02d1b87326Better error handling for the license scripts
Mauricio Carneiro
2013-01-18 16:01:08 -0500
0fb7b73107Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-18 15:03:42 -0500
826c29827bchange the default VCFs gatherer of the GATK (not just the UG)
Ami Levy-Moonshine
2013-01-18 15:03:12 -0500
63e1a377ccAutomatic license information git-hook
Mauricio Carneiro
2013-01-18 12:13:52 -0500
cac439bc5eOptimized the Allele Biased Downsampling: now it doesn't re-sort the pileup but just removes reads from the original one. Added a small fix that slightly changed md5s.
Eric Banks
2013-01-18 11:17:31 -0500
08d2da9057Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2013-01-18 10:28:45 -0500
bf5748a538Forgot to actually put in the md5. Also with the new change to record pairing and filtering, the multiple-records integration test changed: the indel records (T/TG | T/TGACA) are matched up (rather than left separate) resulting in properly identifying mismatching alleles, rather than HET-UNAVAILABLE and UNAVAILABLE-HET. Very nice.
Chris Hartl
2013-01-18 10:25:36 -0500
f99bd5be6aSmall fix to make the script more generic (thanks Yossi)
Mauricio Carneiro
2013-01-18 10:06:50 -0500
91030e9afaBugfix: records that get paired up during the resolution of multiple-records-per-site were not going into genotype-level filtering. Caught via testing.
Chris Hartl
2013-01-18 09:49:48 -0500
39c73a6cf51. Ryan and I noticed that the FisherStrand annotation was completely busted for indels with reduced reads; fixed. 2. While making the previous fix and unifying FS for SNPs and indels, I noticed that FS was slightly broken in the general case for indels too; fixed. 3. I also fixed a minor bug in the Allele Biased Downsampling code for reduced reads.
Eric Banks
2013-01-18 03:35:48 -0500
6a903f2c23I finally gave up on trying to get the Haplotype/Allele merging to work in the HaplotypeCaller. I've resigned myself instead to create a mapping from Allele to Haplotype. It's cheap so not a big deal, but really shouldn't be necessary. Ryan and I are talking about refactoring for GATK2.5.
Eric Banks
2013-01-18 01:21:08 -0500
6db3e473afBetter error message for bad qual
Eric Banks
2013-01-17 10:30:04 -0500
953592421bI think we got out of sync with the HC tests as we were clobbering each other's changes. Only differences here are to some RankSumTest values.
Eric Banks
2013-01-17 09:19:21 -0500
ded659232bMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-16 22:49:56 -0500
a623cca89aBug fix for HaplotypeCaller, as reported on the forum: when reduced reads didn't completely overlap a deletion call, we were incorrectly trying to find the reference position of a base on the read that didn't exist. Added integration test to cover this case.
Eric Banks
2013-01-16 22:47:58 -0500
fcb3c6dc2afix small bugs in scala files
Ami Levy-Moonshine
2013-01-16 22:42:20 -0500
dbb69a1e10Need to use ints for quals in HaplotypeScore instead of bytes because of overflow (they are summed when haplotypes are combined)
Eric Banks
2013-01-16 22:33:16 -0500
e15d4ad278Addition of moltenize argument for moltenized tabular output. NRD/NRS not moltenized because there are only two columns.
Chris Hartl
2013-01-16 18:00:23 -0500
738c24a3b1Add tests to ensure that all insertion reads appear in the active region traversal
Mark DePristo
2013-01-16 16:25:11 -0500
3c476a92a2Add dummy functionality (currently throws an error) to allow HC to include unmapped reads during assembly and calling
Mark DePristo
2013-01-16 15:56:03 -0500
79bc818022Bug fix for VariantsToVCF: old dbSNP files can have '-' as reference base and those records always need to be padded.
Eric Banks
2013-01-16 16:15:58 -0500
4cf34ee9daBug fix to FisherStrand: do not let it output INFINITY. This all needs to be unit tested, but that's coming on the horizon.
Eric Banks
2013-01-16 15:35:04 -0500
2a42b47e4aMassive expansion of ActiveRegionTraversal unit tests, resulting in several bugfixes to ART
Mark DePristo
2013-01-16 15:29:26 -0500
ddcb33fcf8Cache result of getLocation() in Shard so we don't performance expensive calculation over and over
Mark DePristo
2013-01-16 12:09:36 -0500
4d0e7b50ecArtificialBAMBuilder utility class for creating streams of GATKSAMRecords with a variety of properties
Mark DePristo
2013-01-15 16:45:45 -0500
ec1cfe6732Oops, forgot to add 1 of my files
Eric Banks
2013-01-16 15:05:49 -0500
e47a389b26Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-16 14:59:11 -0500
d18dbcbac1Added tests for changing IUPAC bases to Ns, for failing on bad ref bases, and for the HaplotypeCaller not failing when running over a region with an IUPAC base.
Eric Banks
2013-01-16 14:55:33 -0500
4ffb43079fRe-committing the following changes from Dec 18: Refactored interval specific arguments out of GATKArgumentCollection into InvtervalArgumentCollection such that it can be used in other CommandLinePrograms. Updated SelectHeaders to print out full interval arguments. Added RemoteFile.createUrl(Date expiration) to enable creation of presigned URLs for download over http: or file:.
