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  • 52345f0aec Meaningful documentation string Mark DePristo 2011-10-19 15:47:36 -0400
  • 1b38aa1a7e Cleaning up reduced read code accessors Mark DePristo 2011-10-19 15:46:44 -0400
  • d8d73fe4f2 Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown. Eric Banks 2011-10-19 15:11:13 -0400
  • 7928b287fc GATKSamRecord now produced by SAMFileReaders by default Mark DePristo 2011-10-19 13:15:27 -0400
  • 5a6468c11e Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it. Eric Banks 2011-10-19 11:52:05 -0400
  • 48c4a8cb33 Make error messages clearer (even I was confused) Eric Banks 2011-10-19 11:49:16 -0400
  • 6cadaa84c9 Just use validate() from super class since it does the same thing Eric Banks 2011-10-19 11:48:23 -0400
  • df3e4e1abd First working code to use SamRecordFactory to produce objects of our own design in SAMFileReader Mark DePristo 2011-10-19 11:22:35 -0400
  • d79b57d6f4 Fixing cases where the Object equals function wasn't being properly overridden in the haplotype caller classes. Ryan Poplin 2011-10-19 08:57:38 -0400
  • c27e2fb676 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Mauricio Carneiro 2011-10-18 15:23:05 -0400
  • 2125c4f38f Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2011-10-18 14:49:00 -0400
  • e5fc828546 With Khalid's implicit approval, I have removed this line that overrides the memory limit of the VCF-gathering function, so that the inherited limit remains Menachem Fromer 2011-10-18 14:47:39 -0400
  • f77f2eeb7d Fix for new ID structure Mark DePristo 2011-10-18 13:04:43 -0400
  • 1a92ee3593 No longer adds a binding of ID -> . when the ID field is dot in the VCF Mark DePristo 2011-10-18 10:57:02 -0400
  • e5b793f4ce A VCFToPED writer for bridging VCF files to Haploview Mark DePristo 2011-10-18 10:55:46 -0400
  • e45fcb66eb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-10-17 15:56:19 -0400
  • 1e6794c539 fixing typo in VariantsToTable docs Ryan Poplin 2011-10-17 15:56:02 -0400
  • 92e1cbfb6c Updating docs and adding option to use a very large file for GATK vs. Tribble comparison Eric Banks 2011-10-17 15:52:41 -0400
  • 0de8550f17 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-17 15:29:53 -0400
  • c1329c4dde Fixing a binary to logical or Mark DePristo 2011-10-17 15:29:45 -0400
  • 9e4963efc8 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-17 15:27:38 -0400
  • ec911ce5bb Even better error messages Mark DePristo 2011-10-17 15:27:22 -0400
  • d065bf1715 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-17 15:25:47 -0400
  • a7cf9cdc67 Fixing error message typo Mark DePristo 2011-10-17 15:25:35 -0400
  • 589df6b7cf Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-10-17 14:35:14 -0400
  • 6b02354d84 Adding a new getter in VariantsToTable to extract the indel event length. Ryan Poplin 2011-10-17 14:34:52 -0400
  • 3550798c4c Merged bug fix from Stable into Unstable Mark DePristo 2011-10-17 13:58:56 -0400
  • 4108a294f7 Better error message when a RodBinding file doesn't exist Mark DePristo 2011-10-17 13:58:46 -0400
  • cc76826f78 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-17 13:38:11 -0400
  • 09a09cacef Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable Mark DePristo 2011-10-17 13:38:00 -0400
  • fd4540cd32 Fixed extraordinarily subtle race condition with contracts invariant Mark DePristo 2011-10-17 13:37:55 -0400
  • 2193da6bfb Merged bug fix from Stable into Unstable David Roazen 2011-10-16 07:37:20 -0400
  • dcd4eee15f Revert "Intentionally breaking the binary release as a test." David Roazen 2011-10-16 07:24:33 -0400
  • 88c9a35b2a Merged bug fix from Stable into Unstable David Roazen 2011-10-15 20:28:48 -0400
