12:04:45 -0400
  • c6fb215faf GATKDocs for VariantsToTable Mark DePristo 2011-08-17 12:02:41 -0400
  • 5f794d16a7 Fixed bad character in documentation Mark DePristo 2011-08-17 12:00:32 -0400
  • 9d1d5bd27a Revert "Fixed bad character in documentation" Mark DePristo 2011-08-17 11:57:31 -0400
  • 78deb3f195 Fixed bad character in documentation Mark DePristo 2011-08-17 11:57:00 -0400
  • 79dcfca25f Fixed bad character in documentation Mark DePristo 2011-08-17 11:56:51 -0400
  • c365da3c51 Fixed final old rodBinding from PipelineTest Mark DePristo 2011-08-17 11:56:30 -0400
  • b3b5d608ca Adding docs to yet more walkers Eric Banks 2011-08-17 09:57:19 -0400
  • fadcbf68fd Adding docs to QC walkers Eric Banks 2011-08-17 09:39:33 -0400
  • 5d6a6fab98 Renamed softUnclipped functions to refCoord* Mauricio Carneiro 2011-08-16 18:56:28 -0400
  • ed8f769dce Fixed index for getSoftUnclippedEnd() Mauricio Carneiro 2011-08-16 18:54:28 -0400
  • 5f3f46aad1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-16 16:26:33 -0400
  • 946f5c53fe Adding docs to more walkers Eric Banks 2011-08-16 16:26:26 -0400
  • 6e828260a0 Removed -B support. Now explodes with error if -B provided. Mark DePristo 2011-08-16 16:13:47 -0400
  • 0c3466d2c3 typo Chris Hartl 2011-08-16 15:25:35 -0400
  • 008aa281e7 add interval list Chris Hartl 2011-08-16 15:24:05 -0400
  • 7cb42efccb Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-16 15:23:13 -0400
  • 99e7e53744 script it Chris Hartl 2011-08-16 14:37:49 -0400
  • b36b047eb8 val --> var Chris Hartl 2011-08-16 14:36:09 -0400
  • edd39da2ea Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git Chris Hartl 2011-08-16 14:32:48 -0400
  • 880de6ccb0 RFCombine alteration Chris Hartl 2011-08-16 14:32:06 -0400
  • 632cd9bed1 script to scatter-gather left align variants Chris Hartl 2011-08-16 14:31:12 -0400
  • 2d5bbecd9e Merged bug fix from Stable into Unstable Ryan Poplin 2011-08-16 14:19:04 -0400
  • 07c1e113cd Fixed interval traversal for previously hard clipped reads. Mauricio Carneiro 2011-08-16 14:18:05 -0400
  • 9d4add3268 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Ryan Poplin 2011-08-16 14:18:03 -0400
  • 170d1ff7b6 Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode Ryan Poplin 2011-08-16 14:17:46 -0400
  • b135565183 Added low quality clipping Mauricio Carneiro 2011-08-16 13:51:25 -0400
  • 9f3328db53 fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one Andrey Sivachenko 2011-08-16 13:45:40 -0400
  • a684233265 Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable Andrey Sivachenko 2011-08-16 13:40:59 -0400
  • c71a4e1832 this is a bug fix; reverting in unstable and pushing from stable instead Andrey Sivachenko 2011-08-16 13:40:35 -0400
  • 801659c1d7 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-16 13:24:51 -0400
  • 637f3e0756 Commenting out the @Argument so queue will build -- still unsure where the bug is, but this walker can't be brought properly onto the new ROD system yet Christopher Hartl 2011-08-16 13:24:30 -0400
  • 335421820e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-16 13:08:25 -0400
  • ab0b56ed11 Minor doc fixes Eric Banks 2011-08-16 12:55:45 -0400
  • 125ad0bcfa Added docs to RTC Eric Banks 2011-08-16 12:46:48 -0400
  • ef9216011e Added docs to IR Eric Banks 2011-08-16 12:24:53 -0400
  • b9725d6ce5 Merge branch 'incoming' Christopher Hartl 2011-08-16 12:15:54 -0400
