02cc1afdc8
remove RodBed and all it's dependencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 19:12:30 +00:00
ffb1b46166
Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3395 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 18:49:51 +00:00
0036df7b03
adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 17:40:20 +00:00
ca386439be
only emit a warning if the tribble index is out of date, don't remove and replace it for them. Added a test case where the log4j appender checks the logging messages for the appropriate output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3393 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 15:12:48 +00:00
017ab6b690
Experimental versions of downsampler and Ryan's deduper are now available either
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 05:40:05 +00:00
46ba88018d
Updated to the new readHeader(..) api
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 04:06:34 +00:00
984c51efd3
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:42:12 +00:00
42ee16f256
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3389 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:41:37 +00:00
d8469e2fba
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:40:47 +00:00
d65b2d32d1
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:34 +00:00
b82116f488
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3386 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:20 +00:00
6b96f025f5
Tribble integration for indexing the AnnotatorInputTable format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3385 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:54 +00:00
2f3933148d
Added fast split(str, delimiter) methodf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:26 +00:00
aedb9f6734
Bring SAMPileupCodec into compliance with new interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 01:23:29 +00:00
7cfb9ff3dc
updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 19:34:45 +00:00
635f61c22d
Clone the other guy too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3381 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 18:56:01 +00:00
9e15299475
Misc cleanup in variant recalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3380 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:37:01 +00:00
eb200e4cce
Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:13:44 +00:00
e016491a3d
Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3377 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 16:58:13 +00:00
3c022e4b0c
Improved command-line-arg validation at startup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:46:17 +00:00
35b4bba35e
Refactored so it could be used for knownGene and CCDS as well as refGene
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3372 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:44:10 +00:00
bb86c0e03a
Improved error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:43:13 +00:00
68719615be
For multiple matches, shifted counter to be 1-based
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:41:50 +00:00
73e2e32837
Fix typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:04:00 +00:00
ebd0fabf86
First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:02:13 +00:00
0791beab8f
Checking in downsampling iterator alongside LocusIteratorByState, and removing
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the reference implementation. Also implemented a heap size monitor that can
be used to programmatically report the current heap size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:00:44 +00:00
b7d21627ab
Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 17:23:00 +00:00
4235164359
Removed the confusionMatrix column (of *course* this is a confusion matrix... what else would it be?!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3365 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:55:37 +00:00
95b29f608b
Specify default values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 21:42:53 +00:00
6efd05831b
Encapsulating annotation decoding function in order to use same fixed random seed in both VariantOptimizer and ApplyVariantClusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3363 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 20:03:38 +00:00
32389dc0a9
Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 19:17:46 +00:00
1538dc0144
optimizer now uses -an arguments instead of exclude and force for clarity. command-line length reduced by 50%
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3361 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 15:41:44 +00:00
88bd7a2045
Reenabling UG parallelization performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3360 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 16:28:08 +00:00
0490909285
Fixed epic generic paths fail.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3359 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:59:57 +00:00
7ef87e5126
An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less
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than a minute and fell over instantly in the case of the Tribble parallelism issue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 15:40:43 +00:00
ceec525420
Got rid of stray unicode characters in copyright message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3357 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 14:47:39 +00:00
3e9ad4bbd0
Porting SAM pileup ROD to Tribble as a case study.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 00:22:59 +00:00
6839c194cb
although holding on to memories can be fun, it's bound to hurt performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 19:26:58 +00:00
c81b910f73
Commenting out the parallelization test which is failing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3354 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 18:39:53 +00:00
cac98ba5ef
a couple of small documentation fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 17:40:27 +00:00
3f07611187
Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:36:31 +00:00
2c55ac1374
fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 06:13:26 +00:00
6868ce988f
Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an
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indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 17:31:19 +00:00
34969f304c
Adding dbsnp to all UG performance tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3347 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:48:05 +00:00
140e43b93b
Checking in to see whether it fails. If I start getting bombarded with Bamboo error reports, I'm commenting it out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3346 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 15:39:42 +00:00
572b383fe2
Make VA annotate dbsnp again
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 14:06:53 +00:00
b09e7231d1
A quick implementation of the experimental covariates for the TGen folks to work with.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 01:08:52 +00:00
aec5f7b630
Can now threshold results based on minimum base and/or mapping quality.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3343 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 19:58:07 +00:00
13fd182b7c
For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 15:17:05 +00:00
4a7902bb8e
Bases 'A' and 'a' (etc.) no longer considered different.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:53:38 +00:00
aaron
chartl
hanna
weisburd
rpoplin
kiran
ebanks
depristo