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  • 2bb77a7978 Docs for all VariantAnnotator annotations Mark DePristo 2011-09-23 09:04:16 -0400
  • 68d5544ec9 Accurate docs for IOCrusher Mark DePristo 2011-09-23 09:03:50 -0400
  • dd65ba5bae @Hidden for DocumentationTest and GATKDocsExample Mark DePristo 2011-09-23 09:03:37 -0400
  • dfce301beb Looks for @Hidden annotation on all classes and excludes them from the docs Mark DePristo 2011-09-23 09:03:04 -0400
  • 106a26c42d Minor file cleanup Mark DePristo 2011-09-23 08:25:20 -0400
  • a9f073fa68 Genotype merging unit tests for simpleMerge Mark DePristo 2011-09-23 08:24:49 -0400
  • 4397ce8653 Moved removePLs to VariantContextUtils Mark DePristo 2011-09-23 08:23:46 -0400
  • 054c475416 Updating md5 because the file changed Eric Banks 2011-09-23 07:49:59 -0400
  • a8e0fb26ea Updating md5 because the file changed Eric Banks 2011-09-23 07:33:20 -0400
  • c49cc623de Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-22 17:26:21 -0400
  • dab7232e9a simpleMerge UnitTest for not annotating and annotating to different info key Mark DePristo 2011-09-22 17:26:11 -0400
  • 30ab3af0c8 A few more simpleMerge UnitTest tests for filtered vcs Mark DePristo 2011-09-22 17:14:59 -0400
  • 5cf82f9236 simpleMerge UnitTest tests filtered VC merging Mark DePristo 2011-09-22 17:05:12 -0400
  • 46ca33dc04 TestDataProvider now can be named Mark DePristo 2011-09-22 17:04:32 -0400
  • 96c875399c Merging many bug fixes to reduce reads Mauricio Carneiro 2011-09-22 17:04:11 -0400
  • f1f7335e7b In the trim to 95% curation function, ensure that no filtering happens when the sd is zero (e.g. when BAD_CYCLES is uniformly zero across all relevant samples). Matt Hanna 2011-09-22 16:46:38 -0400
  • 4040d1c7d6 More conservative defaults for reduce reads Mauricio Carneiro 2011-09-22 15:53:23 -0400
  • 39b54211d0 Fixed hard clipping soft clipped bases after hard clips Mauricio Carneiro 2011-09-22 15:46:55 -0400
  • 5bca1f732f Little bug fixes in preQC: - Filter out per-library information in per-sample metrics so that our aggregator doesn't crash out while we figure out how to handle data per-library rather than per-sample. - Compare preQC metrics for custom captures to all exome data. Note that not every metric makes sense when compared to every other bait set, so a warning message is emitted on the summary page. Matt Hanna 2011-09-22 15:18:40 -0400
  • 68da555932 UnitTest for simpleMerge for alleles Mark DePristo 2011-09-22 15:16:37 -0400
  • 1acf7945c5 Fixed hard clipped cigar and alignment start Mauricio Carneiro 2011-09-22 14:51:14 -0400
  • 80d7300de4 Unit test was passing in FORMAT as one of the sample names. There used to be a hack in the VCFHeader to check for this and remove it and I couldn't figure out why, but now I know. Hack was removed and now the unit test passes in only the sample names as per the contract. Eric Banks 2011-09-22 13:28:42 -0400
  • 4e9020c9f7 Fixed alignment start for hard clipping insertions Mauricio Carneiro 2011-09-22 13:28:25 -0400
  • 9c1728416c Revert "Updating md5 for fixed file" because this was fixed properly in unstable (but will break SnpEff if put into Stable). Eric Banks 2011-09-22 13:16:42 -0400
  • 888d8697b1 Merged bug fix from Stable into Unstable Eric Banks 2011-09-22 13:16:31 -0400
  • 15a410b24b Updating md5 for fixed file Eric Banks 2011-09-22 13:15:41 -0400
  • 8811bb8668 Merge branch 'stable' Mark DePristo 2011-09-22 12:11:01 -0400
  • ba5f83fee2 start of VariantContextUtils UnitTest Mark DePristo 2011-09-22 12:10:39 -0400
  • 5e06a45628 Fix the AnalayzeCovariates packaging. Eric Banks 2011-09-22 11:55:40 -0400
  • 8ca4b5e938 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-22 11:42:19 -0400
  • d3cc25454c Updating the MDCP Mauricio Carneiro 2011-09-22 11:27:40 -0400
  • 93dd1faa5f Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-22 11:20:10 -0400
