41b5f25bf3Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
Kristian Cibulskis
2012-10-23 13:34:43 -0400
9d451b5154DEV-116 #resolve #time 3m
Kristian Cibulskis
2012-10-23 13:34:11 -0400
0cce1ae8b2When gathering VCFs, using CombineVariants from the current classpath, and not the GATK used to run the command. This was a concern for external modules that bundled the engine but not CombineVariants.
kshakir
2012-10-23 12:38:39 -0400
c210b7cde4Merge GATK repo into CMI-GATK
Mauricio Carneiro
2012-10-23 10:59:11 -0400
bbf7a0fb09Adding integration test to ReduceReads coreduction DEV-117 #resolve
Mauricio Carneiro
2012-10-22 16:09:49 -0400
1ec137a40cAdd support for calculating DoC with flanking intervals added
Menachem Fromer
2012-10-23 10:41:07 -0400
118da1cd1cMore test data for fastq-bam: new short.interval_list with correct header based on reference dict. b) New interval/bait sets with corrected header for decoy contig in b37 c) New metadata file for test fastqs d) Updated test fastqs as previous version was generated with bad intervals
Guillermo del Angel
2012-10-23 09:24:09 -0400
f838815343Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc
Mark DePristo
2012-10-23 06:47:53 -0400
7860ff7981a) Resolve [#DEV-56] - test data with indels in new directory private/testdata/CMITestData/. b) Skeleton (not yet working) of fastq-BAM unit test, c) misc bug fixes for QC functions to work (not done yet)
Guillermo del Angel
2012-10-22 19:59:15 -0400
15b28e61cdRetiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine
Mark DePristo
2012-10-22 16:54:38 -0400
fd59e7d5f6Better error message when generic types are erased from scala collections.
Khalid Shakir
2012-10-22 16:27:31 -0400
008df54575Bug fix in GATKSAMRecord.getSoftEnd() for reads that are entirely clipped.
Ryan Poplin
2012-10-22 14:21:52 -0400
90f59803fdMaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels
Mark DePristo
2012-10-22 09:58:43 -0400
97dc3664c9Fixed yet another NPE related to the ArgumentTypeDescriptor vs. ArgumentMatchValue. Added integration test based on GSA-621.
Khalid Shakir
2012-10-22 12:04:23 -0400
ccae6a5b92Fixed the RR bug I (knowingly) introduced last week: turns out we can't trust a context size's worth of data from the previous marking. I think Mauricio warned me about this but I forgot.
Eric Banks
2012-10-22 11:48:34 -0400
1da4ad9607new class to test the quals of reduced bam vs non-reduced bam
Ami Levy Moonshine
2012-10-22 10:45:53 -0400
5640661368Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-10-22 08:21:43 -0400
9f2851d769Updating UnifiedGenotyperGeneralPloidyIntegrationTest following rebasing
Mark DePristo
2012-10-21 20:23:11 -0400
eb6c9a1a79Disable EfficiencyMonitoringThreadFactoryUnitTest
Mark DePristo
2012-10-21 09:57:31 -0400
5296de8251Fix UnifiedArgumentCollection constructor logic error
Mark DePristo
2012-10-21 08:20:39 -0400
d21e42608aUpdating integration tests for minor changes due to switching to EXACT_INDEPENDENT model by default
Mark DePristo
2012-10-21 08:10:43 -0400
6b6caf8e3aBugfix for indel DP calculations using reduced reads
Mark DePristo
2012-10-19 14:42:00 -0400
0fcd358aceOriginal EXACT model implementation lives, providing another reference (bi-allelic only) EXACT model
Mark DePristo
2012-10-19 19:33:47 -0400
0fb8274507Fix contact on sorting of AFCalcResults
Mark DePristo
2012-10-19 17:11:31 -0400
eaffb814d3IndependentExactAFCalc is now the default EXACT model implementation
Mark DePristo
2012-10-18 13:34:51 -0400
326f429270Bugfixes to make new AFCalc system pass integrationtests
Mark DePristo
2012-10-19 14:06:41 -0400
695cf83675More docs and contracts for classes in genotyper.afcalc
Mark DePristo
2012-10-18 07:38:32 -0400
99c9031cb4Merge AFCalcResultTracker into StateTracker, cleanup
Mark DePristo
2012-10-17 20:41:33 -0400
9c63cee9fcMoving pnrm to UnifiedArgumentCollection so it's available with the HaplotypeCaller
Mark DePristo
2012-10-17 18:36:14 -0400
e9b7324dc1Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-21 12:38:49 -0400
67b9e7319eFix for integration tests: new criterion in AF exact calculation model to trim alleles based on likelihoods does produce better results and resulting alleles changed in 2 sites at integration tests (and all subsequent sites after this had minor annotation differences due to RankSum dithering)
Guillermo del Angel
2012-10-21 12:38:33 -0400
0616b98551Not sure why we were setting the UAC variables instead of the simpleUAC ones when that's what we wanted.
