f0bd1b5ae5
Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.
2013-01-08 15:46:32 -05:00
245fcc8bb5
Merged bug fix from Stable into Unstable
2013-01-08 12:59:15 -05:00
d6146d369a
Remove all of the references to ProgramElementDoc
2013-01-08 12:58:31 -05:00
b099e2b4ae
Moving integration tests to protected
2013-01-08 09:34:08 -05:00
47d030a52d
Oops, move the covariates over too
2013-01-07 15:47:25 -05:00
35699a8376
Move bqsr utils to protected
2013-01-07 15:41:21 -05:00
5371613ad1
Tests seem to pass (can't be positive though because I ran before Tad's recent push), so I'm going to push now (this push touches so many files that I don't want to keep it around much longer).
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Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-07 15:27:43 -05:00
8bbb9e1cc2
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-07 15:07:25 -05:00
d4b4f95e12
move CatVariants to public
2013-01-07 15:07:16 -05:00
1a4b112865
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-07 15:00:35 -05:00
a0219acfaa
Collapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone
2013-01-07 14:55:21 -05:00
d3e2352072
Moved processing pipelines to private
...
These pipelines were supposed to serve as an example for the community, they were written a long-long-long time ago and are being used today by users as the 'best practice pipeline'. Unless we decide we want to support and maintain an example best-practices pipeline, I'm moving these to private.
2013-01-07 14:49:57 -05:00
35d9bd377c
Moved (nearly) all Walkers from public to protected and removed GATKLite utils
2013-01-07 14:42:40 -05:00
78f7a4e300
Received permission from Mauricio to archive the DPP and PBPP PipelineTests
2013-01-07 14:03:08 -05:00
b4e7b3d691
Fixed precision problem in the Bayesian calculation of Qemp: we need to cap below max integer because the MathUtils code add +1.
...
Added unit tests for handling large number of observations.
2013-01-07 13:07:36 -05:00
04e3978b04
Fixed VariantEval tests
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-Added sorting by rows to VariantEval
2013-01-07 12:45:32 -05:00
4f95f850b3
Bug fix in the HC's allele mapping for multi-allelic events. Using the allele alone as a key isn't sufficient because alleles change when the reference allele changes during VariantContextUtils.simpleMerge for multi-allelic events.
2013-01-07 11:05:44 -05:00
d3c2c97fb2
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-06 23:35:47 -05:00
c554d9db25
add TODO
2013-01-06 23:04:38 -05:00
81eef3aa37
merge development branchs of log-less HMM and FastGatherer to master
2013-01-06 23:01:58 -05:00
0249e1f497
Resolving merge conflicts from VCF move
2013-01-06 14:32:31 -05:00
8822b8e7c8
Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.
2013-01-06 14:30:45 -05:00
ef638489d5
Fixing BQSR gatherer test to keep up to date with latest changes
2013-01-06 14:07:59 -05:00
ea21dc9cfb
I just committed this - why didn't it work before? Trying again...
2013-01-06 12:44:13 -05:00
52067f0549
Handle merge conflicts
2013-01-06 12:29:12 -05:00
bf25e151ff
Handle long->int precision in Bayesian estimate
2013-01-06 12:26:32 -05:00
b73d72fe94
update docs for LEftAlignVariants
2013-01-06 01:56:57 -05:00
b403c269e9
Make multi-threaded progress meter daemon unit test more robust
2013-01-05 12:59:18 -05:00
2ab55e4ee7
Fixing bug in TraverseDuplicates.printProgress call: only passes in single location of genome loc
2013-01-05 12:50:27 -05:00
69bf70c42e
Cleanup and more unit tests for RecalibrationTables in BQSR
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-- Added unit tests for combining RecalibrationTables. As a side effect now has serious tests for incrementDatumOrPutIfNecessary
-- Removed unnecessary enum.index system from RecalibrationTables.
-- Moved what were really static utility methods out of RecalibrationEngine and into RecalUtils.
2013-01-05 12:50:27 -05:00
9df30880cb
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-04 17:15:22 -05:00
01738e70c3
Archive the experimental Active Region Traversals
2013-01-04 17:05:31 -05:00
7b7efa0fff
Add in the AAL as an experimental covariate, in case it's wanted.
2013-01-04 16:47:26 -05:00
41bc416b65
Remove AAL and update MD5s.
2013-01-04 16:46:14 -05:00
bce6fce58d
Resolving merge conflicts after Mark's latest push
2013-01-04 14:46:39 -05:00
dd7f5e2be7
Hooking up the Bayesian estimate code for calculating Qemp in BQSR; various fixes after adding unit tests.
2013-01-04 14:43:11 -05:00
80b531f695
emit all sites where more than 90% of the samples have good coverage
2013-01-04 14:27:50 -05:00
ab5526b372
More TODOs
2013-01-04 14:09:02 -05:00
fe06912a87
Removed sorting by row from walkers
2013-01-04 11:52:33 -05:00
810e2da1d4
Cleanup and unit tests for EventType and ReadRecalibrationInfo in BQSR
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-- Added unit tests for EventType and ReadRecalibrationInfo
-- Simplified interface of EventType. Previously this enum carried an index with it, but this is redundant with the enum.ordinal function. Now just using that function instead.
2013-01-04 11:39:25 -05:00
a5901cdd20
Bugfix for printProgress in TraverseReadsNano
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-- Must provide a single bp position (1:10) not the range of the read (1:1-50). ProgressMeter now checks at runtime for this problem as well.
2013-01-04 11:39:24 -05:00
bbdf9ee91b
BQSR cleanup: merge Advanced and Standard recalibration engine into just the RecalibrationEngine
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-- As we are no longer maintaining a public/protected system we need only have one RecalibrationEngine.
-- Misc. code cleanup and docs along the way
2013-01-04 11:39:24 -05:00
7df47418d8
BQSR optimization: make RecalibrationTables thread-local, and merge results in onTraversalDone
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-- With the newer, faster BQSR, scaling was limited by the NestedIntegerArray. The solution to this is to make the entire table thread-local, so that each nct thread has its own data and doesn't have any collisions.
-- Removed the previous partial solution of having a thread-local quality score table
-- Added a new argument -lowMemory
2013-01-04 11:39:24 -05:00
1ba8d47a81
Unit tests for ProgressMeterDaemon
2013-01-04 11:39:24 -05:00
fbee4c11f1
Unit tests for ProgressMeterData
2013-01-04 11:39:23 -05:00
319d651e4a
Initial updates for ActiveRegionShard
2013-01-03 17:00:13 -05:00
e7553545ef
Initial updates for ReadShard
2013-01-03 17:00:13 -05:00
14a3ac0e3c
Enable the use of alternate shards
2013-01-03 17:00:13 -05:00
4cc372f53b
LocusShardDataProvider doesn't need its own GenomeLocParser
2013-01-03 17:00:13 -05:00
ffbd4d85f2
No need to pass fields as parameters
2013-01-03 17:00:12 -05:00
Eric Banks
Ami Levy-Moonshine
Mauricio Carneiro
Tad Jordan
Ryan Poplin
Mark DePristo
Chris Hartl
Joel Thibault
Chris Hartl