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• 62011403b0 Constrains evaluation to places where both the unphased and rbp-phased data show the same genotype. Kiran V Garimella 2011-07-25 13:00:29 -0400
• 90947ab359 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-07-25 12:53:56 -0400
• 44bd9ae703 Restoring UninstantiableWalker, as it is not going to be possible to run ant test; ant gatkdocs without ant clean in between Mark DePristo 2011-07-25 12:53:06 -0400
• acda8eb09c Commented out test that causes new CommandLineGATK() to fail Mark DePristo 2011-07-25 12:43:27 -0400
• 95b48eface Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable into repval Mauricio Carneiro 2011-07-25 12:09:09 -0400
• 987e889137 Merge branch 'desktop' Kiran V Garimella 2011-07-25 11:50:15 -0400
• 0eecda6be4 Forgot to toggle switch state when genotypes are first seen in a reversed or consistent phase. Kiran V Garimella 2011-07-25 11:50:02 -0400
• 357f503a21 Merge branch 'desktop' Kiran V Garimella 2011-07-25 11:36:27 -0400
• 6389b29c4f Computes the switch error rate for many samples at a time. Kiran V Garimella 2011-07-25 11:36:08 -0400
• 0b43ee117c Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default). Kiran V Garimella 2011-07-25 11:35:34 -0400
• bbb8473f03 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-25 10:59:00 -0400
• 1a268ff1fd Refactor so that GenotypeAnnotation and InfoFieldAnnotation share common superclass VariantAnnotatorAnnotation Mark DePristo 2011-07-25 10:55:09 -0400
• 7f8e6a97ee InfoFieldAnnotation now an abstract class extended by annotations so doc system works Mark DePristo 2011-07-25 10:47:11 -0400
• 5db05d2873 Refactored Mills codecs so that they're in correct packages Guillermo del Angel 2011-07-25 10:25:25 -0400
• 115879b31f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-07-25 10:13:16 -0400
• 4c6c16f895 Documented following the new gatkdoc framework Mauricio Carneiro 2011-07-25 00:25:08 -0400
• 2039ce6102 Default values now displayed in arguments Mark DePristo 2011-07-24 22:56:55 -0400
• c43b5981f2 Hidden variables are hidden by default. Settable by command line option Mark DePristo 2011-07-24 20:52:44 -0400
• 1c1f1da349 Fixing compilation Mark DePristo 2011-07-24 20:01:59 -0400
• 9f06f6c493 Split GATKDoclet from ResourceBundleDoclet. Refactored GaTKDocWorkUnit Mark DePristo 2011-07-24 20:00:04 -0400
• e602166f78 First fully functional version outputting a full vcf Guillermo del Angel 2011-07-24 19:38:59 -0400
• 7b84347047 Main index is sorted by the template now. Mark DePristo 2011-07-24 18:19:40 -0400
• ff85687679 Merge branch 'master' into help Mark DePristo 2011-07-24 18:14:32 -0400
• 83996f7951 Enumerated types are working. Mark DePristo 2011-07-24 18:14:21 -0400
• 3c34e9fa65 Cleanup emuns and tables Mark DePristo 2011-07-24 17:45:58 -0400
• c620d96c96 Inline enum documentation is working Mark DePristo 2011-07-24 17:22:14 -0400
• 793e7d3d1d Improved header and argument details Mark DePristo 2011-07-24 16:36:25 -0400
• c6af4efcdc Implemented see also and version header Mark DePristo 2011-07-24 16:10:17 -0400
• b8db0510e0 Sytle sheet and common functions Mark DePristo 2011-07-24 15:43:23 -0400
• 5e0fe2d0f9 Support for style.css via refactored common.html included in all files Mark DePristo 2011-07-24 15:42:39 -0400
• d0ab6bf7a9 Now links to sub and superclass documentation, where possible. Mark DePristo 2011-07-24 09:56:17 -0400
• e2dabb70b8 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-07-24 08:57:47 -0400
• 1ef964c92c Merge branch 'contig' Mauricio Carneiro 2011-07-24 02:40:42 -0400
• e0cb403b33 A read walker for contig statistics Mauricio Carneiro 2011-07-24 02:36:17 -0400
• 7ffedf211c Contig comparator -- sorting contigs like Picard Mauricio Carneiro 2011-07-24 02:24:04 -0400
• 6b501e267b Includes non-concrete classes in docs Mark DePristo 2011-07-23 22:15:01 -0400
