c405a75f54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 13:28:25 -04:00
575303ae6b
Renaming for consistency and bringing up to speed with new rod system
2011-08-17 13:28:19 -04:00
6d629c176c
Adding docs
2011-08-17 13:27:36 -04:00
a21e193a9e
Adding docs to 3 more walkers
2011-08-17 12:35:08 -04:00
98acb546a9
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 12:22:29 -04:00
d1bb302d12
Added GatkDocs documentation
2011-08-17 12:21:37 -04:00
3da71a9bb6
Clean up summary
2011-08-17 12:04:45 -04:00
c6fb215faf
GATKDocs for VariantsToTable
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-- Made a previously required argument optional, as this was a long-standing bug
2011-08-17 12:02:41 -04:00
5f794d16a7
Fixed bad character in documentation
2011-08-17 12:01:08 -04:00
9d1d5bd27a
Revert "Fixed bad character in documentation"
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This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
2011-08-17 11:57:31 -04:00
78deb3f195
Fixed bad character in documentation
2011-08-17 11:57:00 -04:00
79dcfca25f
Fixed bad character in documentation
2011-08-17 11:56:51 -04:00
c365da3c51
Fixed final old rodBinding from PipelineTest
2011-08-17 11:56:30 -04:00
b3b5d608ca
Adding docs to yet more walkers
2011-08-17 09:57:19 -04:00
fadcbf68fd
Adding docs to QC walkers
2011-08-17 09:39:33 -04:00
5d6a6fab98
Renamed softUnclipped functions to refCoord*
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These functions return reference coordinates, so they should be named accordingly.
2011-08-16 18:56:28 -04:00
ed8f769dce
Fixed index for getSoftUnclippedEnd()
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Unclipped end can be calculated simply by looking at the last cigar element and adding it's length in case it's a soft clip.
2011-08-16 18:54:28 -04:00
5f3f46aad1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 16:26:33 -04:00
946f5c53fe
Adding docs to more walkers
2011-08-16 16:26:26 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
0c3466d2c3
typo
2011-08-16 15:25:35 -04:00
008aa281e7
add interval list
2011-08-16 15:24:05 -04:00
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
99e7e53744
script it
2011-08-16 14:37:49 -04:00
b36b047eb8
val --> var
2011-08-16 14:36:09 -04:00
edd39da2ea
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-08-16 14:32:48 -04:00
880de6ccb0
RFCombine alteration
2011-08-16 14:32:06 -04:00
632cd9bed1
script to scatter-gather left align variants
2011-08-16 14:31:12 -04:00
2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -04:00
07c1e113cd
Fixed interval traversal for previously hard clipped reads.
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If a read was hard clipped for being low quality and no does not overlap the interval anymore, this read will now be discarded instead of treated as an error by the GATK traversal engine.
2011-08-16 14:18:05 -04:00
9d4add3268
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-16 14:18:03 -04:00
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
b135565183
Added low quality clipping
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Clips both tails of a read if the tails are below a given quality threshold (default Q2).
*Added special treatment for reads that get completely clipped.
2011-08-16 13:51:25 -04:00
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
a684233265
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 13:40:59 -04:00
c71a4e1832
this is a bug fix; reverting in unstable and pushing from stable instead
2011-08-16 13:40:35 -04:00
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
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
335421820e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 13:08:25 -04:00
ab0b56ed11
Minor doc fixes
2011-08-16 12:55:45 -04:00
125ad0bcfa
Added docs to RTC
2011-08-16 12:46:48 -04:00
ef9216011e
Added docs to IR
2011-08-16 12:24:53 -04:00
b9725d6ce5
Merge branch 'incoming'
2011-08-16 12:15:54 -04:00
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
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
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
d0d2e9eb2a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 10:44:52 -04:00
ee4be4e5cc
Detailed docs. Index loaded only once. Linear threads
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-- Final testing version
-- Detailed docs on all arguments
-- Runs nThreads linearly from 1, 2, ..., maxThreads
-- Only loads a single index
2011-08-16 10:44:36 -04:00
6c0b9a7fc7
Moving RFCombine to the new ROD system
2011-08-16 09:47:57 -04:00
21afdbfff0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 01:03:12 -04:00
Eric Banks
Menachem Fromer
Mark DePristo
Mauricio Carneiro
Chris Hartl
Ryan Poplin
Andrey Sivachenko