dce6b91f7dAdd a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.
Eric Banks
2012-03-16 11:14:37 -0400
41068b6985The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.
Eric Banks
2012-03-15 16:08:58 -0400
e86ce8f3d6updating HaplotypeCaller integration tests to reflect all the recent changes.
Ryan Poplin
2012-03-15 14:56:35 -0400
0c6b34e9dfFixing a bug identified by the ActivityProfile unit tests
Ryan Poplin
2012-03-15 14:24:30 -0400
252b830aa8Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-15 11:56:04 -0400
0fa5a7af05Adding contracts and unit tests for HaplotypeCaller GenotypingEngine
Ryan Poplin
2012-03-15 11:55:48 -0400
c1f454fbe6cleaning up and expanding LikelihoodCalculationEngine unit tests
Ryan Poplin
2012-03-15 08:53:11 -0400
c865950923fixing my typo on the md5.
Mauricio Carneiro
2012-03-14 22:00:03 -0400
1212a65140Adding contracts and unit tests for HaplotypeCaller LikelihoodCalculationEngine
Ryan Poplin
2012-03-14 21:26:01 -0400
1429ddcf55Adding contracts and unit tests for HaplotypeCaller LikelihoodCalculationEngine
Ryan Poplin
2012-03-14 21:25:43 -0400
c045542442ReduceReads default downsampling strategy is now NORMAL
Mauricio Carneiro
2012-03-14 16:16:06 -0400
7c5cdb51c2UnitTests for ActivityProfile and minor ART cleanup
Mark DePristo
2012-03-14 17:26:06 -0400
e440c9be98Clean up logic for adding reads to ART cache
Mark DePristo
2012-03-14 14:59:31 -0400
5bcb5c7433Preliminary refactoring of ART
Mark DePristo
2012-03-14 11:21:31 -0400
e73406b9b5CountReadsInActiveRegions now emits a detailed GATK report
Mark DePristo
2012-03-14 09:43:45 -0400
86eed6de07Updating 1000G summary table to use new CNVs list
Mark DePristo
2012-03-13 10:40:04 -0400
66411ea1e9misc minor cleanup
Ryan Poplin
2012-03-14 16:10:25 -0400
1da8928407HC GenotypingEngine marginalizes over haplotypes when outputing events that were found on a subset of the called haplotypes.
Ryan Poplin
2012-03-14 15:22:21 -0400
eca055ccadAdd option in ValidationAmplicons to only output SNPs and INDELs, ignoring complex variants (or SVs, etc.)
Guillermo del Angel
2012-03-14 14:26:40 -0400
f7c2c818feExact model memory optimization: instead of having a later matrix column pull in data from earlier ones (requiring us to keep them around until all dependencies are hit), the earlier columns push data into their dependents immediately and then are removed. This does trade off speed a little bit (because we need to call approximateLog10Sum each time we add to a dependent instead of once in an array at the end). Note that this commit would normally not get pushed into stable, but I'm about to make a very disruptive push into stable that would make merging this from unstable a nightmare.
Eric Banks
2012-03-14 14:02:36 -0400
8e96969744Support for exception-class in analyzeRunReports.py
Mark DePristo
2012-03-14 12:26:59 -0400
6a40ca6becMerged bug fix from Stable into Unstable
Mark DePristo
2012-03-14 12:19:33 -0400
bb2c10b785Capture the class of the exception in GATKRunReport
Mark DePristo
2012-03-14 12:16:04 -0400
78a4e7e45eMajor restructuring of HaplotypeCaller's LikelihoodCalculationEngine and GenotypingEngine. We no longer create an ugly event dictionary and genotype events found on haplotypes independently by finding the haplotype with the max likelihood. Lots of code has been rewritten to be much cleaner.
Ryan Poplin
2012-03-14 12:05:05 -0400
47e5a80d0fTrivial submission script that's useful to have for next time
Eric Banks
2012-03-14 10:17:14 -0400
06340a3c48Code cleanup now that we have Tableau analysis
Mark DePristo
2012-03-14 08:06:31 -0400
841d200688Always use long format
Mark DePristo
2012-03-13 17:05:16 -0400
77243d0df1Splitting up the MultiallelicSummary module into the standard part for use by all and the dev piece used just by me
Eric Banks
2012-03-13 16:31:51 -0400
f76da1efd2Updating md5s because MultiallelicSummary is now standard
Eric Banks
2012-03-13 16:31:13 -0400
ae65d86b81Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-03-13 16:26:51 -0400
568a1362f5Splitting up the MultiallelicSummary module into the standard part for use by all and the dev piece used just by me
Eric Banks
2012-03-13 16:19:15 -0400
2d5ca8bcfeAdding my AnalyzeCovariates R script for Mauricio to use
Ryan Poplin
2012-03-13 13:05:10 -0400
6e18ecfc9aAdding integration test to cover errors from my previous commit (GENOTYPE_GIVEN_ALLELE bugs reported by Sara Pulit and Chris Hartl)
Eric Banks
2012-03-13 12:43:40 -0400
5d7c761784Merged bug fix from Stable into Unstable
Eric Banks
2012-03-13 11:01:03 -0400
5200f7f919When creating a synthetic VC based on the passed in alleles, set the reference base for indel.
