0ca7428e76Allow processing of empty intervals, but warn user when this case is encountered.
Eric Banks
2011-10-28 12:12:14 -0400
649dfe98f0Add VCF header for any expressions that are requested
Eric Banks
2011-10-28 10:22:19 -0400
8b1a62da27Adding unit test to cover overlapping intervals from the same source with the intersection rule.
Eric Banks
2011-10-28 09:59:43 -0400
057a79f598This argument should be annotated as @Input
Eric Banks
2011-10-28 09:44:49 -0400
4ba7c0cecdMoving to private
Eric Banks
2011-10-28 09:29:28 -0400
1bdd76c2f2These tools now use the IntervalBinding system to handle intervals instead of doing it all manually
Eric Banks
2011-10-28 09:28:12 -0400
6ba08a103dEmpty ROD files should generate an exception when used for creating intervals. Moved some now obsolete files to the archive as the realigner will now read all target intervals into memory.
Eric Banks
2011-10-28 09:23:25 -0400
3d04bb5608Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-10-27 23:55:18 -0400
19e27d4568Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
Eric Banks
2011-10-27 23:55:11 -0400
cafc245a43For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?
Eric Banks
2011-10-27 23:54:28 -0400
cbc43683eeMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-10-27 20:54:18 -0400
8907e42007First fully functional implementation of ValidationSiteSelectorWalker. User gives a) a set of input variants, b) a desired number of output variants, b) Optionally, a set of samples which will restrict sites to be polymorphic in those samples, c) a frequency selection mode: either uniform (no AF matching), or matching AF so that output sites mirror the input AF spectrum as closely as possible. More testing is needed and docs need improving but so far all functionality seems up and running
Guillermo del Angel
2011-10-27 20:53:48 -0400
ccfd853b34Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.
Eric Banks
2011-10-27 20:43:50 -0400
648a17a30bMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-10-27 16:27:30 -0400
1ecd08a296Better docs for VariantsToPed
Mark DePristo
2011-10-27 16:27:19 -0400
c2f343773eOops, working too quickly last time. This is the proper fix for the potential NPE in the equals() test.
Eric Banks
2011-10-27 15:32:08 -0400
4d0e34109fCompacting pdfs when running under R 2.13+.
Khalid Shakir
2011-10-27 14:51:56 -0400
b80d407dc7No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. Other minor cleanup.
Khalid Shakir
2011-10-26 23:05:41 -0400
8c4dbce6d8Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.
Eric Banks
2011-10-27 13:58:19 -0400
4a7e6fee3fRemove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.
Eric Banks
2011-10-27 13:38:08 -0400
f7df8bdeccMerged bug fix from Stable into Unstable
Matt Hanna
2011-10-27 11:31:17 -0400
41ddc7bce7Make sure we output a full stack trace when we encounter Tribble error messages on VCF header merge.
Matt Hanna
2011-10-27 11:30:04 -0400
9ca2828547Bug fix for multiallelic records: When combining SNP and indel record the original alleles are reference padded in one case but not in the other. Added missing normalization of the haplotype likelihood matrix. Unfortunately turning the banded approach off for now because it kills specificity.
Ryan Poplin
2011-10-27 09:51:40 -0400
44f905b5e5Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-10-26 23:31:11 -0400
68283b1651Fixing docs and adding GATKdocs for the new interval functionality
Eric Banks
2011-10-26 22:14:43 -0400
c9978316a3Merge branch 'FragmentUtils'
Mark DePristo
2011-10-26 19:51:49 -0400
add9ad97ecNo scatter gather for VQSR or ApplyVQSR.
Mauricio Carneiro
2011-10-26 15:34:23 -0400
6b3aa7ce62Script to evaluate VQSR on reduce reads
Mauricio Carneiro
2011-10-26 15:22:35 -0400
74aeb22eebMerged bug fix from Stable into Unstable
Ryan Poplin
2011-10-26 15:57:30 -0400
86871bd1e3Throw a UserException in the BQSR when there is no data instead of creating an empty csv file
Ryan Poplin
2011-10-26 15:56:41 -0400
034a997d07Generalized Reads -> Fragment calculation
Mark DePristo
2011-10-26 15:31:24 -0400
2f21b6ecfbRemoved debugging output
Eric Banks
2011-10-26 15:50:20 -0400
b39fcb1beaMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-10-26 15:44:25 -0400
b6ce6ed3f8Go around the ROD system for now so that we can just call decodeLoc() for efficiency. Noted that we should go through the ROD system once it gets cleaned up. This means that currently gzipped files are not supported with -L.
Eric Banks
2011-10-26 15:42:53 -0400
3273c20c98Added integration tests for Tribble-based intervals and fixed up some of the other tests based on some method changes.
Eric Banks
2011-10-26 15:29:18 -0400
9424e8b2caInitial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed.
