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
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
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
ea2d9aa4fe
Merge branch 'incoming'
2013-01-02 15:10:28 -05:00
3753209584
One md5sum slipped past in the HC integration test.
2013-01-02 15:09:28 -05:00
c515175313
Ensure that active region extensions stay on contig
2013-01-02 14:46:24 -05:00
dcb7735d3c
Active Region extensions must stay on contig
2013-01-02 14:46:24 -05:00
09199366b7
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-02 14:44:49 -05:00
e1d09ab0db
QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.
2013-01-02 14:41:29 -05:00
a15f368bdc
Re-enable testIsActiveRangeLow/High
2013-01-02 11:57:50 -05:00
7188a4a921
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-02 11:39:53 -05:00
12f4c6307e
AutoFormattingTime cleanup and complete unittests
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-- Underlying system now uses long nano times to be more consistent with standard java practice
-- Updated a few places in the code that were converting from nanoseconds to double seconds to use the new nanoseconds interface directly
-- Bringing us to 100% test coverage with clover with AutoFormattingTimeUnitTest
2013-01-02 11:29:25 -05:00
c1c5737f80
Re-enabling contracts in tests in build.xml
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-- Left contracts turned off in original clover commit
2013-01-02 11:29:25 -05:00
3d1c107f9d
Detect if clover is present in build.xml. Automatically clean clover db in ant clean, if present
2013-01-02 11:29:24 -05:00
429567cd3f
Rename to TraverseActiveRegionsUnitTest
2013-01-01 19:20:30 -05:00
57d38aac8a
Temporarily disable due to unknown contracts problem
2013-01-01 19:20:04 -05:00
7748b3816f
Delete the test BAI file as well as the BAM
2013-01-01 19:20:02 -05:00
5afeb465aa
TODOs
2013-01-01 19:19:17 -05:00
03780578bc
Archiving SomaticIndelDetector, RemapAlignments, ReadPair, and associated library code
2012-12-29 14:37:22 -05:00
5558a6b8f7
Deleting / archiving no longer classes
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-- AminoAcidTable and AminoAcid goes to the archive
-- Removing two unused SAMRecord classes
2012-12-29 14:34:17 -05:00
38cc496de8
Move SomaticIndelDetector and associated tools and libraries into private/andrey package
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-- Intermediate commit on the way to archiving SomaticIndelDetector and other tools.
-- SomaticIndelDetector, PairMaker and RemapAlignments tools have been refactored into the private andrey package. All utility classes refactored into here as well. At this point, the SomaticIndelDetector builds in this version of the GATK.
-- Subsequent commit will put this code into the archive so it no longer builds in the GATK
2012-12-29 14:34:08 -05:00
5f84a4ad82
Clover report excludes test files and other non-interesting files from the clover reports
2012-12-29 13:31:07 -05:00
275575462f
Protect against non-standard ref bases. Ryan, please review.
2012-12-26 15:46:21 -05:00
75d5b88a3d
Enabling the Recal Report unit test (which looks like it was never ever enabled)
2012-12-26 15:35:50 -05:00
efceb0d48c
Check for well-encoded reads while fixing mis-encoded ones
2012-12-26 14:30:51 -05:00
f2b7c6f0e1
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2012-12-26 09:20:32 -05:00
64c3a0ff62
Remove dependance on clover in build.xml
2012-12-24 13:53:29 -05:00
af9746af52
Fix merge failure
2012-12-24 13:43:04 -05:00
04cc75aaec
Minor cleanup and expansion of the RecalDatum unit tests
2012-12-24 13:35:58 -05:00
Eric Banks
Joel Thibault
Ryan Poplin
Tad Jordan
Mark DePristo
Chris Hartl
Chris Hartl