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  • c0653514b3 minor update to comment in UG Ryan Poplin 2011-08-02 13:34:48 -0400
  • 2ba57bb502 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-02 13:30:46 -0400
  • 38e4ae4176 minor update to comment in UG Ryan Poplin 2011-08-02 13:30:38 -0400
  • 821bbfa9e0 Bug fixes and enhancements to run whole-genome indel VQSR, removed old chr20-only code and cleanup Guillermo del Angel 2011-08-02 13:17:20 -0400
  • 65c5d55b72 Not sure how I missed these. These lines are now superfluous. Eric Banks 2011-08-02 12:48:36 -0400
  • b9d0d2af22 Adding back temporarily removed integration test now that the file permissions have been fixed. Eric Banks 2011-08-02 12:39:11 -0400
  • 9497c303e6 Temporarily comment out annotation from the pipeline test; David will re-enable. Eric Banks 2011-08-02 12:38:47 -0400
  • 1c387848de No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests. Eric Banks 2011-08-02 10:39:50 -0400
  • a2ca994e9a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-02 10:34:53 -0400
  • 2c5e526eb7 Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed. Eric Banks 2011-08-02 10:34:46 -0400
  • 5626199bb6 The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD Eric Banks 2011-08-02 10:14:21 -0400
  • a6a87006a5 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-02 08:26:05 -0400
  • 3b2d1dee66 Final changes to indel project consensus script Guillermo del Angel 2011-08-02 08:25:50 -0400
  • 184030dd56 RefMetaDataTracker no longer automagically converts inputs to VariantContexts Mark DePristo 2011-08-01 15:21:16 -0400
  • 8b1adb8c95 Removed getVariantContext() code Mark DePristo 2011-08-01 13:41:09 -0400
  • f69bff5dd6 Commented out, because these fail the now removed dbSNP conversion. Mark DePristo 2011-08-01 13:34:25 -0400
  • 3a9b6eacdf Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-01 11:23:18 -0400
  • 4f8d830960 Updated to reflect new parse() function Mark DePristo 2011-07-30 15:34:20 -0400
  • 7b07c4e04e RefMetaDataTracker now has get() methods accepting RodBindings Mark DePristo 2011-07-30 15:34:11 -0400
  • e7b4959ebe Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-07-30 02:06:45 -0400
  • 2d94037ad0 Remove temporary index files (*.bai) Mauricio Carneiro 2011-07-30 02:05:22 -0400
  • a6691ab2fd List<RodBinding<T>> now working (sort of). Mark DePristo 2011-07-29 16:11:22 -0400
  • 6acb4aad3b RodBinding<T> are properly generic now. Mark DePristo 2011-07-29 14:37:12 -0400
  • 3b799db61a RefMetaDataTracker cleanup and unit tests Mark DePristo 2011-07-29 13:23:17 -0400
  • b06deac9ea Merged bug fix from Stable into Unstable Ryan Poplin 2011-07-29 10:02:36 -0400
  • c0d4110ffd Correcting redundant warning text. Ryan Poplin 2011-07-29 10:01:11 -0400
  • a58ddab93b minQual and minPower filters added. VCF output added. Mauricio Carneiro 2011-07-28 18:58:36 -0400
  • 39b4e76fde Continuing refactoring of RefMetaDataTracker. Mark DePristo 2011-07-28 17:48:28 -0400
  • 7c5c656b46 Uncovered fundamental accounting bug in VariantEval. Will be fixed by dev. team Mark DePristo 2011-07-28 14:19:27 -0400
  • 33b32c4211 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-07-28 13:57:22 -0400
  • 7a2a65155f Merged bug fix from Stable into Unstable Eric Banks 2011-07-28 13:56:43 -0400
  • 1afc49a297 There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor. Eric Banks 2011-07-28 13:55:58 -0400
  • f7a126722b Cleaned up VariantContext accessors in RefMetaDataTracker Mark DePristo 2011-07-28 00:16:34 -0400
  • c83f9432eb Cleaned up RefMetaDataTracker Mark DePristo 2011-07-27 23:25:52 -0400
  • 1865211b6d Merged bug fix from Stable into Unstable Eric Banks 2011-07-27 22:52:06 -0400
  • 6230315ff2 Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now. Eric Banks 2011-07-27 22:51:21 -0400
