| 26e7992 | Eddie Belter | 11 September 2012, 20:10:43 UTC | AQID: switch from ref seq names to ids | 13 September 2012, 21:39:07 UTC |
| 4e3c04d | Eddie Belter | 11 September 2012, 19:38:39 UTC | AQID: mv additional 454 logic into add pp to pse from execute | 13 September 2012, 21:39:06 UTC |
| f8308b9 | Eddie Belter | 11 September 2012, 19:24:46 UTC | AQID: Move checking pps added to pse out of add pp to pse | 13 September 2012, 21:39:06 UTC |
| c8160fa | Brian Derickson | 13 September 2012, 17:42:51 UTC | added INT/TERM handlers during archive/unarchive that kills HPSS job and cleans up archive directory | 13 September 2012, 21:39:06 UTC |
| 5767316 | Brian Derickson | 13 September 2012, 16:45:53 UTC | new method that kills a given LSF job | 13 September 2012, 21:39:06 UTC |
| eaf56f8 | Travis Abbott | 13 September 2012, 17:21:09 UTC | fix generation of Sample_List.txt sample names from the vcf file were being compared to sample objects from the population group rather than their names. | 13 September 2012, 21:39:06 UTC |
| 8fa26ff | Travis Abbott | 13 September 2012, 17:05:53 UTC | eliminate uninitialized string warning | 13 September 2012, 21:39:06 UTC |
| ac932c4 | Nathan Dees | 13 September 2012, 16:21:18 UTC | added doc to describe funding and manuscript citation | 13 September 2012, 21:39:06 UTC |
| ffcf365 | Nathan Dees | 13 September 2012, 16:20:23 UTC | Fixed case if one puts NA in the model file in the variant / gene name column | 13 September 2012, 21:39:06 UTC |
| ab2465e | David Morton | 13 September 2012, 01:48:10 UTC | Cosmetic improvement to genome pp view clean up whitespace around strelka args. | 13 September 2012, 21:39:06 UTC |
| f6bb57b | David Morton | 13 September 2012, 01:47:05 UTC | Cleanup tree_to_string fn | 13 September 2012, 21:39:05 UTC |
| 9503228 | David Morton | 12 September 2012, 22:23:52 UTC | Created genome individual view The most likely user will be people looking at individuals to see if they are candidates for clin-seq, so defaults are made sensible for that purpose. | 13 September 2012, 21:39:05 UTC |
| 368160d | David Morton | 12 September 2012, 22:23:15 UTC | genome pp view has option for showing model info | 13 September 2012, 21:39:05 UTC |
| 19fc038 | David Morton | 12 September 2012, 20:43:26 UTC | genome pp view uses IO::Handle refactor that is cleaner and makes view more responsive because it prints lines immediately instead of big chunks at a time. | 13 September 2012, 21:39:05 UTC |
| a851984 | David Morton | 12 September 2012, 20:42:02 UTC | Make Utility::Text export fns And various small fn fixes. | 13 September 2012, 21:39:05 UTC |
| 1e48c23 | Mark Burnett | 13 September 2012, 15:10:48 UTC | Improve UCSC table resolution for builds | 13 September 2012, 21:39:05 UTC |
| b00266b | Travis Abbott | 13 September 2012, 03:44:35 UTC | always validate clinical data in phenotype correlation. | 13 September 2012, 21:39:05 UTC |
| 95fcfa7 | Travis Abbott | 13 September 2012, 02:24:20 UTC | add vcf identifiers to variant names in varmatrix | 13 September 2012, 21:39:05 UTC |
| 1edce2a | Travis Abbott | 13 September 2012, 01:56:37 UTC | ClinicalData: coerce_to_binary => convert_attr_to_factor In PhenotypeCorrelation's ClinicalData class, the coerce_to_binary function has been updated to support converting into factors with an arbitrary number of specified levels. Example: $cd->coerce_to_binary($name, zero => "x", one => "y") is now $cd->convert_attr_to_factor($name, levels => ["x", "y"]) Both of these verify that attr $name contains only 'x', 'y', and undef, and converts x => 0, y => 1. | 13 September 2012, 21:39:04 UTC |