Eric Banks
2011-10-26 14:11:49 -0400
7fa943aef1Renamed FragmentPileup to FragmentUtils
Mark DePristo
2011-10-26 14:01:45 -0400
1f044faedd- Genotype assignment in case of equally likeli combination is now random - Genotype combinations with 0 confidence are now left unphased
Laurent Francioli
2011-10-26 19:57:09 +0200
751d66174aMinor additions to the shared .gitignore file, now that Mark has checked one in.
David Roazen
2011-10-26 12:22:00 -0400
62cff266d4GQ calculation corrected for most likely genotype
Laurent Francioli
2011-10-26 14:40:04 +0200
be4eb83041Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-10-25 22:20:53 -0400
2d5a22f4c3Copying Guillermo's indel model optimizations into the haplotype caller which cuts the runtime in half.
Ryan Poplin
2011-10-25 22:19:48 -0400
af3613cc5fGATKSAMRecord commit branch summary
Mark DePristo
2011-10-25 20:52:56 -0400
2822f0dc27Merge branch 'SamRecordFactory'
Mark DePristo
2011-10-25 20:34:47 -0400
05730884c6More ignores
Mark DePristo
2011-10-25 20:29:35 -0400
221c944ee0Including private parts
Mark DePristo
2011-10-25 20:29:17 -0400
0f44066640Ignore common files
Mark DePristo
2011-10-25 20:26:46 -0400
7d092c859fRemoving ugly mapping probability hack because it is no longer necessary.
Ryan Poplin
2011-10-25 16:48:43 -0400
1b722c21cfmerge master
Mark DePristo
2011-10-25 16:08:39 -0400
56fdf0b865Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-10-25 15:58:56 -0400
ea5857c618More misc cleanup.
Ryan Poplin
2011-10-25 15:58:28 -0400
4a34c1862emisc cleanup. We now filter out haplotypes when it is obvious that the assembly has failed to find a parsimonious event rather than use haplotypes with large numbers of SNPs and small indels on them.
Ryan Poplin
2011-10-25 15:22:28 -0400
9eaa62f3f3Tmp. SAM-JDK rev. Better google caliper example
Mark DePristo
2011-10-25 15:15:52 -0400
2794e5c1d4Modified the VCFJarClassLoadingUnitTest to play nice with the packaged-jar test targets.
David Roazen
2011-10-25 14:06:12 -0400
b559936b7aa)New variant eval stratification module for indel size. b) Next iteration on indel caller runtime optimization: when computing likelihood of each haplotype for a given read, many computations will be redundant since pieces of haplotypes will be common to both REF and ALT haplotypes. So, we keep HMM matrices from one haplotype to the next one and recompute starting at the part where either haplotype is different or GOP/GCP are different.
Guillermo del Angel
2011-10-25 09:56:43 -0400
bf61393a7dMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2011-10-25 07:47:22 -0400
9afe6fc7acPicard upgrade to 1.55.
Matt Hanna
2011-10-24 17:02:27 -0400
fac9932938Embedding gsalib source and queueJobReport R scripts in the dist and package jars. Moved gsalib and queueJobReport.R to embeddable namespaced locations. Updated packager dependencies/dir to add an @includes which filters the embedded fileset. RScriptExecutor can now JIT compiles the gsalib. RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG. Refactored ProcessController and IOUtils from Queue to Sting Utils. Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count. Replaced uses of some IOUtils with Apache Commons IO. ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown. Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
Khalid Shakir
2011-10-24 15:49:02 -0400
89a581a66fAdded ability to specify arguments in files via -args/--arg_file Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
Khalid Shakir
2011-10-14 12:06:41 -0400
502592671dCleanup FragmentPileup before main repo commit
Mark DePristo
2011-10-24 14:40:05 -0400
166174a551Google caliper example execution script
Mark DePristo
2011-10-24 14:04:53 -0400
13702939acHaplotypeCaller now calculates multi-sample likelihoods and passes them to the exact model to make multi-sample calls.
Ryan Poplin
2011-10-24 10:15:58 -0400
090382ce03Now calculates proper multi-allelic likelihoods and sends them to the exact model if appropriate.
Ryan Poplin
2011-10-24 08:21:05 -0400
62477a0810Added documentation and comments
Laurent Francioli
2011-10-24 13:45:21 +0200
38ebf3141a- Now supports parent/child pairs - Sites with missing genotypes in pairs/trios are handled as follows: -- Missing child -> Homozygous parents are phased, no transmission probability is emitted -- Two individuals missing -> Phase if homozygous, no transmission probability is emitted -- One parent missing -> Phased / transmission probability emitted - Mutation prior set as argument
Laurent Francioli
2011-10-24 12:30:04 +0200
7312e35c71Now makes use of standard Allele and Genotype classes. This allowed quite some code cleaning.
Laurent Francioli
2011-10-24 10:25:53 +0200
01b16abc8dGenotype quality calculation modified to handle all genotypes the same way. This is inconsistent with GQ output by the UG but is correct even for cases of poor quality genotypes.