• 7420ed098e Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another Mark DePristo 2011-07-23 22:07:30 -0400
• 999acacfa1 Merge branch 'master' into help Mark DePristo 2011-07-23 20:19:33 -0400
• 1d3bcce2c4 Merge branch 'master' into NoDistributedGATK Mark DePristo 2011-07-23 20:04:50 -0400
• e262f4e10b gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs Mark DePristo 2011-07-23 20:00:35 -0400
• ac3eaf5d54 Next intermediate version of MillsGenotypeDecoderWalker Guillermo del Angel 2011-07-23 17:30:37 -0400
• 1f8fc4a041 Added edu.mit.broad.picard to Queue packaged jar. Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems. Khalid Shakir 2011-07-23 14:40:29 -0400
• dcf21f379a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Mauricio Carneiro 2011-07-23 12:59:53 -0400
• f0a6dd27a1 Renaming the plot output directory names. Mauricio Carneiro 2011-07-23 12:59:37 -0400
• 0b36b6540f Merge branch 'laptop' Kiran V Garimella 2011-07-23 01:44:54 -0400
• e23cb27451 Modified MD5 to account for the triple hets that shouldn't be phased Kiran V Garimella 2011-07-23 01:44:44 -0400
• 1dba8b768c Merge branch 'laptop' Kiran V Garimella 2011-07-23 01:39:15 -0400
• 57e3d136eb Don't try to phase triple-hets either. Kiran V Garimella 2011-07-23 01:38:58 -0400
• f366124778 Merge branch 'laptop' Kiran V Garimella 2011-07-23 01:25:36 -0400
• 45f2ca8d99 Changed MD5 to reflect latest changes to PhaseByTransmission. Kiran V Garimella 2011-07-23 01:21:07 -0400
• 5af9d50183 Merge branch 'laptop' Kiran V Garimella 2011-07-23 01:12:06 -0400
• 5521919cc9 Fixed bug where variants to phase were not being selected properly. Kiran V Garimella 2011-07-23 01:11:28 -0400
• 7da99388ac Merge branch 'laptop' Kiran V Garimella 2011-07-23 01:01:11 -0400
• 58eed20b83 Copy all entries from the attributes map, rather than attempting to modify an unmodifiable map. Kiran V Garimella 2011-07-23 01:00:46 -0400
• b5deff48e6 Merge branch 'laptop' Kiran V Garimella 2011-07-23 00:56:50 -0400
• 5638017137 Removed the nofilters argument specification in the integrationtest Kiran V Garimella 2011-07-23 00:56:23 -0400
• ffa361f57f Merge branch 'laptop' Kiran V Garimella 2011-07-23 00:50:38 -0400
• 9417ba8c2c Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field. Kiran V Garimella 2011-07-23 00:48:26 -0400
• 28b9432d26 Docs for read filters, the engine, and the UserExceptions. Mark DePristo 2011-07-22 16:09:21 -0400
• 98d6cf9886 Added superclass to the probability models. Mauricio Carneiro 2011-07-22 16:01:21 -0400
• 051c1dc639 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Kiran V Garimella 2011-07-22 15:59:00 -0400
• d7b3f40259 Merge remote-tracking branch 'unstable/master' Eric Banks 2011-07-22 14:45:24 -0400
• 4f78025b0b Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-07-22 14:42:04 -0400
• 4080e2cd88 * Added the decoy reference to the bundle under the b37 resources. * Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki). Mauricio Carneiro 2011-07-22 14:41:22 -0400
• f0be7348be Generalized handler to allow it to be used with any arbitrary class structure. DocumentedGATKFeature now includes a field for the group name. Build.xml works with public / private now. Mark DePristo 2011-07-22 14:07:40 -0400
• f50145b872 Reinitialize random seed in the bwa bindings from the fixed seed stored in the BWA support files every time the support files are loaded. Matt Hanna 2011-07-22 13:41:53 -0400
• 453954182e Generalized the documentation system to use a class-specific annotation and processor. Need to generalize and bug fix the system. But at a high level it's working now. Mark DePristo 2011-07-22 13:18:33 -0400
• b8a0fd2a8d Multiply fractionRandom by 100.0 so that the line that indicates the percentage of variants that will be output says (for instance) 90%, not 0.9% Kiran V Garimella 2011-07-22 11:54:59 -0400
• aab527064e debug version Guillermo del Angel 2011-07-22 10:32:56 -0400
• 9e88d51db9 Removed now unused @version tags from walker docs. Mark DePristo 2011-07-22 09:57:03 -0400