  • a05c959e5a Empty unit tests for VariantContextUtils Mark DePristo 2011-09-22 11:20:07 -0400
  • 3fdee2b9ed Merge from stable into unstable Mark DePristo 2011-09-22 11:19:43 -0400
  • 623c49765d NO BAQ ON EXOMES! Mauricio Carneiro 2011-09-22 11:13:40 -0400
  • 63758efc17 Adding in a qscript for running the ILG (as calculating the insert size distribution needs to happen first). Christopher Hartl 2011-09-22 11:02:26 -0400
  • 4f4a0fc38a Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git Christopher Hartl 2011-09-22 11:01:58 -0400
  • 982c47bfa7 Remove duplicate effort in ReadUtils (with apologies to Mauricio) Big (but not major) cleanup of code in ILG - mostly excising the old likelihood model Activated the early-abort check for ILG. I think it should be better this way. Christopher Hartl 2011-09-22 10:58:26 -0400
  • c514df6d18 Merge of stable into unstable Mark DePristo 2011-09-22 10:34:27 -0400
  • f81a41b889 Updating MD5s for CombineVariants Mark DePristo 2011-09-22 10:30:25 -0400
  • b8ea9ceb68 Adding integration test that uses the -V:dbsnp binding to make sure it won't fail later on if someone messes with Tribble. Eric Banks 2011-09-21 22:43:31 -0400
  • 8f8b59a932 My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs. Eric Banks 2011-09-21 22:23:28 -0400
  • e53cb79d42 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-09-21 20:26:54 -0400
  • 5d0f284305 Fixing exome specific arguments to the VQSR in the methods development calling pipeline Ryan Poplin 2011-09-21 20:26:28 -0400
  • dc96f6da79 Merge branch 'master' of ssh://chartl@gsa2/humgen/gsa-scr1/chartl/dev/git Christopher Hartl 2011-09-21 18:18:41 -0400
  • f9cdc119af Added a method to ReadUtils that converts reads of the form 10S20M10S to 40M (just unclips the soft-clips). Christopher Hartl 2011-09-21 18:16:42 -0400
  • faff6e4019 Failed to commit changes to the GATKReport required for more easy access when using the files as data sources (read: histograms) for walkers Christopher Hartl 2011-09-21 18:15:23 -0400
  • 96768c8a18 Sending latest bug fixes to Reduce Reads to the main repository Mauricio Carneiro 2011-09-21 17:43:11 -0400
  • 70335b2b0a Hard clipping soft clipped reads to fix misalignments. Mauricio Carneiro 2011-09-21 17:12:01 -0400
  • 1b47dcb1b5 Removing old intron loss genotyper (though all of the development tree got rebased away, I hope); committing a new version of the likelihood calculation model and the genotyper, as well as the sequence simulator (and a QualityScoreHisotgramWalker to help with the simulation of read qualities). RFA will remain local for now. Christopher Hartl 2011-09-21 16:55:09 -0400
  • ef05827c7b Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-09-21 16:40:47 -0400
  • 3b51d9106a Adding in likelihood calculations for mendelian violations. Also fixing a minor and rare bug in SelectVariants when specifying family structure on the command line. Christopher Hartl 2011-09-21 16:40:29 -0400
  • 04968c88b3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-21 15:43:25 -0400
  • c6ba944719 Adding bgzip vcf file for unit tests Mark DePristo 2011-09-21 15:39:45 -0400
  • 6bcfce225f Fix for dynamic type determination for bgzip files Mark DePristo 2011-09-21 15:39:19 -0400
  • 9f6f0c443c Marginally cleaner isVCFStream() function Mark DePristo 2011-09-21 15:25:01 -0400
  • 5fef6dc5d0 Merged bug fix from Stable into Unstable Ryan Poplin 2011-09-21 15:23:06 -0400
  • 2585fc3d6c Updating Rscript path doc text for Broad users Ryan Poplin 2011-09-21 15:22:26 -0400
  • 74f9ccf6dd Merge Mark DePristo 2011-09-21 11:30:11 -0400
  • 6592972f82 Putative fix for BAQ array out of bounds Mark DePristo 2011-09-21 11:25:08 -0400
  • 174859fc68 Don't allow whitespace in the INFO field Eric Banks 2011-09-21 11:14:54 -0400
  • ecc7f34774 Putative fix for BAQ problem. Mark DePristo 2011-09-21 11:09:54 -0400
  • 7d11f93b82 Final bugfix for CombineVariants Mark DePristo 2011-09-21 10:58:32 -0400
