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
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
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -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
d4b4f95e12
move CatVariants to public
2013-01-07 15:07:16 -05:00
a0219acfaa
Collapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone
2013-01-07 14:55:21 -05:00
35d9bd377c
Moved (nearly) all Walkers from public to protected and removed GATKLite utils
2013-01-07 14:42:40 -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
Mark DePristo
Mauricio Carneiro
Eric Banks
Ami Levy-Moonshine
Ryan Poplin
Tad Jordan
Chris Hartl
Joel Thibault