  • 9528cb4c33 A nicer version of the Intron Loss Genotyper that breaks out an engine for future modifications. Chris Hartl 2011-08-16 12:14:30 -0400
  • ea3dfcfb4f Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-16 11:04:21 -0400
  • 9e1d443c47 fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one Andrey Sivachenko 2011-08-16 10:55:51 -0400
  • d0d2e9eb2a Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-16 10:44:52 -0400
  • ee4be4e5cc Detailed docs. Index loaded only once. Linear threads Mark DePristo 2011-08-16 10:44:36 -0400
  • 6c0b9a7fc7 Moving RFCombine to the new ROD system Chris Hartl 2011-08-16 09:47:57 -0400
  • 21afdbfff0 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-16 01:03:12 -0400
  • ab1e3d6a98 Use the right set of sample names Eric Banks 2011-08-16 01:03:05 -0400
  • fd37da13af Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-15 21:44:16 -0400
  • c3c11b2462 A simple utility that evaluates parallel performance in tribble Mark DePristo 2011-08-15 21:42:23 -0400
  • 3e9ef0622d Revert "1) RFCombine switched to the new ROD system" David Roazen 2011-08-15 18:45:38 -0400
  • 1968b65ca8 Revert "Remove merge-added ======'s so this compiles" David Roazen 2011-08-15 18:45:21 -0400
  • 5aa61fefec Remove merge-added ======'s so this compiles Christopher Hartl 2011-08-15 16:53:05 -0400
  • cf3e826a69 1) RFCombine switched to the new ROD system 2) TreeReduce added to useful RODWalkers, but doesn't help very much due to scaling problems 3) RFA refactored, and a genotype-free calculation model added to calculate skew in a genotype-free way (still needs generalization to any ploidy) 4) Added walker to genotype intron loss events, calls into the UG engine to do so. This is very much a first-pass walker. 5) Documentation added for ValidationAmplicons Christopher Hartl 2011-07-29 15:53:56 -0400
  • 36c7f83208 Refactoring VE stratifications so that they don't pass around bulky data; instead just pull needed data from the VE parent. This allows us stop using deprecated features of the rod system. Eric Banks 2011-08-15 16:31:57 -0400
  • 1246b89049 Forgot to initialize variants on the merge Eric Banks 2011-08-15 16:00:43 -0400
  • 993ecb85da Added Hard Clipping Tail Ends Mauricio Carneiro 2011-08-15 15:22:54 -0400
  • 045e8a045e Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker Eric Banks 2011-08-15 14:05:23 -0400
  • fc2c21433b Updating random walkers to new rod system Eric Banks 2011-08-15 13:29:31 -0400
  • 3d56bbf087 Resolving merge conflicts Eric Banks 2011-08-15 12:28:05 -0400
  • 9ddbfdcb9f Check filtered status before applying to alt reference Eric Banks 2011-08-15 12:25:23 -0400
  • 0d976d6211 Fixed second time clipping Mauricio Carneiro 2011-08-15 12:04:53 -0400
  • 489c15b99d Fixed indexing issue in coordinate conversion Mauricio Carneiro 2011-08-15 01:42:34 -0400
  • ca9bb841c3 disabling ReduceReads integration tests Mauricio Carneiro 2011-08-14 17:35:30 -0400
  • c7b69a4574 Fixed integration tests Mauricio Carneiro 2011-08-14 16:38:20 -0400
  • 6ae3f9e322 Wrapped clipping op information Mauricio Carneiro 2011-08-14 15:44:48 -0400
  • 8a51732049 Fixes to ReadClipper and added Reference Coordinate clipping. Mauricio Carneiro 2011-08-14 14:34:29 -0400
  • 291d8c7596 Fixed HardClipping and Interval containment Mauricio Carneiro 2011-08-13 21:02:24 -0400
  • 0be1dacddb Refactored interval clipping utility Mauricio Carneiro 2011-08-13 19:33:53 -0400