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  • 7fb620dce7 Generalize and fixup ContigComparator Mark DePristo 2013-02-09 09:50:43 -0500
  • a3dc7dc5cb Extend AWS timeout for uploads of the GATK run reports to 30 seconds Mark DePristo 2013-02-08 17:37:03 -0500
  • db5b5e3482 Merge pull request #21 from broadinstitute/mc_base_coverage_distribution_GSATDG-45 depristo 2013-02-08 09:45:14 -0800
  • d004bfbe6f walker to calculate per base coverage distribution Mauricio Carneiro 2013-02-07 10:43:14 -0500
  • 5f49c95cc1 Added distance across contigs calculation to GenomeLocs Mauricio Carneiro 2013-01-31 11:51:13 -0500
  • cd4aec177a Merge pull request #20 from broadinstitute/aw_reduceread_perf_1_GSA-761 depristo 2013-02-07 12:11:05 -0800
  • 8f9d317a52 Merge pull request #19 from broadinstitute/eb_add_alignment_utils_tests_GSA-735_GSA-736_GSA-737_GSA-738 depristo 2013-02-07 12:10:35 -0800
  • 9826192854 Added contracts, docs, and tests for several methods in AlignmentUtils. There are over 74K tests being run now for this class! Eric Banks 2013-02-06 14:06:10 -0500
  • e88bc753aa Replace with map.containsKey followed by map.get with map.get followed by null check. Alec Wysoker 2013-02-07 11:58:41 -0500
  • 72e496d6f3 Eliminate unnecessary zeroing out of primitive arrays immediately after new. Alec Wysoker 2013-02-07 11:57:43 -0500
  • cc7731d61f Merge pull request #18 from broadinstitute/eb_fix_RR_tests depristo 2013-02-06 10:02:13 -0800
  • 481982202d Fixing the failing RR integration tests. * After consulting Tim/David/Mauricio we determined that the md5 changes were due to different encodings of binary arrays in samjdk * However, it made no functional difference to the results (confirmed by Eric) so we agreed to update md5s * Also, the header of one of the test bams was malformed but old picard jar didn't perform checks so it only started failing now * Fixed the bam Eric Banks 2013-02-06 12:40:56 -0500
  • 462da7da8f Merge pull request #17 from broadinstitute/dr_variant_migration_cleanup depristo 2013-02-06 08:32:14 -0800
  • df142a389f Minor build.xml cleanup post-variant-migration David Roazen 2013-02-06 11:15:03 -0500
  • bd0349e570 Merge pull request #12 from broadinstitute/md_exact_fast_path_GSA-726 eitanbanks 2013-02-06 07:43:02 -0800
  • 59df329776 Fast path for biallelic variants in IndependentAllelesDiploidExactAFCalc Mark DePristo 2013-02-05 10:11:05 -0500
  • 584899329c Merge pull request #13 from broadinstitute/dr_variant_migration_GSA-692 eitanbanks 2013-02-06 07:22:30 -0800
  • bee127482b Merge pull request #16 from broadinstitute/eb_bqsr_fails_on_RR depristo 2013-02-06 07:20:42 -0800
  • 562f2406d7 Added check that BaseRecalibrator is not being run on a reduced bam. Eric Banks 2013-02-05 23:42:15 -0500
  • c677aa327c Merge pull request #15 from broadinstitute/eb_hapcaller_dbsnp_fix depristo 2013-02-06 04:29:23 -0800
  • 4e5ff3d6f1 Bug fix for NPE in HC with --dbsnp argument. - I had added the framework in the VA engine but should not have hooked it up to the HC yet since the RefMetaDataTracker is always null. - Added contracts and docs to the relevant methods in the VA engine so that this doesn't happen in the future. Eric Banks 2013-02-05 21:59:19 -0500
  • e7c35a907f Fixes to BQSR for the --maximum_cycle_value argument. - It's now written into the recal report so that it can be used in the PrintReads step. - Note that we also now write the --deletions_default_quality value which accidentally wasn't being written before! - Added tests to make sure that the value of the --maximum_cycle_value is being used properly by PR with -BQSR. (This is my last non-branch commit; all future pushes will follow new GATK practices) Eric Banks 2013-02-05 17:38:03 -0500
  • e7e76ed76e Replace org.broadinstitute.variant with jar built from the Picard repo David Roazen 2013-02-05 17:20:23 -0500
  • cb2dd470b6 Moving the random number generator over to using GenomeAnalysisEngine.getRandomGenerator in the logless versus exact pair hmm unit test. We don't believe this will fix the problem with the non-deterministic test failures but it will give us more information the next time it fails. Ryan Poplin 2013-02-05 12:44:59 -0500