Eric Banks
2012-10-21 08:26:26 -0400
d44d5b8275Fix RawHapMapCodec so that it can build indexes. Minor fixes to VCF codec.
Eric Banks
2012-10-21 01:29:59 -0400
841a906f21Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet.
Eric Banks
2012-10-20 23:31:56 -0400
2c624f76c8Refactoring the Unified (and Standard) Argument Collections because it was really ugly that the subclass had to do all the cloning for the super class. The clone() method is really not recommended best practice in Java anyways, so I changed it so that we use standard overloaded constructors. Confirmed that the Haplotype Caller --help docs do not include UG-specific arguments.
Eric Banks
2012-10-20 20:35:54 -0400
a647f1e076Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.
Ryan Poplin
2012-10-20 16:38:18 -0400
25e7dcc46fPerformance tests: only need 1 iteration now that we're no longer running on the farm
David Roazen
2012-10-19 22:11:59 -0400
45f64425a3Update read metrics per shard rather than locus
Joel Thibault
2012-10-19 14:29:02 -0400
637e0cf151CountReads does not permit the use of output files
Joel Thibault
2012-10-11 13:59:21 -0400
a5333006bbMark @Output as required
Joel Thibault
2012-10-18 14:00:22 -0400
6557b7e364Qscript for validating the pooledCaller against a single validation set
Yossi Farjoun
2012-10-19 14:39:57 -0400
2ef456d51aAdded explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems. Changed ReflectionUtils.getGenericTypes' order of looking for @ClassType since the primitive generic wasn't completely erased, only changed to Object which is incorrect. More fixes to @Arguments labeled as java.io.File via incorrect @Input annotation. Put in a default undocumented implementation of @Argument doc() to match the one added to @Input.
Khalid Shakir
2012-10-19 13:19:56 -0400
4622896312Oops, killed contracts
Eric Banks
2012-10-19 13:04:05 -0400
9c088fe3feActually a better implementation of GATKSAMRecord.getSoftStart(). Last commit was all wrong. Oops.
Eric Banks
2012-10-19 12:41:24 -0400
4f768e2f58redo QC picard parts
Guillermo del Angel
2012-10-19 12:25:46 -0400
860ab1e539Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-10-19 12:16:30 -0400
f7bd4998fcNo need for dummy GLs
Eric Banks
2012-10-19 12:13:59 -0400
f08e5a44daBetter implementation of GATKSAMRecord.getSoftStart()
Eric Banks
2012-10-19 12:11:18 -0400
deca564aefMerge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-10-19 12:01:49 -0400
d3cf37dfafBug fix for general ploidy model: when choosing the most likely alternate allele(s), you need to weight the likelihood mass by the ploidy of the specific alleles (otherwise all alt alleles will have the same probability). This fixes Yossi's issue with pooled validation calling. This may brek integration tests, but I will leave that to GdA to handle.
Eric Banks
2012-10-19 12:01:45 -0400
27d8d3f51eRR optimization: don't recalculate the entire bitset of variant sites for every read added to the sliding window. Instead, reuse as much of the previously calculated bitset as you can (basically from the window start until the start of the new read minus the context size). In some awfully performing regions this cuts down the runtime in half, although in others this doesn't seem to help much (so clearly something else is going on). Note that I still need to fix one last bug here, but it's almost done.
