5222f9c397Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Chris Hartl
2013-01-10 14:40:16 -0500
b109b124bdRemove non-ASCII chars
Eric Banks
2013-01-10 14:39:56 -0500
535c4c0d34Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Chris Hartl
2013-01-10 14:39:34 -0500
1b535f6d91I'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
Chris Hartl
2013-01-10 14:37:27 -0500
1e083b2388private/protected licenses updated to the version from legal; public should be the old GATK license.
Eric Banks
2013-01-10 14:37:07 -0500
80dec72c53Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2013-01-10 14:35:59 -0500
31a5f88c4fExpanded unit tests to cover the Concordance Metrics class fairly uniformly.
Chris Hartl
2013-01-10 14:33:47 -0500
f801cb3be5Updating Queue maven version to 0.0.2 - After changes to the repositories, we are making sure that cmi-queueext is getting the right file.
Mauricio Carneiro
2013-01-10 13:46:49 -0500
3e52ce5fa8Remove DepthOfCoverage.java because it is no longer public - Move Pileup.java and PrintReads.java to their new homes
Joel Thibault
2013-01-10 11:44:24 -0500
4a8466783aLicense Parser and update all license scripts
Mauricio Carneiro
2013-01-07 14:46:28 -0500
1a18947abfAdding 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.
Ryan Poplin
2013-01-09 15:54:02 -0500
487fb2afb4Bug 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.
Ryan Poplin
2013-01-09 15:30:46 -0500
077ea8f30cAdded more options to control RBP behavior; raised default RBP PQ threshold to 20
Menachem Fromer
2013-01-09 14:44:22 -0500
6089a4bf62Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2013-01-09 13:26:40 -0500
6787f86803Eliminate the import of DiploidGenotype, which switched public/private underneath me but for some reason didn't stop me from compiling...
Chris Hartl
2013-01-09 13:23:24 -0500
c1de92b511Add in some todo items
Chris Hartl
2013-01-09 13:16:06 -0500
8d126161e2Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2013-01-09 13:15:04 -0500
3a0dd4b175Oops, I broke the build. NOW we shouldn't have any more public->protected dependancies.
Eric Banks
2013-01-09 11:12:28 -0500
a921b06e02Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-09 11:06:17 -0500
4fa439d89eMove 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
Eric Banks
2013-01-09 11:06:10 -0500
da3aa68492Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2013-01-09 11:04:53 -0500
396bce1f28Reverting this change until we can figure out the right thing to do here.
Ryan Poplin
2013-01-09 10:51:30 -0500
676e79542aBring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.
Eric Banks
2013-01-09 10:39:48 -0500
c87ad8c0efBug 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.
Ryan Poplin
2013-01-09 10:00:46 -0500
ad7c2a08d4Normalize by the event type counts, not the total genotype counts: more useful normalization.
Chris Hartl
2013-01-09 09:12:41 -0500
b56754606bInitial break-out of GenotypeConcordance as a standalone walker. Some basic functionality testing. Currently performs only a pairwise comparison, but is very careful about proper tabulation through the GenotypeType enum.
Chris Hartl
2013-01-09 00:34:07 -0500
15ca5015cdMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-08 21:53:36 -0500
d6071728e8add new walker to find sites with good coverage
Ami Levy-Moonshine
2013-01-08 17:10:38 -0500
13c05a6cf2Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2013-01-08 16:40:44 -0500
6984ab0c78Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing
Menachem Fromer
2013-01-08 16:40:32 -0500
264cc9e78dResolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class. Instead of the GATK Engine creating a new BaseRecalibrator (not clean), it just keeps track of the arguments (clean).
Eric Banks
2013-01-08 16:23:29 -0500
ee7d85c6e6Move around the DiploidGenotype classes (so it can be used by the GATKPaperGenotyper)
Eric Banks
2013-01-08 15:53:11 -0500
0e2e672521Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-08 15:46:39 -0500
f0bd1b5ae5Okay, 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.
