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
ab1e3d6a98
Use the right set of sample names
2011-08-16 01:03:05 -04:00
fd37da13af
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-15 21:44:16 -04:00
c3c11b2462
A simple utility that evaluates parallel performance in tribble
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Tests low-level multi-threading performance of tribble Creates a thread pool that reads the input VCF file in parallel with N threads from 1 to maxThreads (in powers of 2) and emits the wall time needed to process the entire file. Assumes the VCF file has a chromosome named 1 that has at least 250 Mb.
The output is a nice table showing performance of Tribble
THREAD: 1-250000001 read 2288096 objects
TIME: 1 thread runtime 12.58
THREAD: 125000001-250000001 read 1098468 objects
THREAD: 1-125000001 read 1189628 objects
TIME: 2 thread runtime 8.66
THREAD: 124000001-186000001 read 406935 objects
THREAD: 62000001-124000001 read 569656 objects
THREAD: 1-62000001 read 619972 objects
THREAD: 186000001-248000001 read 678173 objects
TIME: 4 thread runtime 8.57
THREAD: 124000001-155000001 read 101636 objects
THREAD: 93000001-124000001 read 271390 objects
THREAD: 62000001-93000001 read 298266 objects
THREAD: 155000001-186000001 read 305299 objects
THREAD: 31000001-62000001 read 297745 objects
THREAD: 1-31000001 read 322227 objects
THREAD: 217000001-248000001 read 334136 objects
THREAD: 186000001-217000001 read 344037 objects
TIME: 8 thread runtime 9.68
2011-08-15 21:42:23 -04:00
3e9ef0622d
Revert "1) RFCombine switched to the new ROD system"
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This reverts commit cf989bd3cfae119ba9011873c5f5d5b80e37f67b.
2011-08-15 18:45:38 -04:00
1968b65ca8
Revert "Remove merge-added ======'s so this compiles"
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This reverts commit be028b6513a129f81aa6f3593ea7d396c0e8fc25.
2011-08-15 18:45:21 -04:00
5aa61fefec
Remove merge-added ======'s so this compiles
2011-08-15 16:53:05 -04:00
cf3e826a69
1) RFCombine switched to the new ROD system
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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
2011-08-15 16:37:31 -04:00
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.
2011-08-15 16:31:57 -04:00
1246b89049
Forgot to initialize variants on the merge
2011-08-15 16:00:43 -04:00
Mark DePristo
Eric Banks
Mauricio Carneiro
Chris Hartl
Ryan Poplin
Andrey Sivachenko
David Roazen