2a0cd556d3Further cleanup of Sample
Mark DePristo
2011-09-29 10:34:51 -0400
e76f381628Moved sample package from DataSources to gatk, and renamed it samples
Mark DePristo
2011-09-29 09:57:15 -0400
e197dcd1f3Pre-cleanup commit of Sample and SampleDataSource
Mark DePristo
2011-09-29 09:44:18 -0400
4d31673cc5No longer supporting YAML file allows us to delete 75% of the sample's codebase
Mark DePristo
2011-09-29 09:43:31 -0400
e366ee18bcAdding ability to read in and make use of kmer quality tables during HMM evaluation
Ryan Poplin
2011-09-29 07:46:19 -0400
9e32ede5b2Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-29 07:40:08 -0400
fc86cd6fd8Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/carneiro/gatk/RR into rr
Mauricio Carneiro
2011-09-29 00:12:15 -0400
4fd5630f6aAdded ReadClipper Unit Test
Roger Zurawicki
2011-09-28 23:13:50 -0400
f49a12de6bUpdating latest changes from the repository to reduce reads repo
Mauricio Carneiro
2011-09-28 22:31:57 -0400
9272ed03b5Merged bug fix from Stable into Unstable
Matt Hanna
2011-09-28 21:26:43 -0400
0acaf2df65Fix an embarrassing issue where a specific configuration of minimal coverage over small intervals could cause reads to be dropped from the pileup. Nothing to see here...
Matt Hanna
2011-09-28 21:23:01 -0400
07b0a75d96Added SlidingRead Unit Test
Roger Zurawicki
2011-09-28 21:22:57 -0400
c5f1a4325fUpdated preQC: - full 8.5x11 - concating multiple initiatives / bait_sets - Using NA instead of python None when WR dates are unavailable - In new aggregations where the sample may have per library metrics, only using the sample level metrics, i.e. library is null Updated postQC: - Renamed some variables to assist with traceback() - Fixed crashes on batches with two alleles or two samples such as Seminara_MC_1_09222011 or Engle_MC_2_09222011 - Added dependency tracking to PostCallingQC.scala so that the R script does try to run before the evals are complete Other minor cleanup. Tried to use R 2.13 compactPDF but a few issues to work out with fingerprint boxplots in preQC and geom_text font size in postQC.
Khalid Shakir
2011-09-28 20:23:30 -0400
edf852d47dAdding lists to ReduceReads script
Mauricio Carneiro
2011-09-28 18:40:03 -0400
64e7b3000cFix read spans deletion through the entire interval
Mauricio Carneiro
2011-09-28 17:28:52 -0400
c8d3a720f9Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-28 18:17:34 -0400
7e3cb45093Further performance optim in banded hmm, about 60% speed improvement over current implementation now
Guillermo del Angel
2011-09-28 16:27:28 -0400
1b1ca80df2Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-28 16:17:39 -0400
3b73dc89feMaking several esoteric arguments in the BQSR @Hidden. Adding basic support for Complete Genomics machine cycle.
Ryan Poplin
2011-09-28 16:17:31 -0400
5c9b659c02clipping both ends of the reads was modifying the original read
Mauricio Carneiro
2011-09-28 12:10:47 -0400
fe23e4d10cMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-28 15:53:11 -0400
e2b9030e93First mostly fully functional implementation of banded pair HMM likelihood computation for indel caller. More experimentation to follow but it right now works in small data sets and at least it doesn't break existing things. Disabled by default at this point
Guillermo del Angel
2011-09-28 15:51:48 -0400
1b45f21774Removing this command-line tool. Purposely not doing this in stable so that users who may still use it have time to find other options. But the docs are no longer on the wiki.
Eric Banks
2011-09-28 13:18:32 -0400
1f0e354faeMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-09-28 13:13:21 -0400
bb619a9a3cFixing docs
Eric Banks
2011-09-28 13:13:03 -0400
5812004e06Merge branch 'stable'
Mark DePristo
2011-09-28 11:36:40 -0400
a88b7c1203Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-28 11:36:33 -0400
a5006831d7Shows "" not empty space when default string value is ""
Mark DePristo
2011-09-28 11:35:52 -0400
1e32281a15Fix to not show -null when missing short name argument
Mark DePristo
2011-09-28 11:31:20 -0400
fd287da189Final tweaking of Smith-Waterman parameters based on large-scale parameter search with Queue
Ryan Poplin
2011-09-28 11:22:01 -0400
2e2463633fQueue script to find missing calls between full and reduced bams
Mark DePristo
2011-09-28 11:17:25 -0400
af0d16e741Adding context dependent gap penalty code into the haplotype likelihood model. Adding ContextCovariate to indel CountCovariates for use in generating k-mer quality tables. Bug fix: make sure to clear the assembly graphs between active regions.