  • 46badee76a Intentionally breaking the binary release as a test. David Roazen 2011-10-15 20:20:41 -0400
  • 900eb19acb Merged bug fix from Stable into Unstable David Roazen 2011-10-14 23:05:01 -0400
  • c756da1798 Remove unnecessary debugger port listening from GATKDoclet invocation. David Roazen 2011-10-14 22:59:12 -0400
  • 88d6b8bc1f Merged bug fix from Stable into Unstable David Roazen 2011-10-14 20:13:38 -0400
  • bd8bb93811 Split RScriptExecutorUnitTest into public and private test classes. David Roazen 2011-10-14 20:04:42 -0400
  • aad99563be Merged bug fix from Stable into Unstable David Roazen 2011-10-14 03:26:35 -0400
  • 442d33ba18 Enable testing of the jars produced by the packaging system. David Roazen 2011-09-28 16:23:54 -0400
  • 4f01a742cb Merged bug fix from Stable into Unstable David Roazen 2011-10-13 21:39:52 -0400
  • edfd6f8a06 Removing a public -> private dependency from the test suite. David Roazen 2011-10-13 21:32:52 -0400
  • 404ef741f1 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-13 18:02:06 -0400
  • 2ebdff074c Update MD5s for SOLiD recalibration Mark DePristo 2011-10-13 18:01:51 -0400
  • 5a881360df Merged bug fix from Stable into Unstable Mark DePristo 2011-10-13 15:54:43 -0400
  • 7cab6f6bb0 Bug fixes for thread unsafe simple timer and bad Ns treatment in AlignmentUtils Mark DePristo 2011-10-13 15:53:12 -0400
  • e12ffb6547 Updating docs for GCContentByInterval Mauricio Carneiro 2011-10-13 13:27:00 -0400
  • 0939d16a8d String not empty bug Mauricio Carneiro 2011-10-13 13:22:05 -0400
  • 22b432c404 Tool to expand intervals Mauricio Carneiro 2011-10-13 13:19:54 -0400
  • baa1c60b80 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Mauricio Carneiro 2011-10-13 12:59:57 -0400
  • 9aecd50473 Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it. Eric Banks 2011-10-12 15:44:54 -0400
  • e53a952aeb Added ION Torrent support to CountCovariates. Mauricio Carneiro 2011-10-12 01:57:02 -0400
  • a2733a451f Added NotCalled feature to GAV Mauricio Carneiro 2011-10-11 19:31:45 -0400
  • 66b5646f95 Adding hidden options to the DPP Mauricio Carneiro 2011-10-11 13:56:00 -0400
  • ae83420637 Merged bug fix from Stable into Unstable David Roazen 2011-10-11 12:26:08 -0400
  • 794f275871 SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation. David Roazen 2011-10-11 12:08:56 -0400
  • cfd0ac8410 Merged bug fix from Stable into Unstable David Roazen 2011-10-11 12:03:51 -0400
  • 24b72334b3 UnifiedGenotyper now correctly initializes the VariantAnnotator engine. David Roazen 2011-10-11 11:32:27 -0400
  • 0429b38021 Merged bug fix from Stable into Unstable Guillermo del Angel 2011-10-11 11:19:38 -0400
  • 1c485d8b5e Forgot that no matter how trivial a change it's a good idea to compile first Guillermo del Angel 2011-10-11 11:18:41 -0400
  • 6418f4d69b Merged bug fix from Stable into Unstable Guillermo del Angel 2011-10-11 11:13:18 -0400
  • 1975de1b32 Second try: hide --do_indel_quality in AnalyzeCovariates Guillermo del Angel 2011-10-11 11:11:29 -0400
  • 6506ea83e8 Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through. Guillermo del Angel 2011-10-11 11:03:12 -0400
  • 4c1d8c8d44 Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users Guillermo del Angel 2011-10-11 11:01:06 -0400
  • cffc959e58 Moving to archive instead, since no one owns it Eric Banks 2011-10-10 23:55:57 -0400
  • 77c983c5b5 No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public. Eric Banks 2011-10-10 15:17:54 -0400
  • fb72bcf732 DiffObjects no longer prints out the file name in the status so MD5 are stable Mark DePristo 2011-10-10 15:10:57 -0400
  • ac41b303fd Merge branch 'vcfAlleles' Mark DePristo 2011-10-10 13:23:52 -0400
  • 0c0a619b08 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-10 13:23:40 -0400
