6a91902aa2
Fix final merge conflicts
2013-01-11 15:17:18 -05:00
b9a33d3c66
Split original and optimized ART into largely independent pieces
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-- Allows us to cleanly run old and new art, which now have different traversal behavior (on purpose). Split unit tests as well.
2013-01-11 15:17:18 -05:00
02130dfde7
Cleanup ART
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-- Initialize routine captures essential information for running the traversal
2013-01-11 15:17:17 -05:00
9b2be795a7
Initial working version of new ActiveRegionTraversal based on the LocusIteratorByState read stream
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-- Implemented as a subclass of TraverseActiveRegions
-- Passes all unit tests
-- Will be very slow -- needs logical fixes
2013-01-11 15:17:17 -05:00
8b83f4d6c7
Near final cleanup of PileupElement
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-- All functions documented and unit tested
-- New constructor interface
-- Cleanup some uses of old / removed functionality
2013-01-11 15:17:17 -05:00
fb9eb3d4ee
PileupElement and LIBS cleanup
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-- function to create pileup elements in AlignmentStateMachine and LIBS
-- Cleanup pileup element constructors, directing users to LIBS.createPileupFromRead() that really does the right thing
2013-01-11 15:17:17 -05:00
2f2a592c8e
Contracts and documentation for AlignmentStateMachine and LocusIteratorByState
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-- Add more unit tests for both as well
2013-01-11 15:17:17 -05:00
cc1d259cac
Implement get Length and Bases of OfImmediatelyFollowingIndel in PileupElement
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-- Added unit tests for this behavior. Updated users of this code
2013-01-11 15:17:17 -05:00
2c38310868
Create LIBS using new AlignmentStateMachine infrastructure
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-- Optimizations to AlignmentStateMachine
-- Properly count deletions. Added unit test for counting routines
-- AlignmentStateMachine.java is no longer recursive
-- Traversals now use new LIBS, not the old one
2013-01-11 15:17:17 -05:00
80d9b7011c
Complete rewrite of low-level machinery of LIBS, not hooked up
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-- AlignmentStateMachine does what SAMRecordAlignmentState should really do. It's correct in that it's more accurate than the LIB_position tests themselves. This is a non-broken, correct implementation. Needs cleanup, contracts, etc.
-- This version is like 6x slower than the original implementation (according to the google caliper benchmark here). Obvious optimizations for future commit
2013-01-11 15:17:16 -05:00
0ac4352614
LIBS can now (optionally) track the unique reads it uses from the underlying read iterator
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-- This capability is essential to provide an ordered set of used reads to downstream users of LIBS, such as ART, who want an efficient way to get the reads used in LIBS
-- Vastly expanded the multi-read, multi-sample LIBS unit tests to make sure this capability is working
-- Added createReadStream to ArtificialSAMUtils that makes it relatively easy to create multi-read, multi-sample read streams for testing
2013-01-11 15:17:16 -05:00
b3ecfbfce8
Refactor LIBS into component parts, expand unit tests, some code cleanup
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-- Split out all of the inner classes of LIBS into separate independent classes
-- Split / add unit tests for many of these components.
-- Radically expand unit tests for SAMRecordAlignmentState (the lowest level piece of code) making sure at least some of it works
-- No need to change unit tests or integration tests. No change in functionality.
-- Added (currently disabled) code to track all submitted reads to LIBS, but this isn't accessible or tested
2013-01-11 15:17:16 -05:00
2e5d38fd0e
Updating to latest google caliper code
2013-01-11 15:17:16 -05:00
b2990497e2
Refactor LIBS into utils.locusiterator before refactoring
2013-01-11 15:17:16 -05:00
9ed922d562
Updating licenses to Eric's last commit
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- for now we're still running the script by hand, soon automated solution will be in place.
GSATDG-5
2013-01-11 14:33:00 -05:00
bc64d4240f
Licensing update -- batch #2
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- caught all scala files that didn't have proper package information / class names
- included all source files in archive as well
GSATDG-5
2013-01-11 13:38:11 -05:00
28235f57f2
Adding package information to scala scripts that were missing it. Including archived ones.
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GSATDG-5
2013-01-11 13:38:05 -05:00
e7906713d9
Moving some random walkers back to public as requested by Mark. Mauricio will the licenses get updated automatically?
2013-01-11 02:03:43 -05:00
352cb831d0
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 21:27:06 -05:00
fac0bce916
add RunCoveredByNSamplesSites; changes in CoveredByNSamplesSites so it can work in parallel; also, move it to diagnostics
2013-01-10 21:26:49 -05:00
ea8c8573d2
Fixing ParseLicense script for scala syntax
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- Scala allows package objects in its syntax, so the script needs to be aware of that and not add "*/" every time it sees it.
GSATDG-5
2013-01-10 18:24:24 -05:00
e5913e50b2
Updating licenses for all scala files
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GSATDG-5
2013-01-10 17:46:10 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
3e52ce5fa8
Remove DepthOfCoverage.java because it is no longer public
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- Move Pileup.java and PrintReads.java to their new homes
2013-01-10 11:45:38 -05:00
487fb2afb4
Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.
2013-01-09 15:30:46 -05:00
4fa439d89e
Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now
2013-01-09 11:06:10 -05:00
676e79542a
Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.
2013-01-09 10:39:48 -05:00
c87ad8c0ef
Bug fixes related to HC's GGA mode. Tracking just the artificial allele isn't sufficient when there are multiple GGA records that change the reference basis. Also, duplicated records screw up the tracking of merged alleles.
2013-01-09 10:00:46 -05:00
15ca5015cd
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-08 21:53:36 -05:00
d6071728e8
add new walker to find sites with good coverage
2013-01-08 17:10:38 -05:00
264cc9e78d
Resolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class.
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Instead of the GATK Engine creating a new BaseRecalibrator (not clean), it just keeps track of the arguments (clean).
There are still some dependency issues, but it looks like they are related to Ami's code. Need to look into it further.
2013-01-08 16:23:29 -05:00
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
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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.
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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
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
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
f450cbc1a3
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-12-27 21:23:59 -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
Mark DePristo
Mauricio Carneiro
Eric Banks
Ami Levy-Moonshine
Joel Thibault
Ryan Poplin
Tad Jordan
Chris Hartl
Chris Hartl