Ryan Poplin
2011-09-28 08:51:50 -0400
eacbee3fe5Merged bug fix from Stable into Unstable
Eric Banks
2011-09-27 20:35:18 -0400
43b0c98298Fix docs
Eric Banks
2011-09-27 20:34:46 -0400
232a6df11cAdd longhand form to the error message.
Eric Banks
2011-09-27 20:29:31 -0400
1d6fcb6eb1Revert "Add longhand form to the error message to prevent users from posting borderline dumb posts to GS."
Eric Banks
2011-09-27 20:27:00 -0400
269b9826b6Add longhand form to the error message to prevent users from posting borderline dumb posts to GS.
Eric Banks
2011-09-27 20:26:36 -0400
84bd355690Merged bug fix from Stable into Unstable
Khalid Shakir
2011-09-27 14:34:39 -0400
b090751f62Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths. Updates to HybridSelectionPipeline: - Added annotations back via snpEff - Minor updates to VQSR paths and lowered memory
Khalid Shakir
2011-09-27 14:33:57 -0400
db785eb50dFix a bug where no fingerprint LODs across an entire project would cause the R script to blow up.
Matt Hanna
2011-09-27 12:39:25 -0400
e5ce5e265aMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2011-09-27 11:07:01 -0400
26e71f6688The Omni files have multiple records (with the same ALT) at a particular location, with one PASSing and the other(s) filtered. Chris, this is why using this file as both eval and comp leads to ref/no-call cells in the GenotypeConcordance table. However, this led to non-determinism in VE because the VCs were placed in a HashSet; we use a LinkedHashMap instead to bring back determinism.
Eric Banks
2011-09-27 11:03:17 -0400
ceffefa6a6Intermediate version with banded pair HMM
Guillermo del Angel
2011-09-27 10:18:58 -0400
e99ff3caaeRemoved lots of old, and not to be used, HMM options
Mark DePristo
2011-09-27 10:08:40 -0400
17dc0e44bcMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-27 07:10:58 -0400
77ba59e30aMerge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Khalid Shakir
2011-09-27 00:51:45 -0400
648b959361Minor change to log an info message when a signal such as Ctrl-C is caught.
Khalid Shakir
2011-09-27 00:50:19 -0400
6d8b3b882fMerged bug fix from Stable into Unstable
Matt Hanna
2011-09-26 15:16:54 -0400
6478681c0cMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
Matt Hanna
2011-09-26 15:12:52 -0400
82bb3acba0Merged bug fix from Stable into Unstable
Matt Hanna
2011-09-26 14:59:23 -0400
059cdcb1beChanging packaging system path for GATK-only Tribble codecs.
Matt Hanna
2011-09-26 14:58:19 -0400
fa0efbc4caRefactoring of PairHMM to support reduced reads
Mark DePristo
2011-09-26 13:28:56 -0400
a6b65d6347Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-26 13:26:21 -0400
4f09453470Refactored reduced read utilities
Mark DePristo
2011-09-26 12:58:31 -0400
234b74dd05Merged bug fix from Stable into Unstable
Eric Banks
2011-09-26 11:47:23 -0500
317b95fa57Fixing some annotator docs
Eric Banks
2011-09-26 11:46:45 -0500
763fcfc96bAdding support to splitting one read into multiple reads
Mauricio Carneiro
2011-09-26 09:24:40 -0400
9afccd11b1Minor refactoring: add ability to MathUtils.normalizeFromLog10 to not go to linear domain but just substract max value from log values and return. Use this function in snp and indel GL computation.
Guillermo del Angel
2011-09-25 21:18:56 -0400
8c4eb5827fcleaning up parameter/variable names
Mauricio Carneiro
2011-09-24 18:52:46 -0400
3eedb40c3eCleaning up old code from ReduceReads
Mauricio Carneiro
2011-09-24 18:39:24 -0400
3eef800889Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-24 21:20:11 -0400
4707ab4a7dAdded unit tests to test genotype merges with PL's
Guillermo del Angel
2011-09-24 21:17:15 -0400
203517fbb7a) Cleanups/bug fixes to previous commit to CombineVariants. b) Change md5 to reflect records that are now merged correctly. c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.