  • b1124b2b61 Trivial Qscript to evaluate the impact of max deletion fraction in UG Mark DePristo 2011-10-10 13:22:59 -0400
  • e3ff4f4266 Failing MD5 because output now contains absolute path Mark DePristo 2011-10-10 11:05:02 -0400
  • 3e6c16d961 CombineVariants preserves allele order Mark DePristo 2011-10-10 11:04:38 -0400
  • a4bb842958 RankSum tests have lightly different MD5 results based on allele order Mark DePristo 2011-10-10 11:04:07 -0400
  • 46e7370128 this.allele, getAlleles(), and getAltAlleles() now return List not set Mark DePristo 2011-10-09 11:45:55 -0700
  • 822654b119 UnitTests for allele getting functions in VC in prep for move from set to list Mark DePristo 2011-10-09 10:36:14 -0700
  • e19dba86a6 Merged bug fix from Stable into Unstable Matt Hanna 2011-10-08 22:37:12 -0400
  • 0016c707a3 Codecs other than VCF accidentally bled into vcf.jar. Unfortunately, vcf.jar turned out to be the *only* home for these other codecs. This change pushes them back into StingUtils.jar. Matt Hanna 2011-10-08 22:24:35 -0400
  • c67f6c076b simpleMerge now preserves allele order Mark DePristo 2011-10-08 17:39:53 -0700
  • e94e6ba101 A UnitTest to ensure that the order of alleles is maintained Mark DePristo 2011-10-08 08:47:58 -0700
  • ff3dccd062 Fixing errors in queueJobReport runtime unit Mark DePristo 2011-10-07 12:04:53 -0700
  • ec14a4a606 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-07 08:38:50 -0700
  • 6fbd41724a Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-10-07 11:20:00 -0400
  • 4514bc350f More reliable way of finding the Tribble jar. Matt Hanna 2011-10-07 11:19:29 -0400
  • 181c76750e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-10-06 22:38:55 -0400
  • ca9cd9b688 Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC. Eric Banks 2011-10-06 22:38:44 -0400
  • f91b015e0e Made the BaseTest.testDir absolute Khalid Shakir 2011-10-06 22:33:21 -0400
  • c7864c7256 Filter application order is now deterministic, in the order defined by the walker Mark DePristo 2011-10-06 18:51:40 -0700
  • 0b88af4af9 Counts of records failing filters are displayed sorted Mark DePristo 2011-10-06 18:42:26 -0700
  • d1e70d6ec2 Removed Nx counting of reads in metrics with -nt > 1 Mark DePristo 2011-10-06 18:29:26 -0700
  • d367945dec Extending InsertSizeDistribution to compute stats by sample and by read group Mark DePristo 2011-10-06 15:14:17 -0700
  • c61804a450 Rename the long version of the argument name to more accurately reflect its purpose. Eric Banks 2011-10-06 16:14:04 -0400
  • 61a3dfae24 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-10-06 15:58:04 -0400
  • 6eb87bf58a RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop. Eric Banks 2011-10-06 15:57:49 -0400
  • 6d9c210460 Updating MD5s for updated BAM with read groups Mark DePristo 2011-10-06 12:15:48 -0700
  • c528233578 Now uses exampleBAM and exampleFASTA instead of the misc. copies in validation_data Mark DePristo 2011-10-06 12:03:45 -0700
  • ab357ef900 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-06 10:50:02 -0700
  • 1b0735f0a3 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-10-06 13:41:45 -0400
  • c4dfc1fb8b Temporary commit of parallelization support for RealignerTargetCreator. Tim begged us for this and I got assurances from Khalid/Matt that this would also be extremely helpful for the whole genome calling pipeline, so I spent a while working on this. Needs to be fixed up though because apparently only the leaves in the hierarchical reduce get their output aggregated. Worked out a better solution with Matt. Eric Banks 2011-10-06 13:41:36 -0400
  • 3961733590 Merged bug fix from Stable into Unstable Matt Hanna 2011-10-06 12:54:52 -0400