  • f6bc5be6b4 Fixing license on Yossi's file Mauricio Carneiro 2013-02-05 11:14:43 -0500
  • 050c4794a5 Merge pull request #11 from yfarjoun/per_sample2 MauricioCarneiro 2013-02-05 08:04:29 -0800
  • 00c98ff0cf Need to reset the static counter before tests are run or else we won't be deterministic. Also need to give credit where credit is due: David was right that this was not a non-deterministic Bamboo failure... Eric Banks 2013-02-05 10:41:46 -0500
  • 23c6aee236 Added in some basic unit tests for polyploid consensus creation in RR. - Uncovered small bug in the fix that I added yesterday, which is now fixed properly. - Uncovered massive general bug: polyploid consensus is totally busted for deletions (because of call to read.getReadBases()[readPos]). - Need to consult Mauricio on what to do here (are we supporting het compression for deletions? (Insertions are definitely not supported) Eric Banks 2013-02-05 10:35:45 -0500
  • de03f17be4 -Added Per-Sample Contamination Removal to UnifiedGenotyper: Added an @Advanced option to the StandardCallerArgumentCollection, a file which should contain two columns, Sample (String) and Fraction (Double) that form the Sample-Fraction map for the per-sample AlleleBiasedDownsampling. -Integration tests to UnifiedGenotyper (Using artificially contaminated BAMs created from a mixure of two broadly concented samples) were added -includes throwing an exception in HC if called using per-sample contamination file (not implemented); tested in a new integration test. -(Note: HaplotypeCaller already has "Flat" contamination--using the same fraction for all samples--what it doesn't have is _per-sample_ AlleleBiasedDownsampling, which is what has been added here to the UnifiedGenotyper. -New class: DefaultHashMap (a Defaulting HashMap...) and new function: loadContaminationFile (which reads a Sample-Fraction file and returns a map). -Unit tests to the new class and function are provided. -Added tests to see that malformed contamination files are found and that spaces and tabs are now read properly. -Merged the integration tests that pertain to biased downsampling, whether HaplotypeCaller or unifiedGenotyper, into a new IntegrationTest class. Yossi Farjoun 2013-01-30 14:57:48 -0500
  • 70f3997a38 More RR tests and fixes. * Fixed implementation of polyploid (het) compression in RR. * The test for a usable site was all wrong. Worked out details with Mauricio to get it right. * Added comprehensive unit tests in HeaderElement class to make sure this is done right. * Still need to add tests for the actual polyploid compression. * No longer allow non-diploid het compression; I don't want to test/handle it, do you? * Added nearly full coverage of tests for the BaseCounts class. Eric Banks 2013-02-04 15:55:15 -0500
  • a281fa6548 Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter Mark DePristo 2013-02-04 15:33:57 -0500
  • eb847fa102 Message "script failed" moved to the correct place in the code Tad Jordan 2013-02-04 13:40:40 -0500
  • 79ef41e7b1 Added some docs, unit test, and contracts to SimpleDeBruijnAssembler. Ryan Poplin 2013-02-04 11:03:52 -0500
  • 43e3a040b6 Updated UnifiedGenotyper GATKDoc (note on ploidy model) Geraldine Van der Auwera 2013-02-04 14:17:05 -0500
  • 41a030f4b7 Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again: Chris Hartl 2013-02-04 14:10:32 -0500
  • 3c99010be4 Part 1 of Variant Annotator Unit tests: PerReadAlleleLikelihoodMap Chris Hartl 2013-02-04 10:02:16 -0500
  • d9fd89ecaa Somehow these md5 updates got lost in my previous git rebase disaster. Sorry for the trouble. Ryan Poplin 2013-02-04 13:26:18 -0500
  • 2d518f3063 More RR-related updates and tests. - ReduceReads by default now sets up-front ReadWalker downsampling to 40x per start position. - This is the value I used in my tests with Picard to show that memory issues pretty much disappeared. - This should hopefully take care of the memory issues being reported on the forum. - Added javadocs to SlidingWindow (the main RR class) to follow GATK conventions. - Added more unit tests to increase coverage of BaseCounts class. - Added more unit tests to test I/D operators in the SlidingWindow class. Eric Banks 2013-02-04 12:57:43 -0500