• 88bbd9581a debug version Guillermo del Angel 2011-07-22 09:53:20 -0400
• 1e80d715ff debug version Guillermo del Angel 2011-07-22 09:47:10 -0400
• 421b70ca4f Removed previous, and largely unused, help system extensions. This involved deleting the utils/help/*Taglet.java classes, which parsed out these fields unnecessarily This also involved removing the few uses of these from the codebase. For these uses, though, almost all were an identical copy of the first line of the docs, which is the default javadoc behavior anyway. Mark DePristo 2011-07-22 09:42:44 -0400
• 9c1bd3b75a debug version Guillermo del Angel 2011-07-22 09:21:44 -0400
• 172b35372b Moved all of the distributed GATK code to archive. Mark DePristo 2011-07-22 09:20:32 -0400
• e922ebc29d Missed this template for walker index. Mark DePristo 2011-07-22 09:13:33 -0400
• 90b887372c debug version Guillermo del Angel 2011-07-22 09:03:33 -0400
• 3d0853149b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-07-22 08:13:58 -0400
• 6afe63690d Two more true oneoffs (committed mostly for didactic purposes): codec that reads Mills/Devine indel table into a vcf and another (in progress) that will read indel chip genotype data and produce a vcf Guillermo del Angel 2011-07-22 08:13:05 -0400
• 8b8f121cfb Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Khalid Shakir 2011-07-21 23:01:11 -0400
• 59eb1f4663 Memory limits changed from Int to Double. Updated LSF calls to read memory units from config along with tweaks to select hosts. Moved some common code from GridEngine and LSF to super classes. Khalid Shakir 2011-07-21 22:57:18 -0400
• e1b9cf2595 getting rid of useless imports Mauricio Carneiro 2011-07-21 21:48:05 -0400
• eb104156ae now takes -sp (number of samples per pool) instead of estimating the maxAlleleCount from the total number of samples in the file (this was only good for test runs). Mauricio Carneiro 2011-07-21 21:45:20 -0400
• 8d7ef1bb51 Complete refactor of the ReplicationValidation framework, plus the following new functionality: * merges all pools in a lane. * merges all lanes in a site. Mauricio Carneiro 2011-07-21 21:39:00 -0400
• 81d0cab27e Walker index html now emited. Mark DePristo 2011-07-21 16:01:54 -0400
• e892489696 V2 of the document system. Now uses GATKDoc class to organize documentation for arguments. Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class. Mark DePristo 2011-07-21 15:20:34 -0400
• 87f991aee7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-07-21 13:35:24 -0400
• 2f5d10d16b Fix bug wherein aligner could be closed prior to its being used to lowercase sequences. Christopher Hartl 2011-07-21 13:21:48 -0400
• 7054c5342f When using the BWA bindings, you have to explicitly call close() to get the bindings to release memory. It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA. Matt Hanna 2011-07-21 12:13:29 -0400
• 84c66d4b92 Bug fixes Guillermo del Angel 2011-07-21 11:52:51 -0400
• c4684f4659 A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order Guillermo del Angel 2011-07-21 11:20:46 -0400
• 623143454b Merge branch 'laptop' Kiran V Garimella 2011-07-21 11:07:02 -0400
• bf6388fa8c Print haplotype start locus Kiran V Garimella 2011-07-21 11:06:45 -0400
• 15610ce0c3 Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage. Christopher Hartl 2011-07-21 11:04:22 -0400
• 1aefc02d2e Merge branch 'laptop' Kiran V Garimella 2011-07-21 10:54:15 -0400
• 45e536dca8 Reenable haplotype printing Kiran V Garimella 2011-07-21 10:40:40 -0400
• 664246937c Try to resolve merge conflict Guillermo del Angel 2011-07-21 10:19:26 -0400
• 1933be36b4 Ignore sites where the alleles don't match between the two files Kiran V Garimella 2011-07-21 03:44:02 -0400
• d9909537ef Merge branch 'laptop' Kiran V Garimella 2011-07-21 03:22:59 -0400
• 58873c391f Don't print the haplotypes anymore - the metrics will do Kiran V Garimella 2011-07-21 03:22:44 -0400