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
b53286cc3c
HaplotypeCaller mode to skip assembly and genotyping for performance testing
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-- Added HCPerformance evaluation Qscript
-- Added some docs about one of the HC integration tests
-- HaplotypeCaller / ART performance evaluation script
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
009d2f5705
Removed CMI specific script from GATK repo
2013-01-11 14:33:00 -05:00
e9a8b1a403
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-11 14:18:26 -05:00
9519c3fd6f
(1) add scala script to merge bam files; (2) few change in Queue script that run the new CoveredByNSamplesSites walker
2013-01-11 13:47:05 -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
4ea2c5df43
Updating updateAllLicenses scripts to include archived files
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GSATDG-5
2013-01-11 13:38:05 -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
cc9a2aaee7
Script to identify code without package info
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- package information is critical for the licensing scripts. All java and scala files MUST contain package information.
GSATDG-5
2013-01-11 13:38:05 -05:00
85baf71b39
Merged bug fix from Stable into Unstable
2013-01-11 11:05:27 -05:00
d78539774f
Another RR bug: off by one error led to ArrayIndexOutOfBoundsException when working with multiple samples and the variant region ended 1 base after the end of the last read for a given sample.
2013-01-11 11:05:09 -05:00
79b93f659c
Merged bug fix from Stable into Unstable
2013-01-11 09:20:13 -05:00
67fafbb625
Forgot an include
2013-01-11 09:19:46 -05:00
6bf0cc32f9
When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed.
2013-01-11 09:16:19 -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
3a51823c2a
Clean up imports
2013-01-10 23:35:01 -05:00
e4b7b1955c
Forgot to add the note about length normalization to the QD docs
2013-01-10 23:34:06 -05:00
ff5ac986d8
Fix docs for QD
2013-01-10 23:31:46 -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
9b45e54ae6
Adding package information to stray scala files
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GSATDG-5
2013-01-10 17:45:36 -05:00
6623148838
Removing CMI scripts from the GATK repo
2013-01-10 17:45:36 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
75a0d0b193
Cleaning CRLF terminations in the licenses
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- made all unix style line endings
- removed private license since it was similar to protected license. Made it a symlink.
GSATDG-5
2013-01-10 17:06:29 -05:00
dd177b1714
Removing fully commented out varianteval evaluators
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- Files were completely commmented out, and were screwing up my license script. Dont like them. Removed them.
GSATDG-5
2013-01-10 17:06:12 -05:00
5222f9c397
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 14:40:16 -05:00
b109b124bd
Remove non-ASCII chars
2013-01-10 14:39:56 -05:00
535c4c0d34
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 14:39:34 -05:00
1b535f6d91
I'd like to put these under version control just to be safe. They are components of the LD-corrected PCA/VarianceComponent tool in private/python
2013-01-10 14:37:27 -05:00
1e083b2388
private/protected licenses updated to the version from legal; public should be the old GATK license.
2013-01-10 14:37:07 -05:00
80dec72c53
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-10 14:35:59 -05:00
31a5f88c4f
Expanded unit tests to cover the Concordance Metrics class fairly uniformly.
2013-01-10 14:33:47 -05:00
f801cb3be5
Updating Queue maven version to 0.0.2
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- After changes to the repositories, we are making sure that cmi-queueext is getting the right file.
2013-01-10 13:46:49 -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
4a8466783a
License Parser and update all license scripts
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* Implemented a script that parses and replaces the license (to be used by git on every commit)
* Implemented a shell script that makes use of the license parser to add the license to all java files in the repo
GSA-685 GSATDG-6 GSATDG-16
2013-01-09 15:56:50 -05:00
1a18947abf
Adding new command line argument requested on the forum to control the maximum number of haplotypes that are sent forward for genotyping. In the presence of a large degree of heterozygosity the current algorithm breaks down and so this argument would need to be increased.
2013-01-09 15:54:02 -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
6787f86803
Eliminate the import of DiploidGenotype, which switched public/private underneath me but for some reason didn't stop me from compiling...
2013-01-09 13:23:24 -05:00
Mark DePristo
Mauricio Carneiro
Ami Levy-Moonshine
Eric Banks
Chris Hartl
Chris Hartl
Joel Thibault
Ryan Poplin