  • 9b77cdec4b Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-02-04 12:03:42 -0500
  • 971ded341b Swap java Random generator for GATK one to ensure test determinism Guillermo del Angel 2013-02-04 10:57:34 -0500
  • 5521bf3dd7 Fix bad contract implementation Guillermo del Angel 2013-02-03 16:15:14 -0500
  • f31bf37a6f First step in better BQSR unit tests for covariates (not done yet): more test coverage in basic covariates, test logging several read groups/read lengths and more combinations simultaneously. Add basic Javadocs headers for PerReadAlleleLikehoodMap. Guillermo del Angel 2013-02-03 15:31:30 -0500
  • e504806b91 GATKRunReport paranoid unit testing continues: now ensure that the public GATK cannot list buckets, objects, or delete them Mark DePristo 2013-02-03 14:01:09 -0500
  • 8d08780582 GATKRunReport now tracks the errorMessage and errorThrown during post for later analysis Mark DePristo 2013-02-02 19:24:31 -0500
  • 6382d5bdc9 Final cleanup and unit testing for GATKRunReport Mark DePristo 2013-02-02 15:05:13 -0500
  • eb17230c2f Update AWS access and private keys to the new GATK2LogUploader user Mark DePristo 2013-02-01 14:29:13 -0500
  • de35ce800d Consolidate and cleanup GATK Log infrastructure Mark DePristo 2013-02-01 12:33:49 -0500
  • 03df5e6ee6 - Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops. - Added RR qual correctness tests (note that this is a case where we don't add code coverage but still need to test critical infrastructure). - Also added minor cleanup of BaseUtils Eric Banks 2013-02-01 15:37:19 -0500
  • 24ba81c062 Merge branch 'master' of github.com:broadinstitute/gsa-unstable auto-merge Ryan Poplin 2013-02-01 13:58:31 -0500
  • 2fee000dba Adding unit tests for KBestPaths class and fixing edge case bugs. Ryan Poplin 2013-02-01 13:50:38 -0500
  • c6581e4953 Update MD5s to reflect version number change in the BAM header David Roazen 2013-02-01 12:14:31 -0500
  • c4b0ba4d45 Temporarily back out the Picard team's patches to GATKBAMIndex from December David Roazen 2013-02-01 00:36:54 -0500
  • a520058ef6 Add option to specify maximum STR length to RepeatCovariates from command line to ease testing Guillermo del Angel 2013-02-01 11:13:10 -0500
  • 1fb182d951 Restore Utils.appendArray() David Roazen 2013-02-01 01:18:51 -0500
  • 6d9816f1a5 Cleanup unused utils functions, and add unit test for one (append) Mark DePristo 2013-01-31 17:46:18 -0500
  • 22f7fe0d52 Expanded unit tests for AlignmentUtils Mark DePristo 2013-01-31 17:26:22 -0500
  • 206eab80e3 Expanded unit tests for AlignmentUtils Mark DePristo 2013-01-31 17:26:22 -0500
  • 292037dfda Rev picard, sam-jdk, and tribble David Roazen 2013-01-31 16:00:13 -0500
  • e07cefb058 Updating AlignmentUtils.consolidateCigar() to the GATK coding standards. Ryan Poplin 2013-01-31 15:57:48 -0500
  • 4c0a3b182e Update MD5s to reflect version number change in the BAM header David Roazen 2013-02-01 12:14:31 -0500
  • 874913318a Temporarily back out the Picard team's patches to GATKBAMIndex from December David Roazen 2013-02-01 00:36:54 -0500
  • 2f118c85ed Merge branch 'master' of github.com:broadinstitute/gsa-unstable Guillermo del Angel 2013-02-01 11:15:01 -0500
  • baf2c4c338 Add option to specify maximum STR length to RepeatCovariates from command line to ease testing Guillermo del Angel 2013-02-01 11:13:10 -0500
  • 48b08a0172 Restore Utils.appendArray() David Roazen 2013-02-01 01:18:51 -0500
  • 110f0d4e82 Cleanup unused utils functions, and add unit test for one (append) Mark DePristo 2013-01-31 17:46:18 -0500
  • 59028fe6f3 Expanded unit tests for AlignmentUtils Mark DePristo 2013-01-31 17:26:22 -0500
  • 63e68a725f Expanded unit tests for AlignmentUtils Mark DePristo 2013-01-31 17:26:22 -0500
  • d82b855c4c Rev picard, sam-jdk, and tribble David Roazen 2013-01-31 16:00:13 -0500
  • b4db1d3e7f Adding Clover Mark DePristo 2013-01-31 14:08:52 -0500
  • c3c4e2785b UnitTest for calcNumHighQualityBases in AlignmentUtils Mark DePristo 2013-01-31 13:57:23 -0500
  • 6ec1e613a2 Move AWS keys to a resources subdirectory within the phonehome package David Roazen 2013-01-31 11:40:40 -0500
