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
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
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
0be1dacddb
Refactored interval clipping utility
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reads are clipped in map() and now we cover almost all cases. Left behind the case where the read stretches through two intervals. This will need special treatment later.
2011-08-14 14:54:33 -04:00
e921230e72
Compressor class variables private
2011-08-14 14:54:33 -04:00
3d73b6fe9d
Getting rid of minBpForConsensus
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The minimum is now 1 with the sliding reads, no need for the MBRC parameter anymore.
2011-08-14 14:54:33 -04:00
ec6b1731e8
First implementation of the Sliding Window
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This is the first attempt on the sliding window approach to reduce the memory footprint and increase performance of the ReduceReads walker.
The sliding window creates a running consensus as it traverses the reads without saving them all in memory. It also generalizes the treatment of variable regions.
2011-08-14 14:54:33 -04:00
ed2df49743
Rename so filename matches class
2011-08-14 10:44:28 -04:00
fc10685709
Measure nt scaling with/without ROD system for CC
2011-08-14 10:41:05 -04:00
9d2cda3d41
Removed a public -> private dependency in our test suite.
2011-08-12 17:29:10 -04:00
f55ac40f2b
Moving HLA code into the archive.
2011-08-12 16:06:42 -04:00
bb4ced3201
SnpEff-related fixes.
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-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.
-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
2011-08-12 15:26:24 -04:00
10e873d9c6
Merge branch 'repval'
2011-08-12 15:24:31 -04:00
b3b9b74d2c
got rid of the useless parameter classes
2011-08-12 14:21:30 -04:00
31dc831531
Merged bug fix from Stable into Unstable
2011-08-12 13:26:41 -04:00
9121b8ed65
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 12:24:19 -04:00
7ed120361d
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
2011-08-12 12:23:44 -04:00
7ea9196321
Better error message for name/type clashes.
2011-08-12 11:18:14 -04:00
27f0748b33
Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
2011-08-12 11:11:56 -04:00
f5b2cc4977
I'm really starting to hate this pipeline test.
2011-08-12 10:45:58 -04:00
005bd71be3
Working too quickly earlier. Fixing syntax.
2011-08-12 10:29:36 -04:00
c7ca33cbff
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 10:12:09 -04:00
639a01f382
Updating integration test now that VE has been updated
2011-08-12 07:15:08 -04:00
41f3da75d7
Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.
2011-08-12 02:22:44 -04:00
45f973ab1f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 00:40:18 -04:00
eba316621d
Finish moving VE over to new rod system and fixing up the type inconsistency between eval and comp rods. Now the novel count is always 0 under the known stratification. :)
2011-08-12 00:40:08 -04:00
6ee8a3a8dd
Fixing the javadoc/scaladoc targets in build.xml
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Usable targets are now:
ant javadoc (public-only)
ant javadoc.private (public + private)
ant scaladoc (public-only)
ant scaladoc.private (public + private)
As documented in the comments, you need to set the ANT_OPTS environment
variable to -Xmx1G before using the scaladoc targets.
Will modify bamboo to auto-generate these and post them to the web after
successful builds.
2011-08-11 19:24:41 -04:00
9de06560df
Update to new RodBinding system
2011-08-11 17:54:16 -04:00
f408d5ea93
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 17:04:18 -04:00
f1d1252be2
Fixing syntax of BQSR and UG performance tests.
2011-08-11 17:04:09 -04:00
bd5cdb8a43
The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml
2011-08-11 16:38:29 -04:00
902eb0c61e
Adding dbsnp annotation back into the UG integration tests
2011-08-11 13:55:03 -04:00
90771b74b4
When matching eval to comps, try to choose the one with the same alt allele.
2011-08-11 13:55:01 -04:00
200f73b008
No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
2011-08-11 13:44:07 -04:00
e93538cdf7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 13:39:36 -04:00
265c3d744b
Fixing VariantEval logic and having it use the new rod system.
2011-08-11 13:39:34 -04:00
Mark DePristo
David Roazen
Christopher Hartl
Eric Banks
Mauricio Carneiro
Guillermo del Angel
Menachem Fromer
Ryan Poplin