Eric Banks
2012-10-19 11:59:34 -0400
1658975f43Intermediate fix
Guillermo del Angel
2012-10-19 11:01:56 -0400
6da7fb4132* resolved [DEV-88]
Kristian Cibulskis
2012-10-19 10:47:10 -0400
403654d40aFixed null checkes in ArgumentTypeDescriptor due to ArgumentMatchValue updates. Fixed @Arguments such as scatter count that were labeled as java.io.File via incorrect @Input annotation.
Khalid Shakir
2012-10-18 16:57:15 -0400
5444f33f04Some final touches (pointers --> variables).
Christopher Hartl
2012-10-18 16:45:14 -0400
dd42ca112dNext big holdup: numpy.diag(N*p*(1-p)) is way too slow. Place this into a c routine as well.
Christopher Hartl
2012-10-18 16:08:14 -0400
a4184716d8Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-10-18 15:42:31 -0400
3db38c5a93Bug fix: inbreeding coeff shouldn't be computed in ref-only sites
Guillermo del Angel
2012-10-18 15:42:14 -0400
a0381f15afMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ami Levy Moonshine
2012-10-18 14:49:34 -0400
f665c6ceb9minor chnage (add 129 to the dbSNP name
Ami Levy Moonshine
2012-10-18 14:48:37 -0400
b4e69239ddIn order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.
Ryan Poplin
2012-10-18 14:31:15 -0400
3504f71b6bFixing a null pointer exception bug for DEV-10
Mauricio Carneiro
2012-10-18 13:58:38 -0400
c39578ec89Undo git mess - revert back to origin and THEN comment out QC metrics
Guillermo del Angel
2012-10-18 12:49:26 -0400
38656780b0Revert "comment out QC metrics until picard jar path gets resolved"
Guillermo del Angel
2012-10-18 12:45:21 -0400
d8562298c9comment out QC metrics until picard jar path gets resolved
Guillermo del Angel
2012-10-18 12:43:00 -0400
262c84a459(1) Add RR step to the general calling script. \n (2) add more modularity to the script
Ami Levy Moonshine
2012-10-18 10:47:17 -0400
d3fc797cfeSelectVariants is actually *NOT* NanoSchedulable
Mark DePristo
2012-10-18 10:42:20 -0400
f20fa9d082SelectVariants is actually NanoSchedulable
Mark DePristo
2012-10-18 10:19:34 -0400
97abb98c0bBugfix for bad nt / nct argument detection in MicroScheduler
Mark DePristo
2012-10-18 10:19:21 -0400
54f698422cBetter implementation for getSoftEnd() in GATKSAMRecord
Eric Banks
2012-10-18 09:01:51 -0400
d8ca5028ddAlter the convergence criteria not to focus on beta (which we don't care about here) but rather on the convergence of the predictors. This leads to far quicker convergence in the case where some responses can be completely explained (so some of the true beta values are infinite).
Christopher Hartl
2012-10-18 09:01:31 -0400
ce70230a2eEvaluating the logistic regression given a large matrix of predictors was a killer roadblock (>99% runtime). NumPy's applyOverDimension didn't cut it. Instead: write the appropriate function as a c extension and call into it.
Christopher Hartl
2012-10-17 23:52:47 -0400
acc0fb2f7aMerge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ami Levy Moonshine
2012-10-17 22:16:02 -0400
20ffbcc86eRR optimization: profiling was showing that the BaseCounts class was a major bottleneck because the underlying implementation was a HashMap. Given that the map index was an indexable Enum anyways, it makes a lot more sense to implement as a native array. Knocks 30% off the runtime in bad regions.