Laurent Francioli
2011-10-24 10:24:41 +0200
f6ccac889bMerged bug fix from Stable into Unstable
Mark DePristo
2011-10-23 16:37:12 -0400
585a45b7a3Bug fix for ClipReadsWalker when stats output isn't provided
Mark DePristo
2011-10-23 16:36:48 -0400
f5d910b8a5Haplotype caller now sends genotype likelihoods to the exact model to genotype the events found in the best haplotypes.
Ryan Poplin
2011-10-23 13:29:08 -0400
42bf9adedeInitial version of "fast" FragmentPileup code
Mark DePristo
2011-10-22 21:36:37 -0400
c3cb07fc1dRelocating the ReduceBAM script.
Mauricio Carneiro
2011-10-22 13:35:52 -0400
4913f8a60fMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Mauricio Carneiro
2011-10-21 17:45:07 -0400
86305a5dcfAdjusting the memory limits of the MDCP
Mauricio Carneiro
2011-10-21 17:41:52 -0400
102dafdcbcValidation of GATKSamRecord in read filters
Mauricio Carneiro
2011-10-21 17:40:43 -0400
f4b409fa0dCombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result
Guillermo del Angel
2011-10-21 14:07:20 -0400
b863390cb1Moving reduced read functionality into GATKSAMRecord
Mark DePristo
2011-10-21 13:28:05 -0400
1b01e24e23Moving around comments
Mark DePristo
2011-10-21 13:26:30 -0400
2403e96062Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs.
Mark DePristo
2011-10-21 09:59:24 -0400
110e13bc1eMerge branch 'master' into SamRecordFactory
Mark DePristo
2011-10-21 09:43:52 -0400
be797a8a1fRecalibrator now uses the much more efficient NGSPlatform in the cycle covariates system
Mark DePristo
2011-10-21 09:39:21 -0400
ed74ebcfa1GATKSamRecords with efficiency NGSPlatform method
Mark DePristo
2011-10-21 09:38:41 -0400
94e1898d8fA canonical set of NGS platforms as enums with convenient manipulation methods
Mark DePristo
2011-10-21 09:37:45 -0400
9f867d77cano sort order
Mauricio Carneiro
2011-10-20 18:44:09 -0400
c9d8b22092Added BWASW support to the pipeline
Mauricio Carneiro
2011-10-20 18:36:28 -0400
093cd95c5dMerged bug fix from Stable into Unstable
Mauricio Carneiro
2011-10-20 17:03:22 -0400
d7367c152aFixing 'revert' when not realigning
Mauricio Carneiro
2011-10-20 17:01:54 -0400
558a7a81f0Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Mauricio Carneiro
2011-10-20 16:23:32 -0400
ed402588ccAdding the "gold standard NA12878" target
Mauricio Carneiro
2011-10-20 16:19:13 -0400
edea90786aGenotype quality is now recalculated for each of the phased Genotypes. Small problem is that we unnecessarily loose a little precision on the genotypes that do not change after assignment.
Laurent Francioli
2011-10-20 17:04:19 +0200
1c61a57329Original rewrite of PhaseByTransmission: - Adapted to get the trio information from the SampleDB (i.e. from Pedigree file (ped)) => Multiple trios can be passed as argument - Mendelian violations and trio phasing possibilities are pre-calculated and stored in Maps. => Runtime is ~3x faster - Genotype combinations possible only given two MVs are now given a squared MV prior (e.g. 0/0+0/0=>1/1 is given 10^-16 prior if the MV prior is 10^-8) - Corrected bug: In case the best genotype combination is Het/Het/Het, the genotypes are now set appropriately (before original genotypes were left even if they weren't Het/Het/Het) - Basic reporting added: -- mvf argument let the user specify a file to report remaining MVs -- When the walker ends, some basic stats about the genotype reconfiguration and phasing are output
Laurent Francioli
2011-10-20 13:06:44 +0200
ef6a6fdfe4Added getAsMap -> returns the likelihoods as an EnumMap with Genotypes as keys and likelihoods as values.
Laurent Francioli
2011-10-20 12:49:18 +0200
76dd816e70Added getParents() -> returns an arrayList containing the sample's parent(s) if available
Laurent Francioli
2011-10-20 12:47:27 +0200
6f72b3de6aForgot to add this in too (oops)
Christopher Hartl
2011-10-19 18:46:31 -0400
999a8998aeConstructor for GATKSamRecord with header only, for unit testing
Mark DePristo
2011-10-19 17:51:48 -0400
3227143a1cSystematic test code for FragmentPileup
Mark DePristo
2011-10-19 17:50:27 -0400
bba69701b5Now creates GATKSamRecords now SamRecords
Mark DePristo
2011-10-19 17:49:17 -0400
cd8a6d62bbYou know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.
Christopher Hartl
2011-10-19 17:42:37 -0400
Eric Banks
Guillermo del Angel
Mauricio Carneiro
Mark DePristo
Khalid Shakir
Matt Hanna
Ryan Poplin
Laurent Francioli
David Roazen
Christopher Hartl