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.
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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
38c3f22531
now using variant.jar
2013-01-06 23:33:17 -05:00
a1de84c6c1
remove annotation from LasrgeScalePipeline and change eval to wrok with the srandard interval file
2013-01-06 23:28:38 -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
96efa8b19f
auto-merge
2013-01-04 12:21:03 -05:00
9b993c647f
Adding a manual review site.
2013-01-04 12:20:25 -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
6af1e21758
Minor cleanup of GATKPerformanceOverTime
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
27722a15e5
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-04 11:38:18 -05:00
e89a1d711e
Adding ability to exclude callsets from AssessNA12878.
2013-01-04 11:38:05 -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
47e620dfbc
Create BAM index to test shard boundaries
2013-01-03 17:00:12 -05:00
c1ba12d71a
Added unit test for outputting sorted GATKReport Tables
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- Made few small modifications to code
- Replaced the two arguments in GATKReportTable constructor with an enum used to specify way of sorting the table
2013-01-03 16:53:59 -05:00
10a705b27f
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-03 13:42:31 -05:00
2018285a39
better error message
2013-01-03 13:41:03 -05:00
c7039a9b71
Pushing in implementation of the Bayesian estimate of Qemp for the BQSR.
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This isn't hooked up yet with BQSR; it's just a static method used in my testing walker. I'll hook this into BQSR after more testing and the addition of unit tests.
Most of the changes in this commit are actually documentation-related.
2013-01-02 15:21:44 -05:00
03294ae1c8
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-02 15:11:30 -05:00
Eric Banks
Tad Jordan
Ryan Poplin
Ami Levy-Moonshine
Mark DePristo
Chris Hartl
Joel Thibault
Chris Hartl