Khalid Shakir
2013-01-16 12:43:15 -0500
445735a4a5There was no reason to be sharing the Haplotype infrastructure between the HaplotypeCaller and the HaplotypeScore annotation since they were really looking for different things. Separated them out, adding efficiencies for the HaplotypeScore version.
Eric Banks
2013-01-16 11:10:13 -0500
392b5cbcdfThe CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases. This way walkers won't see anything except the standard bases plus Ns in the reference. Added option to turn off this feature (to maintain backwards compatibility).
Eric Banks
2013-01-16 10:22:43 -0500
4fb3e48099Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2013-01-16 00:13:38 -0500
0d282a7750Bam writing from HaplotypeCaller seems to be working on all my test cases. Note that it's a hidden debugging option for now. Please let me know if you notice any bad behavior with it.
Eric Banks
2013-01-16 00:12:02 -0500
c8de9b92d0Updating CountReadsInActiveRegionsIntegrationTest integration tests due to new ART
Mark DePristo
2013-01-15 15:41:33 -0500
327169b283Refactor the method that identifies the site overlap type into the type enum class (so it can be used elsewhere potentially).
Chris Hartl
2013-01-15 12:13:45 -0500
d3baa4b8caHave Haplotype extend the Allele class. This way, we don't need to create a new Allele for every read/Haplotype pair to be placed in the PerReadAlleleLikelihoodMap (very inefficient). Also, now we can easily get the Haplotype associated with the best allele for a given read.
Eric Banks
2013-01-15 11:36:20 -0500
3c37ea014bRetire original TraverseActiveRegion, leaving only the new optimized version
Mark DePristo
2013-01-15 10:24:45 -0500
94800771e31. Initial implementation of bam writing for the HaplotypeCaller with -bam argument; currently only assembled haplotypes are emitted. 2. Framework is set up in the VariantAnnotator for the HaplotypeCaller to be able to call in to annotate dbSNP plus comp RODs. Until the HC uses meta data though, this won't work.
Eric Banks
2013-01-15 10:19:18 -0500
39bc9e999dAdd a test to LocusIteratorByState to ensure that we aren't holding reads anywhere
Mark DePristo
2013-01-14 08:34:42 -0500
b8b2b9b2deManagingReferenceOrderedView optimization: don't allow a fresh RefMetaDataTracker in the frequent case where there's no reference meta data
Mark DePristo
2013-01-13 20:44:28 -0500
7eea6b8f92ReservoirDownsampler optimizations
Mark DePristo
2013-01-13 20:43:10 -0500
c7f0ca8ac5Optimization for LIBS: PerSampleReadStateManager now uses a simple LinkedList of AlignmentStateMachine
Mark DePristo
2013-01-13 14:36:25 -0500
5a5422e4f8Refactor PerSampleReadStates into a separate class
Mark DePristo
2013-01-13 13:02:17 -0500
5c2799554aRefactor updateReadStates into PerSampleReadStateManager, add tracking of downsampling rate
Mark DePristo
2013-01-13 12:23:51 -0500
a4334a67e0SamplePartitioner optimizations and bugfixes
Mark DePristo
2013-01-12 19:22:36 -0500
19288b007dLIBS bugfix: kept reads now only (correctly) includes reads that at least passed the reservoir
Mark DePristo
2013-01-12 13:39:19 -0500
83fcc06e28LIBS optimizations and performance tools
Mark DePristo
2013-01-12 12:41:13 -0500
ec05ecef60getAdaptorBoundary returns an int, not an Integer, as this was taking 30% of the allocation effort for LIBS
Mark DePristo
2013-01-11 18:05:45 -0500
682c59ff04Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2013-01-14 13:27:34 -0500
61bc334df1Ensure output table formatting does not contain NaNs. For (0 eval ref calls)/(0 comp ref calls), set the proportion to 0.00.
Chris Hartl
2013-01-14 09:21:30 -0500
c33105beadMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2013-01-13 18:27:38 -0500
3a6b4b43b7Backporting LIBSPerformance improvements to original commit
Mark DePristo
2013-01-13 09:53:10 -0500
a7fe334a3fcalculating the md5s for the new tests.