| 470d6e8 | Obi Griffith | 13 September 2012, 00:47:33 UTC | Fixed case of HopkinsGroom category | 13 September 2012, 21:39:04 UTC |
| ffe5b70 | Obi Griffith | 12 September 2012, 23:44:07 UTC | wrote new importer for Hopkins and Groom dataset | 13 September 2012, 21:39:04 UTC |
| d9a84dd | Malachi Griffith | 12 September 2012, 23:01:25 UTC | Added various subroutines for examining status of reference alignment models | 13 September 2012, 21:39:04 UTC |
| 77ac44b | Mark Burnett | 12 September 2012, 21:37:42 UTC | Fix bugs with ImportedAnnotation gap file fetching | 13 September 2012, 21:39:04 UTC |
| 77d9d07 | Mark Burnett | 12 September 2012, 21:36:05 UTC | Add ability to get gap data from multiple tables | 13 September 2012, 21:39:04 UTC |
| 10e756a | Mark Burnett | 12 September 2012, 19:50:26 UTC | Add gap list to reference annotation. | 13 September 2012, 21:39:04 UTC |
| d9a9a53 | Travis Abbott | 12 September 2012, 21:53:43 UTC | make identify_{cases,controls}_by optional | 13 September 2012, 21:39:04 UTC |
| 3b37abc | Travis Abbott | 12 September 2012, 20:54:12 UTC | force 0/1 encoding on binary traits in PhenotypeCorrelation case/control | 13 September 2012, 21:39:03 UTC |
| 6b715ae | Travis Abbott | 12 September 2012, 19:44:25 UTC | move PhenotypeCorrelation case/control test data dir | 13 September 2012, 21:39:03 UTC |
| 93d72ef | Travis Abbott | 12 September 2012, 19:42:11 UTC | use updated ClinicalData to_filehandle method which replaces write_file | 13 September 2012, 21:39:03 UTC |
| 1029f7c | Travis Abbott | 12 September 2012, 19:39:28 UTC | rename ClinicalData tests one tests construction from the database, the other from files | 13 September 2012, 21:39:03 UTC |
| 31265b9 | Travis Abbott | 12 September 2012, 19:36:59 UTC | added coercion to binary for traits in clinical data | 13 September 2012, 21:39:03 UTC |
| d4c8deb | Thomas Mooney | 12 September 2012, 20:53:50 UTC | Use the is_input magic of Models rather than defining explicit relations. | 13 September 2012, 21:39:03 UTC |
| 9ee0b0d | Thomas Mooney | 12 September 2012, 20:49:14 UTC | Better support for inputs that are UR::Values. These changes allow UR::Value inputs to be specified in Model->create() as seen in upcoming G:M:GenePrediction::Bacterial changes. | 13 September 2012, 21:39:03 UTC |
| 3ecd5f6 | Eddie Belter | 12 September 2012, 20:24:37 UTC | Ref Align PP: change default value of seq platform from 3730 to sanger | 13 September 2012, 21:39:03 UTC |
| c24a5b7 | APipe Tester | 12 September 2012, 20:18:51 UTC | updated ur submodule to 8cc655c | 13 September 2012, 21:39:03 UTC |
| 7e9d82d | Brian Derickson | 12 September 2012, 19:31:47 UTC | fixed case where dotfiles were being ignored during archive, updated test | 13 September 2012, 21:39:02 UTC |
| d4eb52b | Brian Derickson | 12 September 2012, 16:31:29 UTC | updated volume query, now checking disk_status | 13 September 2012, 21:39:02 UTC |
| 026c608 | apregier | 12 September 2012, 15:52:40 UTC | Call prepare_output_dir after temp directory has been filled in | 13 September 2012, 21:39:02 UTC |
| b1dd9bb | apregier | 12 September 2012, 15:51:07 UTC | Call prepare_output_directory after temp directory has been filled in | 13 September 2012, 21:39:02 UTC |
| 264ffa4 | Jim Weible | 12 September 2012, 13:32:51 UTC | add tool to remove unpaired reads in an otherwise paired bam file | 13 September 2012, 21:39:02 UTC |