  • f3ad4ec94b Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not. Mark DePristo 2011-07-27 22:06:23 -0400
  • 06374c91d7 Adding standard header Mark DePristo 2011-07-27 21:37:12 -0400
  • 07ec5dd63a Implementation of the parameter classes A generalization of the parameters necessary to each class in the pool caller framework. Should make it more extensible and flexible, but I'm not yet convinced that this is the best approach. Trying it out. Mauricio Carneiro 2011-07-27 17:00:09 -0400
  • ff31fa7990 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-07-27 16:15:23 -0400
  • 5809a61b20 Merged bug fix from Stable into Unstable Eric Banks 2011-07-27 16:14:59 -0400
  • 64aad67b5f Fixing dbSNP adaptor for complex indels (wasn) Eric Banks 2011-07-27 16:13:45 -0400
  • 15be383d5b Merge branch 'master' into rodRefactor Mark DePristo 2011-07-27 15:36:49 -0400
  • 38a2518668 Merge branch 'master' into rodRefactor Mark DePristo 2011-07-27 15:34:54 -0400
  • 60db6cc836 Warnings for old ROD system use. Mark DePristo 2011-07-27 12:39:12 -0400
  • ab69b8e4ee Merged bug fix from Stable into Unstable Kiran V Garimella 2011-07-27 12:37:34 -0400
  • 6ebd83478b Fixed build.xml to reflect path changes for gsalib Kiran V Garimella 2011-07-27 12:37:00 -0400
  • fe52f2dd8c Merged bug fix from Stable into Unstable Kiran V Garimella 2011-07-27 12:30:15 -0400
  • ca35defdcd Moved gsalib sources from private/ to public/ Kiran V Garimella 2011-07-27 12:29:43 -0400
  • ada2f21976 Revert "Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable" Kiran V Garimella 2011-07-27 12:27:17 -0400
  • 097828a466 ParsingEngine now maintains the list of rodBindings Mark DePristo 2011-07-27 11:36:53 -0400
  • 86d38b7f0b Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-27 10:35:19 -0400
  • dc8061e7a6 Moved gsalib from private/ to public/ Kiran V Garimella 2011-07-27 10:34:56 -0400
  • e607461db1 leftover </ol> removed... Mauricio Carneiro 2011-07-26 19:31:33 -0400
  • 20a3b31b61 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Mauricio Carneiro 2011-07-26 19:29:45 -0400
  • 321afac4e8 Updates to the help layout. Mauricio Carneiro 2011-07-26 19:29:25 -0400
  • 405e521d44 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-26 17:56:48 -0400
  • 92a11ed8dc Updated MD5 for PhaseByTransmissionIntegrationTest Kiran V Garimella 2011-07-26 17:52:25 -0400
  • 412c466de6 Bug fix, wherein triple-hets after genotype refinement need to be left unphased, not just prior to refinement Kiran V Garimella 2011-07-26 17:43:43 -0400
  • 81f8e05bfa Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-07-26 17:35:46 -0400
  • f6a5e0e36a Go for global integrationtest path first, if possible. Mark DePristo 2011-07-26 17:35:30 -0400
  • 36daaa7bda Extract GA, AR2, and DR2 from the BEAGLE output Kiran V Garimella 2011-07-26 17:29:23 -0400
  • fec495e292 Fix a nasty little bug in the sharding system: if the last shard in contig n overlaps exactly on disk with the first shard in contig n+1, the shards would be merged together to avoid duplicate extraction. Unfortunately, the interval overlap filter couldn't handle shards spanning contigs, and was choosing to filter out reads from contig n+1 which should have been included. I'm not completely sure why the BAM indexing code would ever specify that the end of one chromosome had the same on-disk location as the start of the next one. I suspect that this is a indexer performance bug. Matt Hanna 2011-07-26 15:43:20 -0400
  • 9dfb57168a RodBinding source is no longer assumed to be a file Mark DePristo 2011-07-26 13:59:44 -0400
  • d0badd5bd6 RodBinding subclassed to VariantContextRodBinding for easy access to VariantContext providing RODs Mark DePristo 2011-07-26 13:54:55 -0400
