d4b4f95e12
move CatVariants to public
2013-01-07 15:07:16 -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
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
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
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
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
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
Ami Levy-Moonshine
Eric Banks
Tad Jordan
Ryan Poplin
Mark DePristo
Chris Hartl
Joel Thibault
Chris Hartl