| d22eda3 | Thomas Mooney | 12 September 2012, 13:06:38 UTC | Set the log directory to our parent's when running under another workflow. | 13 September 2012, 21:39:02 UTC |
| bdec6db | Obi Griffith | 11 September 2012, 23:39:48 UTC | Finished work on script to get Protein members for Hopkins & Groom categories | 13 September 2012, 21:39:02 UTC |
| 1931be7 | Travis Abbott | 11 September 2012, 20:27:13 UTC | add some error checking to ClinicalData | 13 September 2012, 21:39:02 UTC |
| dedb779 | David Morton | 11 September 2012, 21:44:26 UTC | Start library to repair Polymutt Vcfs | 13 September 2012, 21:39:01 UTC |
| 5c0e32c | David Morton | 11 September 2012, 21:42:34 UTC | Add helper routines to Utility::Vcf | 13 September 2012, 21:39:01 UTC |
| af8e517 | Dave Larson | 11 September 2012, 21:42:14 UTC | add special trait type of none to prevent going on to downstream statistical analysis | 13 September 2012, 21:39:01 UTC |
| cda9aa8 | Malachi Griffith | 11 September 2012, 20:55:45 UTC | Add modified version of Clinseq UpdateAnalysis that no longer performs DB lookups in class definition | 13 September 2012, 21:39:01 UTC |
| 10c2b03 | Chris Miller | 11 September 2012, 20:51:04 UTC | genome-build no longer an optional parameter | 13 September 2012, 21:39:01 UTC |
| c4c034c | apregier | 11 September 2012, 20:44:44 UTC | Relax constraints to allow compatible builds in model group qc | 13 September 2012, 21:39:01 UTC |
| 5ead862 | Malachi Griffith | 11 September 2012, 20:20:32 UTC | Revert "Revert "Add clinseq tool to help create and update clinseq commands"" This reverts commit 6bbd940363f0d7accc42c8e31bc6d268a8f328ad. | 13 September 2012, 21:39:01 UTC |
| a3ab416 | Ian Ferguson | 11 September 2012, 18:49:22 UTC | Put ReferenceSequence.t files in /gsc/var/cache. I put supporting files for ReferenceSequence.t in /gsc/var/cache where they belong. It's not like I had tests running out of my homedir. Nope. That never happened. | 13 September 2012, 21:39:01 UTC |
| 7a7abd6 | Nathaniel Nutter | 11 September 2012, 18:43:49 UTC | Revert "Add clinseq tool to help create and update clinseq commands" This reverts commit 70ab376cf1643d27bdff6b9227a0a264aabea29e. This command cause DB connections during use due to default values that hit database. | 13 September 2012, 21:39:00 UTC |
| 7ae7865 | Justin Lolofie | 11 September 2012, 18:04:01 UTC | Stableable makes tmp dir then "promotes" to alloc | 13 September 2012, 21:39:00 UTC |
| 6ddaaa7 | Christopher C. Harris | 11 September 2012, 17:47:48 UTC | first commit of rudimentary workflow agent for any command line commands | 13 September 2012, 21:39:00 UTC |
| cf153a3 | Malachi Griffith | 11 September 2012, 15:52:40 UTC | Add clinseq tool to help create and update clinseq commands | 13 September 2012, 21:39:00 UTC |
| 5ff5237 | Malachi Griffith | 11 September 2012, 15:52:02 UTC | Update tab-complete commands for clinseq | 13 September 2012, 21:39:00 UTC |
| f701197 | Nathaniel Nutter | 11 September 2012, 14:57:12 UTC | updated expected_data_directory | 13 September 2012, 21:39:00 UTC |
| 506d13e | David Morton | 10 September 2012, 22:08:05 UTC | Fix pp view to show Strelka params properly | 13 September 2012, 21:39:00 UTC |
| c91dac8 | Adam Coffman | 10 September 2012, 21:33:18 UTC | Use streaming bam alignment result API in PerLaneTophat | 13 September 2012, 21:39:00 UTC |
| 59af36a | Adam Coffman | 10 September 2012, 21:29:19 UTC | remove double declaration of processing profile | 13 September 2012, 21:38:59 UTC |