Ryan Poplin
2013-01-11 15:43:52 -0500
65afec2a53Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2013-01-11 15:22:52 -0500
85b529ccedUpdating MD5s in HC and UG that changed due to new LIBS
Mark DePristo
2013-01-11 15:16:47 -0500
f204908a94Add some todos for future optimization to LIBS
Mark DePristo
2013-01-11 14:19:32 -0500
e88dae2758LocusIteratorByState operates natively on GATKSAMRecords now
Mark DePristo
2013-01-11 14:01:02 -0500
94cb50d3d6Retire LegacyLocusIteratorByState
Mark DePristo
2013-01-11 11:37:26 -0500
cc0c1b752aDelete old LocusIteratorByState, leaving only new LIBS and legacy
Mark DePristo
2013-01-11 10:59:24 -0500
bd03511e35Updating AlignmentStateMachinePerformance to include some more useful performance assessments
Mark DePristo
2013-01-11 10:44:39 -0500
9e23c592e6ReadBackedPileup cleanup
Mark DePristo
2013-01-10 16:26:51 -0500
e3e3ae29b2Final documentation for LocusIteratorByState
Mark DePristo
2013-01-11 08:35:04 -0500
6a91902aa2Fix final merge conflicts
Mark DePristo
2013-01-10 20:48:55 -0500
b9a33d3c66Split original and optimized ART into largely independent pieces
Mark DePristo
2013-01-10 20:31:26 -0500
02130dfde7Cleanup ART
Mark DePristo
2013-01-10 20:02:07 -0500
9b2be795a7Initial working version of new ActiveRegionTraversal based on the LocusIteratorByState read stream
Mark DePristo
2013-01-10 15:18:17 -0500
8b83f4d6c7Near final cleanup of PileupElement
Mark DePristo
2013-01-10 12:17:48 -0500
fb9eb3d4eePileupElement and LIBS cleanup
Mark DePristo
2013-01-09 16:40:45 -0500
2f2a592c8eContracts and documentation for AlignmentStateMachine and LocusIteratorByState
Mark DePristo
2013-01-09 15:14:42 -0500
cc1d259cacImplement get Length and Bases of OfImmediatelyFollowingIndel in PileupElement
Mark DePristo
2013-01-09 08:36:29 -0500
2c38310868Create LIBS using new AlignmentStateMachine infrastructure
Mark DePristo
2013-01-08 13:12:22 -0500
80d9b7011cComplete rewrite of low-level machinery of LIBS, not hooked up
Mark DePristo
2013-01-07 21:27:55 -0500
b53286cc3cHaplotypeCaller mode to skip assembly and genotyping for performance testing
Mark DePristo
2013-01-07 13:40:06 -0500
0ac4352614LIBS can now (optionally) track the unique reads it uses from the underlying read iterator
Mark DePristo
2013-01-06 15:54:15 -0500
b3ecfbfce8Refactor LIBS into component parts, expand unit tests, some code cleanup
Mark DePristo
2013-01-06 11:55:18 -0500
2e5d38fd0eUpdating to latest google caliper code
Mark DePristo
2013-01-07 21:25:44 -0500
b2990497e2Refactor LIBS into utils.locusiterator before refactoring
Mark DePristo
2013-01-05 13:06:47 -0500
e952296c10Adding HC GGA integration test to cover duplicated input alleles.
Ryan Poplin
2013-01-11 15:01:27 -0500
7f7f40f851Adding additional HC GGA integration tests to cover more complicated input alleles.
Ryan Poplin
2013-01-11 14:36:21 -0500
9ed922d562Updating licenses to Eric's last commit
Mauricio Carneiro
2013-01-11 14:28:21 -0500
009d2f5705Removed CMI specific script from GATK repo
Mauricio Carneiro
2013-01-11 14:27:37 -0500
e9a8b1a403Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-11 14:18:26 -0500
9519c3fd6f(1) add scala script to merge bam files; (2) few change in Queue script that run the new CoveredByNSamplesSites walker
Ami Levy-Moonshine
2013-01-11 13:47:05 -0500
4ea2c5df43Updating updateAllLicenses scripts to include archived files
Mauricio Carneiro
2013-01-11 13:27:31 -0500
28235f57f2Adding package information to scala scripts that were missing it. Including archived ones.
Mauricio Carneiro
2013-01-11 13:17:32 -0500
cc9a2aaee7Script to identify code without package info
Mauricio Carneiro
2013-01-11 13:16:23 -0500
85baf71b39Merged bug fix from Stable into Unstable
Eric Banks
2013-01-11 11:05:27 -0500
d78539774fAnother 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.
Eric Banks
2013-01-11 11:05:09 -0500
79b93f659cMerged bug fix from Stable into Unstable
Eric Banks
2013-01-11 09:20:13 -0500
67fafbb625Forgot an include
Eric Banks
2013-01-11 09:19:46 -0500
6bf0cc32f9When 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.
Eric Banks
2013-01-11 09:16:19 -0500
e7906713d9Moving some random walkers back to public as requested by Mark. Mauricio will the licenses get updated automatically?
Eric Banks
2013-01-11 02:03:43 -0500
3a51823c2aClean up imports
Eric Banks
2013-01-10 23:35:01 -0500
e4b7b1955cForgot to add the note about length normalization to the QD docs
Eric Banks
2013-01-10 23:34:06 -0500
ff5ac986d8Fix docs for QD
Eric Banks
2013-01-10 23:31:46 -0500
352cb831d0Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2013-01-10 21:27:06 -0500
fac0bce916add RunCoveredByNSamplesSites; changes in CoveredByNSamplesSites so it can work in parallel; also, move it to diagnostics
Ami Levy-Moonshine
2013-01-10 21:26:49 -0500
Mauricio Carneiro
Ami Levy-Moonshine
Eric Banks
Chris Hartl
Mark DePristo
Khalid Shakir
Menachem Fromer
Ryan Poplin