Guillermo del Angel
2011-09-24 19:08:00 -0400
466ffa3665Forgot to hide my (shameless) debug techinque
Mauricio Carneiro
2011-09-24 14:39:42 -0400
c31f4cb2f6Cleaning leading insertions
Mauricio Carneiro
2011-09-24 14:33:32 -0400
cd058dd10fa) Fixed md5 for legit change in UG output that now also no-calls genotypes w/0,0,0 in PL's in SNP case. b) First reimplementation of new vc merger of different types. Previous version did it in two steps, first merging all vc's per type and then trying to see if resulting vc's would be merged if alleles of one type were a subset of another, but this won't work when uniquifying genotypes since sample names would be messed up and GT sample names wouldn't match VC sample names. Now, it's actually simpler: when splitting vc's by type before merging, we check for alleles of one vc being a subset of alleles of vc of another type and if so we put them together in same list.
Guillermo del Angel
2011-09-24 13:40:11 -0400
bb11951255Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-24 09:26:45 -0400
8d9e136bbaMerge branch 'stable'
Mark DePristo
2011-09-24 09:26:28 -0400
6804ab6d2fBug fix for NPE in very short GATK runs
Mark DePristo
2011-09-24 09:25:29 -0400
92acff46e5Moved Haplotype into Utils root
Mark DePristo
2011-09-24 09:14:05 -0400
f792353dcdFramework for genotype unit test
Mark DePristo
2011-09-24 08:56:45 -0400
c0bb0cb465Make DiploidGenotype enum private to walkers.genotyper
Mark DePristo
2011-09-24 08:48:33 -0400
3a4469a236Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-23 21:58:34 -0400
0e74cc3c74a) Treat SNP genotype likelihoods just as indels, in the sense that they're always normalized as PL's so one of them will always be zero. This creates minor numerical differences in Qual and annotations due to numerical approximations in AF computation. b) Intermediate CombineVariants fixes, not ready yet
Guillermo del Angel
2011-09-23 21:58:20 -0400
1803bd6ae2Merged bug fix from Stable into Unstable
Khalid Shakir
2011-09-23 21:05:00 -0400
8ceb93b8acFixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE
Khalid Shakir
2011-09-23 21:03:22 -0400
7cac75ae1dMerged bug fix from Stable into Unstable
Mauricio Carneiro
2011-09-23 19:00:43 -0400
fbe3c1e0b3Adding warning on HardClipping
Mauricio Carneiro
2011-09-23 19:00:19 -0400
1f5ed1fbbaFixing Indels in the consensus
Mauricio Carneiro
2011-09-23 17:30:45 -0400
b66841f179Static cache for binomial probability
Mark DePristo
2011-09-23 17:29:34 -0400
1a45c331b2bringing the latest bug fixes to Reduce Reads
Mauricio Carneiro
2011-09-23 16:40:06 -0400
9ea40f2e41Deletions/Insertions in hard clip and bug fixes
Mauricio Carneiro
2011-09-23 16:37:08 -0400
40202c85e0Merged bug fix from Stable into Unstable
David Roazen
2011-09-23 16:35:55 -0400
e1cb5f6459SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers.
David Roazen
2011-09-23 15:00:03 -0400
e388c357caMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2011-09-23 14:53:28 -0400
cc23b0b8a9Fix for recent change modelling unmapped shards: don't invoke optimization to combine mapped and unmapped shards.
Matt Hanna
2011-09-23 14:52:31 -0400
96ffc63caaMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-23 12:57:04 -0400
bf94845801Consensus shall never have indels.
Mauricio Carneiro
2011-09-23 12:36:07 -0400
147c16c8c0Added separate threshold for indels to trigger variant regions
Mauricio Carneiro
2011-09-23 12:35:38 -0400
0d53e184a7Mapping quality name change.
Mauricio Carneiro
2011-09-23 12:16:09 -0400
e3d4efb283Remove N2 EXACT model code, which should never be used
Mark DePristo
2011-09-23 11:55:21 -0400
fb6ac127a1Merged bug fix from Stable into Unstable
Eric Banks
2011-09-23 10:56:58 -0400
bcecc61715Fixing md5 because file changed on disk
Eric Banks
2011-09-23 10:56:16 -0400
27ce3c822eMerge branch 'stable'
Mark DePristo
2011-09-23 09:04:52 -0400
Mark DePristo
Ryan Poplin
Mauricio Carneiro
Roger Zurawicki
Matt Hanna
Khalid Shakir
Guillermo del Angel
Eric Banks
David Roazen