  • 496727ac5e Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-31 11:51:08 -0500
  • ac033ce41a Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference. Ryan Poplin 2013-01-31 11:32:19 -0500
  • 9c0207f8ef Fixing BQSR/BAQ bug: If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases). The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated. Added a unit test to ensure that the tags are removed in such a case. Eric Banks 2013-01-31 11:03:17 -0500
  • 495bca3d1a Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-31 10:12:26 -0500
  • ca6968d038 Use base List and Map types in the GenotypingEngineUnitTest. Ryan Poplin 2013-01-31 10:12:18 -0500
  • 75ceddf9e5 Adding new unit tests for RR. These tests took a frustratingly long time to get to pass, but now we have a framework for testing the adding of reads into the SlidingWindow plus consensus creation. Will flesh these out more after I take care of some other items on my plate. Eric Banks 2013-01-31 09:46:38 -0500
  • 404ee9a6e4 More aggressive checking of AWS key quality upon startup in the GATK Mark DePristo 2013-01-31 09:08:26 -0500
  • b875ff4c8d Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-30 18:44:03 -0500
  • 670bf1e094 few changes in the generalCallingPipeline Ami Levy-Moonshine 2013-01-30 18:43:53 -0500
  • 438c98035b Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-30 17:12:28 -0500
  • bb29bd7df7 Use base List and Map types in the HaplotypeCaller when possible. Ryan Poplin 2013-01-30 17:09:27 -0500
  • b707331332 Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs Mark DePristo 2013-01-30 16:41:23 -0500
  • 5f4a063def Breaking up my massive commits into smaller pieces that I can successfully merge and digest. This one enables downsampling in the HaplotypeCaller (by lowering the default dcov to 20) and removes my long-standing, temporary region-based downsampling. Ryan Poplin 2013-01-30 16:14:07 -0500
  • 591df2be44 Move additional VariantContext utility methods back to the GATK David Roazen 2013-01-30 13:46:59 -0500
  • ff8ba03249 Updating BQSR integration test md5s to reflect the updates to the hierarchicalBayesianQualityEstimate function Ryan Poplin 2013-01-30 13:30:18 -0500
  • 85dabd321f Adding unit tests for hierarchicalBayesianQualityEstimate function Ryan Poplin 2013-01-30 13:26:07 -0500
  • 07fe3dd1ef Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-30 13:19:24 -0500
  • 9985f82a7a Move BaseUtils back to the GATK by request, along with associated utility methods David Roazen 2013-01-30 12:54:57 -0500
  • 51a322fb54 Remove FindContaminatingReadGroups walker and associated untested utils.NamedTable code Mark DePristo 2013-01-30 12:51:50 -0500
  • 2967776458 The Empirical quality column in the recalibration report can't be compared in the BQSRGatherer because the value is calculated using the Bayesian estimate with different priors. This value should never be used from a recalibration report anyway except during plotting. Ryan Poplin 2013-01-30 12:28:14 -0500
  • 1ff78679ca UnitTesting example for copying Mark DePristo 2013-01-30 11:18:58 -0500
  • d067c7f136 Resolving merge conflicts Eric Banks 2013-01-30 10:47:59 -0500
  • 9025567cb8 Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. Moved the merging utility methods into GenomeLoc and moved the unit tests around accordingly. Eric Banks 2013-01-30 10:45:29 -0500
  • 4852c7404e GenomeLocs are already comparable, so I'm removing the less complete GenomeLocComparator class and updating ReduceReads and CompressionStash to use built-in comparator Mark DePristo 2013-01-30 10:12:27 -0500
  • 59311aeea2 Getting back null values from the tables is perfectly reasonable if those covariates don't appear in your table. Need to handle them gracefully. Ryan Poplin 2013-01-30 10:06:14 -0500
  • e7d7d70247 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2013-01-30 10:01:06 -0500
  • 45603f58cd Refactoring and unit testing GenomeLocParser Mark DePristo 2013-01-29 16:51:39 -0500
  • 8562bfaae1 Optimize GenomeLocParser.createGenomeLoc Mark DePristo 2013-01-29 08:10:56 -0500
  • 69dd5cc902 AutoFormattingTimeUnitTest should be in utils Mark DePristo 2013-01-29 19:28:14 -0500