Eric Banks
2013-01-08 15:46:32 -0500
9cbb2b868fErrorRatePerCycleIntegrationTest fix
Tad Jordan
2013-01-08 14:53:07 -0500
0841ce3de5Bug fix to exclude callset capability in AssessNA12878.
Ryan Poplin
2013-01-08 13:26:16 -0500
245fcc8bb5Merged bug fix from Stable into Unstable
Eric Banks
2013-01-08 12:59:15 -0500
d6146d369aRemove all of the references to ProgramElementDoc
Eric Banks
2013-01-08 12:58:31 -0500
b099e2b4aeMoving integration tests to protected
Eric Banks
2013-01-08 09:34:08 -0500
dfe4cf1301When merging the PerReadAlleleLikelihoodMap classes, I forgot to initialize the underlying objects. This was causing the LargeScaleTests to fail.
Eric Banks
2013-01-08 09:24:12 -0500
9e6c2afb28Not sure why IntelliJ didn't add this for commit like the other dirs
Eric Banks
2013-01-07 18:11:07 -0500
3787ee6de7Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-07 17:07:29 -0500
673ed0aaa6remove public-protected dependency by commeting out some code that should be re-included after all the walkers will be in portected (added some todos)
Ami Levy-Moonshine
2013-01-07 17:07:23 -0500
47d030a52dOops, move the covariates over too
Eric Banks
2013-01-07 15:47:25 -0500
35699a8376Move bqsr utils to protected
Eric Banks
2013-01-07 15:41:21 -0500
5371613ad1Tests 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).
Eric Banks
2013-01-07 15:27:43 -0500
8bbb9e1cc2Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-07 15:07:25 -0500
d4b4f95e12move CatVariants to public
Ami Levy-Moonshine
2013-01-07 15:07:16 -0500
1a4b112865Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-07 15:00:35 -0500
a0219acfaaCollapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone
Eric Banks
2013-01-07 14:55:21 -0500
d3e2352072Moved processing pipelines to private
Mauricio Carneiro
2013-01-07 14:49:57 -0500
35d9bd377cMoved (nearly) all Walkers from public to protected and removed GATKLite utils
Eric Banks
2013-01-07 14:42:40 -0500
6904baf458merge branchs
Ami Levy-Moonshine
2013-01-07 14:20:03 -0500
78f7a4e300Received permission from Mauricio to archive the DPP and PBPP PipelineTests
Eric Banks
2013-01-07 14:03:08 -0500
b5faf00fcesame commit as yesterday, since I moved to he new computer
Ami Levy-Moonshine
2013-01-07 13:55:29 -0500
b4e7b3d691Fixed precision problem in the Bayesian calculation of Qemp: we need to cap below max integer because the MathUtils code add +1.
Eric Banks
2013-01-07 13:07:36 -0500
04e3978b04Fixed VariantEval tests
Tad Jordan
2013-01-07 12:08:39 -0500
4f95f850b3Bug 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.
Ryan Poplin
2013-01-07 11:05:44 -0500
d3c2c97fb2Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-06 23:35:47 -0500
38c3f22531now using variant.jar
Ami Levy-Moonshine
2013-01-06 23:33:17 -0500
a1de84c6c1remove annotation from LasrgeScalePipeline and change eval to wrok with the srandard interval file
Ami Levy-Moonshine
2013-01-06 23:28:38 -0500
c554d9db25add TODO
Ami Levy-Moonshine
2013-01-06 23:04:38 -0500
81eef3aa37merge development branchs of log-less HMM and FastGatherer to master
Ami Levy-Moonshine
2013-01-06 23:01:58 -0500
0249e1f497Resolving merge conflicts from VCF move
Eric Banks
2013-01-06 14:32:31 -0500
8822b8e7c8Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.
