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7058 Commits (d1892cd0d77194af26df39008600a7ba03b68aab)

Author SHA1 Message Date
Andrey Sivachenko 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) 2011-08-17 15:17:31 -04:00
Andrey Sivachenko 710d34633e now the reads that are too long are truly ignored (fix of the fix) 2011-08-17 15:16:23 -04:00
Eric Banks 40f64a27be Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-17 14:21:55 -04:00
Eric Banks 2f19046f0c Adding docs to the 2 beasts. Saved the worst for last. 2011-08-17 14:19:14 -04:00
Chris Hartl 8a92143938 Change @argument to @input 2011-08-17 14:18:34 -04:00
Chris Hartl 4dab59bfb5 Added: a simulator for intron loss reads. 2011-08-17 14:14:31 -04:00
Christopher Hartl eea8087c73 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-17 14:06:25 -04:00
Andrey Sivachenko 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 2011-08-17 14:05:19 -04:00
Eric Banks c405a75f54 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-17 13:28:25 -04:00
Eric Banks 575303ae6b Renaming for consistency and bringing up to speed with new rod system 2011-08-17 13:28:19 -04:00
Eric Banks 6d629c176c Adding docs 2011-08-17 13:27:36 -04:00
Eric Banks a21e193a9e Adding docs to 3 more walkers 2011-08-17 12:35:08 -04:00
Menachem Fromer 98acb546a9 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-17 12:22:29 -04:00
Menachem Fromer d1bb302d12 Added GatkDocs documentation 2011-08-17 12:21:37 -04:00
Mark DePristo 3da71a9bb6 Clean up summary 2011-08-17 12:04:45 -04:00
Mark DePristo c6fb215faf GATKDocs for VariantsToTable 
-- Made a previously required argument optional, as this was a long-standing bug
 2011-08-17 12:02:41 -04:00
Mark DePristo 5f794d16a7 Fixed bad character in documentation 2011-08-17 12:01:08 -04:00
Mark DePristo 9d1d5bd27a Revert "Fixed bad character in documentation" 
This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
 2011-08-17 11:57:31 -04:00
Mark DePristo 78deb3f195 Fixed bad character in documentation 2011-08-17 11:57:00 -04:00
Mark DePristo 79dcfca25f Fixed bad character in documentation 2011-08-17 11:56:51 -04:00
Mark DePristo c365da3c51 Fixed final old rodBinding from PipelineTest 2011-08-17 11:56:30 -04:00
Eric Banks b3b5d608ca Adding docs to yet more walkers 2011-08-17 09:57:19 -04:00
Eric Banks fadcbf68fd Adding docs to QC walkers 2011-08-17 09:39:33 -04:00
Eric Banks 5f3f46aad1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 16:26:33 -04:00
Eric Banks 946f5c53fe Adding docs to more walkers 2011-08-16 16:26:26 -04:00
Mark DePristo 6e828260a0 Removed -B support. Now explodes with error if -B provided. 2011-08-16 16:13:47 -04:00
Chris Hartl 0c3466d2c3 typo 2011-08-16 15:25:35 -04:00
Chris Hartl 008aa281e7 add interval list 2011-08-16 15:24:05 -04:00
Christopher Hartl 7cb42efccb Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 15:23:13 -04:00
Chris Hartl 99e7e53744 script it 2011-08-16 14:37:49 -04:00
Chris Hartl b36b047eb8 val --> var 2011-08-16 14:36:09 -04:00
Chris Hartl edd39da2ea Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git 2011-08-16 14:32:48 -04:00
Chris Hartl 880de6ccb0 RFCombine alteration 2011-08-16 14:32:06 -04:00
Chris Hartl 632cd9bed1 script to scatter-gather left align variants 2011-08-16 14:31:12 -04:00
Ryan Poplin 2d5bbecd9e Merged bug fix from Stable into Unstable 2011-08-16 14:19:04 -04:00
Ryan Poplin 9d4add3268 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-16 14:18:03 -04:00
Ryan Poplin 170d1ff7b6 Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode 2011-08-16 14:17:46 -04:00
Andrey Sivachenko 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 2011-08-16 13:45:40 -04:00
Andrey Sivachenko a684233265 Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 13:40:59 -04:00
Andrey Sivachenko c71a4e1832 this is a bug fix; reverting in unstable and pushing from stable instead 2011-08-16 13:40:35 -04:00
Christopher Hartl 801659c1d7 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 13:24:51 -04:00
Christopher Hartl 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 2011-08-16 13:24:30 -04:00
Eric Banks 335421820e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 13:08:25 -04:00
Eric Banks ab0b56ed11 Minor doc fixes 2011-08-16 12:55:45 -04:00
Eric Banks 125ad0bcfa Added docs to RTC 2011-08-16 12:46:48 -04:00
Eric Banks ef9216011e Added docs to IR 2011-08-16 12:24:53 -04:00
Christopher Hartl b9725d6ce5 Merge branch 'incoming' 2011-08-16 12:15:54 -04:00
Chris Hartl 9528cb4c33 A nicer version of the Intron Loss Genotyper that breaks out an engine for future modifications. 2011-08-16 12:14:30 -04:00
Christopher Hartl ea3dfcfb4f Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-08-16 11:04:21 -04:00
Andrey Sivachenko 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 2011-08-16 10:55:51 -04:00