  • b36d396c16 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-21 10:16:24 -0400
  • 34f435565c Accidentally committed unclean tribble jar to repo Mark DePristo 2011-09-21 10:16:17 -0400
  • a91ac0c5db Intermediate commit of bugfixes to CombineVariants Mark DePristo 2011-09-21 10:15:05 -0400
  • ac4f2d6d34 Fixing choppy consensus reads Mauricio Carneiro 2011-09-21 00:49:50 -0400
  • 48c413fee8 Now throws an error when the mismatch fraction is too high Mark DePristo 2011-09-20 21:28:31 -0400
  • 3b9314aecf Max fraction of mismatch test for debugging Mark DePristo 2011-09-20 20:42:18 -0400
  • b04d8eab55 Merged bug fix from Stable into Unstable David Roazen 2011-09-20 17:24:14 -0400
  • 758ecf2d43 Bringing latest updates of ReduceReads to the master repository Mauricio Carneiro 2011-09-20 16:35:09 -0400
  • d9ea764611 SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file. David Roazen 2011-09-20 15:22:27 -0400
  • bffd3cca6f Bug fix for reduced read; only adds regular bases for calculation Mark DePristo 2011-09-20 15:07:06 -0400
  • 83bb91020f Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-20 14:52:54 -0400
  • a97e039a62 Thanks to Chris for instructing me to use VCFExtractIntervals to get proper scattering of Variant Annotation Menachem Fromer 2011-09-20 14:29:39 -0400
  • 827c942c80 Rev tribble Mark DePristo 2011-09-20 14:01:14 -0400
  • a1b4cafe7a Bug fix for NPE when timer wasn't initialized Mark DePristo 2011-09-20 13:59:59 -0400
  • 08ffb18b96 Renaming datasets in the MDCP Mauricio Carneiro 2011-09-20 11:02:51 -0400
  • b7511c5ff3 Fixed long-standing bug in tribble index creation Mark DePristo 2011-09-20 10:53:18 -0400
  • efce2ece9d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-09-20 09:08:38 -0400
  • 5d0705acd6 Adding quality scores to the VCF records created by the Haplotype Caller Ryan Poplin 2011-09-20 09:07:28 -0400
  • 230e16d7c0 Merge branch 'master' into rodrewrite Mark DePristo 2011-09-20 06:54:18 -0400
  • b507bd946c Merged bug fix from Stable into Unstable Khalid Shakir 2011-09-20 00:18:16 -0400
  • 61b89e236a To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1. Khalid Shakir 2011-09-20 00:14:35 -0400
  • aa8afa3899 Merge Mark DePristo 2011-09-19 21:16:47 -0400
  • 56106d54ed Changing ReadUtils behavior to comply with GenomeLocParser Mauricio Carneiro 2011-09-19 14:00:00 -0400
  • 080c957547 Fixing contracts for SoftUnclippedEnd utils Mauricio Carneiro 2011-09-19 13:53:08 -0400
  • ba150570f3 Updating to use new rod system syntax plus name change for CountRODs Eric Banks 2011-09-19 13:30:32 -0400
  • 5e832254a4 Fixing ReadAndInterval overlap comments. Mauricio Carneiro 2011-09-19 13:28:41 -0400
  • ecb8466662 Merged bug fix from Stable into Unstable Christopher Hartl 2011-09-19 12:32:08 -0400
  • 8143def292 Fix the -T argument in the DepthOfCoverage docs Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file Christopher Hartl 2011-09-19 10:29:06 -0400
  • 095f75ff7d Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-09-19 12:24:12 -0400
  • 85626e7a5d We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too. Eric Banks 2011-09-19 12:24:05 -0400
  • 034b868588 Revert "Fix the -T argument in the DepthOfCoverage docs" Christopher Hartl 2011-09-19 12:16:07 -0400
  • cfde0e674b Merge branch 'sgintervals' Mark DePristo 2011-09-19 12:02:41 -0400
  • 3e93f246f7 Support for sample sets in AssignSomaticStatus Mark DePristo 2011-09-19 11:40:45 -0400
  • 41ffb25b74 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-19 10:55:18 -0400
  • ca1b30e4a4 Fix the -T argument in the DepthOfCoverage docs Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file Christopher Hartl 2011-09-19 10:29:06 -0400
  • 4ad330008d Final intervals cleanup Mark DePristo 2011-09-19 10:19:10 -0400
  • 6ea57bf036 Merge branch 'master' into sgintervals Mark DePristo 2011-09-19 09:50:19 -0400