Eric Banks
2013-01-06 14:30:45 -0500
ef638489d5Fixing BQSR gatherer test to keep up to date with latest changes
Eric Banks
2013-01-06 14:07:59 -0500
ea21dc9cfbI just committed this - why didn't it work before? Trying again...
Eric Banks
2013-01-06 12:44:13 -0500
52067f0549Handle merge conflicts
Eric Banks
2013-01-06 12:29:12 -0500
bf25e151ffHandle long->int precision in Bayesian estimate
Eric Banks
2013-01-06 12:26:32 -0500
b73d72fe94update docs for LEftAlignVariants
Eric Banks
2013-01-06 01:56:57 -0500
b403c269e9Make multi-threaded progress meter daemon unit test more robust
Mark DePristo
2013-01-05 12:59:18 -0500
2ab55e4ee7Fixing bug in TraverseDuplicates.printProgress call: only passes in single location of genome loc
Mark DePristo
2013-01-04 17:14:32 -0500
69bf70c42eCleanup and more unit tests for RecalibrationTables in BQSR
Mark DePristo
2013-01-04 17:13:31 -0500
9df30880cbMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Chris Hartl
2013-01-04 17:15:22 -0500
01738e70c3Archive the experimental Active Region Traversals
Joel Thibault
2013-01-04 16:53:50 -0500
7b7efa0fffAdd in the AAL as an experimental covariate, in case it's wanted.
Chris Hartl
2013-01-04 16:47:26 -0500
41bc416b65Remove AAL and update MD5s.
Chris Hartl
2013-01-04 16:46:14 -0500
bce6fce58dResolving merge conflicts after Mark's latest push
Eric Banks
2013-01-04 14:46:39 -0500
dd7f5e2be7Hooking up the Bayesian estimate code for calculating Qemp in BQSR; various fixes after adding unit tests.
Eric Banks
2013-01-04 14:43:11 -0500
80b531f695emit all sites where more than 90% of the samples have good coverage
Ami Levy-Moonshine
2013-01-04 14:27:50 -0500
ab5526b372More TODOs
Joel Thibault
2013-01-04 13:24:57 -0500
96efa8b19fauto-merge
Ryan Poplin
2013-01-04 12:21:03 -0500
9b993c647fAdding a manual review site.
Ryan Poplin
2013-01-04 12:20:25 -0500
fe06912a87Removed sorting by row from walkers
Tad Jordan
2013-01-04 11:52:04 -0500
810e2da1d4Cleanup and unit tests for EventType and ReadRecalibrationInfo in BQSR
Mark DePristo
2013-01-04 11:38:58 -0500
a5901cdd20Bugfix for printProgress in TraverseReadsNano
Mark DePristo
2013-01-04 10:54:02 -0500
6af1e21758Minor cleanup of GATKPerformanceOverTime
Mark DePristo
2013-01-03 16:48:46 -0500
bbdf9ee91bBQSR cleanup: merge Advanced and Standard recalibration engine into just the RecalibrationEngine
Mark DePristo
2013-01-03 16:47:45 -0500
7df47418d8BQSR optimization: make RecalibrationTables thread-local, and merge results in onTraversalDone
Mark DePristo
2013-01-03 14:43:36 -0500
1ba8d47a81Unit tests for ProgressMeterDaemon
Mark DePristo
2013-01-02 16:12:08 -0500
fbee4c11f1Unit tests for ProgressMeterData
Mark DePristo
2013-01-02 15:20:25 -0500
27722a15e5Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2013-01-04 11:38:18 -0500
e89a1d711eAdding ability to exclude callsets from AssessNA12878.
Ryan Poplin
2013-01-04 11:38:05 -0500
319d651e4aInitial updates for ActiveRegionShard
Joel Thibault
2013-01-03 15:49:40 -0500
Mauricio Carneiro
Chris Hartl
Eric Banks
Chris Hartl
Joel Thibault
Ryan Poplin
Menachem Fromer
Ami Levy-Moonshine
Tad Jordan
Mark DePristo