Eric Banks
2012-03-13 10:59:58 -0400
1675bd4dd7When creating a synthetic VC based on the passed in alleles, set the length correctly.
Eric Banks
2012-03-13 10:55:52 -0400
a514257318Output to sdout, not a file
Eric Banks
2012-03-13 10:46:12 -0400
ed69f4ff7cMerge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-03-13 09:28:16 -0400
9b9856ead5quick todo for next time we make a bundle
Eric Banks
2012-03-13 09:28:11 -0400
6dd341ea22Generalized runtime simplifying routines in analyzeRunReports
Mark DePristo
2012-03-13 08:05:04 -0400
5d6a686474Restoring key-related unit/integration tests
David Roazen
2012-03-13 00:58:24 -0400
42ace8bf7bMerge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-03-12 23:20:14 -0400
6e9b8559d8Unfortunately need to bump up memory needed for liftover to get Omni file sorted
Eric Banks
2012-03-12 23:20:00 -0400
7887a06703GATKReport v1.0
Roger Zurawicki
2012-01-09 23:46:48 -0500
10995d349eFix old error message
Eric Banks
2012-03-12 22:56:08 -0400
2314787767Generalizing to avoid JDK 1.7 incompatibilities
Eric Banks
2012-03-12 22:50:59 -0400
359090c4b7Updating dbsnp to v135
Eric Banks
2012-03-12 13:17:58 -0400
7e9a535c4dUpdated the bundle to use the official filtered (final) indel calls
Eric Banks
2012-03-12 12:12:24 -0400
05ef5863cfDon't assume files have .bai and .bas associated with them
Eric Banks
2012-03-12 11:47:48 -0400
6bc92d2bbfBugfix for analyzeRunReports.py: now handles case where hostname is missing
Mark DePristo
2012-03-12 09:45:47 -0400
a63d1f58b6analyzeRunReports cleanup for new minimal GATKRunReport structure
Mark DePristo
2012-03-11 10:41:29 -0400
03223029e3Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-12 09:42:37 -0400
04cafffaa7Merge remote-tracking branch 'unstable/master'
Eric Banks
2012-03-12 08:43:43 -0400
b4749757f8Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.
Eric Banks
2012-03-12 01:07:07 -0400
191a5860cfupdating HaplotypeCaller integration tests
Ryan Poplin
2012-03-11 16:23:25 -0400
2836c161eeMoving trimToVariableRegion out of reduced reads and into a public static ReadClipper function. HaplotypeCaller clips reads to the active region boundries before passing to the HMM. The philosophy of the HC is moving towards genotyping the entire haplotype sequence contained within the active region as a single allele.
Ryan Poplin
2012-03-11 14:45:59 -0400
8db11eb781Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-10 21:00:55 -0500
0cadd4d732Banding approach for PairHMM utility class. Adds bands to a work queue when distinct likelihood masses are detected in the HMM matrices. Works over a wide range of haplotype sizes and GOP values.
