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
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
2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -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
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
045e8a045e
Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker
2011-08-15 14:05:23 -04:00
fc2c21433b
Updating random walkers to new rod system
2011-08-15 13:29:31 -04:00
3d56bbf087
Resolving merge conflicts
2011-08-15 12:28:05 -04:00
9ddbfdcb9f
Check filtered status before applying to alt reference
2011-08-15 12:25:23 -04:00
ca9bb841c3
disabling ReduceReads integration tests
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the new version of the walker is not yet ready for integration tests.
2011-08-14 17:35:30 -04:00
c7b69a4574
Fixed integration tests
2011-08-14 16:38:20 -04:00
6ae3f9e322
Wrapped clipping op information
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The clipping op extra information being kept by this walker was specific to the walker, not to the read clipper. Created a wrapper ReadClipperWithData class that keeps the extra information and leaves the ReadClipper slim.
(this is a quick commit to unbreak the build, performing integration tests and will make further commits if necessary)
2011-08-14 15:44:48 -04:00
8a51732049
Fixes to ReadClipper and added Reference Coordinate clipping.
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* Added reference coordinate based hard clipping functions. This allows you to set a hard cut on where you need the read to be trimmed despite indels.
* soft clipping was messing up cigar string if there was already a hard clip at the beginning of the read. Fixed.
* hard clipping now works with previously hard clipped reads.
2011-08-14 14:54:33 -04:00
291d8c7596
Fixed HardClipping and Interval containment
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* Hard clipping was wrongfully hard clipping unmapped reads while soft clipping then hard clipping mapped reads. Now we throw exception if we try to hard/soft clip unmapped reads and use the soft->hard clip procedure fore every mapped read.
* Interval containment needed a <= and >= to make sure it caught the borders right.
2011-08-14 14:54:33 -04:00
Mark DePristo
Eric Banks
Ryan Poplin
Andrey Sivachenko
Christopher Hartl
David Roazen
Mauricio Carneiro