  • 7ab8b53339 Support for List<RodBinding> argument type Mark DePristo 2011-07-26 11:37:31 -0400
  • 38969b9783 Prototype of RODBinding @Arguments instead of -B syntax Mark DePristo 2011-07-26 11:09:06 -0400
  • d87e6bdea0 Don't process sites where everyone is hom-ref, and print no-call genotypes when necessary Kiran V Garimella 2011-07-26 08:44:27 -0400
  • 4e09f87dfa Debug: fixed bug where position wasn't output. Experimenting with allele and genotype printing Kiran V Garimella 2011-07-26 01:44:19 -0400
  • 075f7683b2 Debug: fixed some typos that ended up referring to the wrong VCs when populating table Kiran V Garimella 2011-07-26 01:31:11 -0400
  • b51d461d09 Debug: declared missing AF columns Kiran V Garimella 2011-07-26 01:23:15 -0400
  • 2d86c0d7d4 Debug: get all attributes as raw Object types, rather than as specific types Kiran V Garimella 2011-07-26 01:19:30 -0400
  • a615556781 Debug: removed restrictions that all VCs had to be non-null Kiran V Garimella 2011-07-26 01:13:33 -0400
  • ef4101b62d Merge branch 'desktop' Kiran V Garimella 2011-07-25 17:38:03 -0400
  • 70b69d8e89 Fixed a typo - should all set(), not addColumn() Kiran V Garimella 2011-07-25 17:37:14 -0400
  • 5854a56366 Merge branch 'desktop' Kiran V Garimella 2011-07-25 17:20:43 -0400
  • 626552481f Check if the tracker is null and, if so, do not process the locus. Kiran V Garimella 2011-07-25 17:20:36 -0400
  • 3361b46add Merge branch 'desktop' Kiran V Garimella 2011-07-25 16:51:29 -0400
  • edaa0c5d7f One-off walker to take a whole bunch of RBP-analysis VCFs and dump them to an R-readable table Kiran V Garimella 2011-07-25 16:40:16 -0400
  • 088fc39308 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-25 15:54:56 -0400
  • 6fd6684e86 Merged bug fix from Stable into Unstable Matt Hanna 2011-07-25 15:21:17 -0400
  • 6f43284053 Switch to including our entire exception tree rather than just UserException. Matt Hanna 2011-07-25 15:19:41 -0400
  • a53aeb75ab Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-07-25 15:10:35 -0400
  • a29554e565 Removing the Genomic Annotator and its supporting classes Eric Banks 2011-07-25 15:10:25 -0400
  • 5136eea7be Merge branch 'desktop' Kiran V Garimella 2011-07-25 15:02:42 -0400
  • 3afcb3415d Max of 1000 records will be loaded and compared to avoid heap size problem. Mark DePristo 2011-07-25 14:58:31 -0400
  • 504b3ef5ef Removed constraint to only evaluate eval and comp tracks at sites where genotypes match. Kiran V Garimella 2011-07-25 14:58:10 -0400
  • af0b5883c3 In unstable, add a reference to DocumentedGATKFeature to vcf.jar, which is now a static dependency of UserExceptions. Matt Hanna 2011-07-25 14:36:12 -0400
  • 6c49197de6 Merged bug fix from Stable into Unstable Matt Hanna 2011-07-25 14:32:33 -0400
  • a00e302321 Fix formatting issue. Matt Hanna 2011-07-25 14:31:40 -0400
  • 29c08ac3c6 Merge branch 'desktop' Kiran V Garimella 2011-07-25 14:06:52 -0400
  • a2d280b85e Forgot to change the name of the switchState columns Kiran V Garimella 2011-07-25 14:06:41 -0400
  • b11765b360 Merge branch 'desktop' Kiran V Garimella 2011-07-25 13:53:43 -0400
  • a0dd166364 Print metrics for both the unphased and rbp-phased data for easier comparison. Kiran V Garimella 2011-07-25 13:53:33 -0400
  • 2a51543693 Actually should have been gone... Mark DePristo 2011-07-25 13:27:42 -0400
  • ebfd8df06c Restoring accidentially deleted unit test Mark DePristo 2011-07-25 13:25:30 -0400
  • f3049fba63 refdata directory cleanup Mark DePristo 2011-07-25 13:21:52 -0400
  • 8014fad6ff Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-07-25 13:20:44 -0400
  • 2ac490dbdf Fix improper detection of command-line arguments with missing values. Matt Hanna 2011-07-25 13:20:00 -0400
  • ac5a11b4f3 Merge branch 'desktop' Kiran V Garimella 2011-07-25 13:18:41 -0400