Ryan Poplin
2012-03-10 20:59:35 -0500
1ee46e5c06Collect only the bare essentials in the GATKRunReport
Mark DePristo
2012-03-10 20:27:14 -0500
92bbb9bbddMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-10 10:09:57 -0500
bd883031a4Final version of QualQuantizer
Mark DePristo
2012-03-09 15:59:27 -0500
4b404cae48Final evaluation script for quantizing quality scores
Mark DePristo
2012-03-09 12:09:20 -0500
e2c62572f9Further upgrades to CalibrateGenotypeLikelihoods.R
Mark DePristo
2012-03-08 11:40:23 -0500
fceb2bf25bUpdating CalibrateGenotypeLikelihoods.R to display Q93 not filter them out
Mark DePristo
2012-03-08 10:11:16 -0500
3ba2e5667cCalibrateGenotypesLikelihoods include pOfDGivenD now
Mark DePristo
2012-03-08 09:43:24 -0500
1011f3862bCalibrateGenotypeLikelihoods now emits the position of the variant for debugging
Mark DePristo
2012-03-08 08:57:29 -0500
8158348e01Prints xlim = 30 and xlim = 99 in CalibrateGenotypeLikelihoods.R
Mark DePristo
2012-03-07 17:15:36 -0500
91d10431d3BAMScheduler: detect contigs from the interval list that are not in the merged BAM header's sequence dictionary
David Roazen
2012-03-09 15:11:59 -0500
bc65f6326fDetect incomplete reads from BAM schedule file in BAMSchedule before they become buffer underflows
David Roazen
2012-03-09 12:13:53 -0500
32dee7ed9bAvoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices
David Roazen
2012-03-08 12:52:11 -0500
c04853eae6Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-03-08 12:30:04 -0500
858acf8616Hidden mode in ValidationAmplicons to support ILMN output format (same as Sequenom, with just shuffled columns)
Guillermo del Angel
2012-03-08 12:29:44 -0500
117ea605acMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Andrey Sivachenko
2012-03-07 18:35:07 -0500
497a1b059etransition to JEXL completed, old parameters setting individual cutoffs now deprecated
Andrey Sivachenko
2012-03-07 18:34:11 -0500
fbd2f04a04JEXL support added; intermediate commit, not yet functional
Andrey Sivachenko
2012-03-07 17:29:42 -0500
20d10dfa35EvalQuantizedQuals now tests the impact on reduced reads as well
Mark DePristo
2012-03-07 13:09:48 -0500
0376d73eceImproved, public version of ErrorRateByCycle
Mark DePristo
2012-03-07 13:08:52 -0500
a6a8fc0521Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-03-07 10:05:43 -0500
c4824a77f5Some to-do items for the reduced reads calling script
Eric Banks
2012-03-07 10:03:10 -0500
155839e901Commit of VQSRV3 with Random Forest Bridge and Decision Tree engines. Lots of code duplication with the variant recalibrator in public, but also some subtle changes (i.e. to the engines and data manager). Code worked when it overwrote the stuff in public, but couldn't commit that. Will push if it works for private as well.
Christopher Hartl
2012-03-07 09:46:43 -0500
26dcec08d5Bugfix for QualQuantizerUnitTest
Mark DePristo
2012-03-07 09:30:03 -0500
8ef654aa77Minor improvements to QuantizeQuals
Mark DePristo
2012-03-06 16:56:17 -0500
569be953b9Bugfix for VariantEval
Mark DePristo
2012-03-06 16:54:59 -0500
5f35f5d338QualQuantizer scales the penalty by the log of the two error rates
Mark DePristo
2012-03-05 15:49:56 -0500
8d2db3f249Emit and visualize quality histogram in QualQuantizer
Mark DePristo
2012-03-04 20:07:50 -0500
b7089a3b05Improvements to QualQuantizer; Walker to quantize quals in BAM file
Mark DePristo
2012-03-04 18:44:11 -0500
811f871f78Do not fail tests that require the GATK private key if the user does not have permission to read it
David Roazen
2012-03-06 15:25:19 -0500
67def6acc8Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-03-06 14:23:14 -0500
20c1fbaf0fFixing a merge (turning off downsampling on DoC)
Christopher Hartl
2012-03-06 14:22:45 -0500
46b470cc69Minor misc updates
Ryan Poplin
2012-03-06 10:14:45 -0500
0702ee1587Public-key authorization scheme to restrict use of NO_ET
David Roazen
2012-02-22 16:45:20 -0500
027843d791I've simply added a "library(grid)" call at the beginning of the R script generation since R 2.14.2 doesn't seem to load the "grid" package as default. I haven't tested it on previous R versions (you may edit the R version comment to be more precise if desired), but I'm almost certain that this library call shouldn't do any harm on them.
Lechu
2012-03-04 03:32:30 +0100
f6905630bbAdding Unit test for Haplotype class. Used in HC's genotype given alleles mode.
Ryan Poplin
2012-03-05 21:08:07 -0500
9b53250befAdding Unit test for Haplotype class. Used in HC's genotype given alleles mode.
Ryan Poplin
2012-03-05 21:07:36 -0500
b37461587dMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-05 17:54:59 -0500
c6ded4d23cBug fix for hard clipping reads when base insertion and base deletion qualities are present in the read. Updating HaplotypeCaller integration tests to reflect all the recent changes.
Ryan Poplin
2012-03-05 17:54:42 -0500
14a77b1e71Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly.
Ryan Poplin
2012-03-05 12:28:32 -0500
e9ad382e74unifying the BQSR argument collection
Mauricio Carneiro
2012-03-03 18:01:55 -0500
a1d6b3818cdont include deletions in the pileup
Mauricio Carneiro
2012-03-02 19:10:50 -0500
Eric Banks
Ryan Poplin
Mauricio Carneiro
Mark DePristo
Guillermo del Angel
David Roazen
Roger Zurawicki
Andrey Sivachenko
Christopher Hartl
Lechu