Eric Banks
2012-10-17 21:44:53 -0400
bfb73e1c5bFix merge conflicts
Guillermo del Angel
2012-10-17 20:13:51 -0400
a30ac7a778Add uniform threading argument and enable multithreading in BQSR - will save over 40 hours of runtime
Guillermo del Angel
2012-10-17 20:08:22 -0400
f45e7ffbd8Updated CMIBAMPP to use latest design of script() generating local paths and pushing bits back to <provided_s3_bucket/<provided_s3_prefix><argument fullName>.
kshakir
2012-10-17 19:59:23 -0400
55ac4ba70bAdded another utility that can convert to RemoteFiles. QScripts will now generate remote versions of files if the caller has not already passed in remote versions (or the QScript replaces the passed in remote references... not good) Instead of having yet another plugin, combined QStatusMessenger and RemoteFileConverter under general QCommandPlugin trait.
kshakir
2012-10-17 19:39:03 -0400
32ee2c7dffRefactored the compression interface per sample in ReduceReadsa
Mauricio Carneiro
2012-10-15 17:04:29 -0400
b57df6cac8Bringing CMI changes into the main GATK repo.
Mauricio Carneiro
2012-10-17 15:23:19 -0400
4dea20b9b5Release of CMI-0.1.0
Mauricio Carneiro
2012-10-17 14:59:36 -0400
8288c30e36Use buffered output for ExactCallLogger
Mark DePristo
2012-10-17 14:14:55 -0400
fa93681f51Scalability test for EXACT models
Mark DePristo
2012-10-17 14:14:41 -0400
c9e7a947c2Improve interface of ExactCallLogger, use it to have a more informative AFCalcPerformanceTest
Mark DePristo
2012-10-17 08:34:47 -0400
097bc2329cMerge branch 'develop'
Guillermo del Angel
2012-10-17 13:55:41 -0400
d6be657966BQSR profiling: execute multiple operations per thread so that threading overhead doesn't dominate
David Roazen
2012-10-16 16:23:42 -0400
98b83421a3A faster implementation of the Plink Bed Reader that's optimized for SNP-major bed files. Reduced runtime from 102 minutes to 12 minutes. Partially tested.
Christopher Hartl
2012-10-17 12:48:14 -0400
0196dbeacaAdded more logging to push/pull of RemoteFiles.
kshakir
2012-10-17 09:52:17 -0400
33df1afe0eMore BaseCounts optimizations for RR.
Eric Banks
2012-10-17 00:55:44 -0400
19e2b5f0d5RR optimization: since total count in BaseCounts is requested so often, don't keep computing it from scratch each time.
Eric Banks
2012-10-17 00:44:23 -0400
f93b279151Moved the class field caching from QScript to a ClassFieldCache utility. Using ClassFieldCache to pull values from QScript for passing to done() method of QStatusMessenger.
kshakir
2012-10-16 18:49:10 -0400
f0e04376ecAdd output file tag so caller can specify output vcf
Guillermo del Angel
2012-10-16 16:05:12 -0400
b30e2a5b7dBQSR: tool to profile the effects of more-granular locking on scalability by # of threads
David Roazen
2012-10-15 11:53:57 -0400
402ce963f9changes in the postQC summary tables foramt
Ami Levy Moonshine
2012-10-16 14:11:54 -0400
62d9de084fChanges to specify outputs from inputs arguments per Khalid's request
Guillermo del Angel
2012-10-16 13:57:35 -0400
9bcefadd4eRefactor ExactCallLogger into a separate class
Mark DePristo
2012-10-16 13:30:09 -0400
b26b7bd8e5fixed problem with isIntermediate flag being interited from FQ2BAM added support for tumor flag in metadata
Kristian Cibulskis
2012-10-16 12:20:41 -0400
c74d7061feAdded AFCalcResultUnitTest
Mark DePristo
2012-10-16 08:10:22 -0400
9b0ab4e941Cleanup IndependentAllelesDiploidExactAFCalc
Mark DePristo
2012-10-15 20:58:55 -0400
Kristian Cibulskis
kshakir
Mauricio Carneiro
Menachem Fromer
Guillermo del Angel
Mark DePristo
Ryan Poplin
Eric Banks
Ami Levy Moonshine
Christopher Hartl
David Roazen
Joel Thibault
Yossi Farjoun