| 6397cde | Adam Coffman | 10 September 2012, 21:25:13 UTC | handle default processing profile without crashing | 13 September 2012, 21:38:59 UTC |
| b4ce683 | David Morton | 10 September 2012, 20:51:15 UTC | Update PhenotypeCorrelation.t with new test-data Old test-data failed diff caused by an update to CreateCrossSampleVcf being changed to use sample->id for directory names instead of sample->name. | 13 September 2012, 21:38:59 UTC |
| 4a2e59e | Gabriel Sanderson | 10 September 2012, 18:44:21 UTC | Optionally region limit inputs | 13 September 2012, 21:38:59 UTC |
| 4992e9d | Jason Walker | 10 September 2012, 19:25:00 UTC | Add the 1.99 additional features such as per Replicate plots, and added statistical comparison plots for Cufflinks/Cummerbund. | 13 September 2012, 21:38:59 UTC |
| 8acdce7 | apregier | 10 September 2012, 19:19:05 UTC | add_assembler interface accepts default_lsf_queue | 13 September 2012, 21:38:59 UTC |
| a627cd7 | apregier | 10 September 2012, 17:53:56 UTC | Specify assembly queue | 13 September 2012, 21:38:59 UTC |
| b3237ac | Jim Weible | 05 September 2012, 14:02:14 UTC | fix syntax | 13 September 2012, 21:38:59 UTC |
| f451d21 | Jim Weible | 05 September 2012, 13:59:00 UTC | enable translation from unalphabatized string to IUB code | 13 September 2012, 21:38:58 UTC |
| 7350450 | David Morton | 10 September 2012, 18:02:55 UTC | Replace subject->name with subject->id Using the subject->name potentially causes problems when the name contains special caracters (such as /). We only used the names to create temporary directories and so the id will be fine to use instead. | 13 September 2012, 21:38:58 UTC |
| 3b3848f | David Morton | 10 September 2012, 17:51:46 UTC | Make option to show latest-build-status in pp view | 13 September 2012, 21:38:58 UTC |
| 88ba74b | David Morton | 10 September 2012, 15:21:39 UTC | Remove switch from Utility::Text It breaks LIMS 5.8 interpreter. | 13 September 2012, 21:38:58 UTC |
| 161ae46 | David Morton | 09 September 2012, 23:41:48 UTC | Fix coloring in genome processing-profile view Also a couple of fault-tolerance improvements. | 13 September 2012, 21:38:58 UTC |
| 68e1e57 | David Morton | 09 September 2012, 23:40:07 UTC | Fix formatting string in genome model build view | 13 September 2012, 21:38:58 UTC |
| b0fb560 | David Morton | 10 September 2012, 15:30:18 UTC | Revert "Revert "Add Utility::Text tools"" This reverts commit ee10a23cf1ef49ce333f9ff50e0b5ba8bb5ccf0e. | 13 September 2012, 21:38:58 UTC |
| 3e53133 | David Morton | 10 September 2012, 15:29:56 UTC | Revert "Revert "Add 'genome processing-profile view'"" This reverts commit 6c4cc39e03b6295df6d12b51a78343ce4f651659. | 13 September 2012, 21:38:57 UTC |
| 0c3e57e | Nathaniel Nutter | 10 September 2012, 14:27:31 UTC | Revert "Add 'genome processing-profile view'" This reverts commit 2e5d0aa15600b5482e07bc5d457a35a6e953821d. | 13 September 2012, 21:38:57 UTC |
| 89bdbd1 | Nathaniel Nutter | 10 September 2012, 14:14:21 UTC | Revert "Add Utility::Text tools" This reverts commit 1748b7b4eecc2b36a977ab57ab99e9cea503e71e. | 13 September 2012, 21:38:57 UTC |
| b998cc6 | Malachi Griffith | 10 September 2012, 01:51:55 UTC | Added pairoscope png generation to clinseq summarizeSvs | 13 September 2012, 21:38:57 UTC |
| fb37977 | Obi Griffith | 08 September 2012, 04:45:56 UTC | created new script for mapping interpro to uniprot, minor fixes to importers | 13 September 2012, 21:38:57 UTC |
| aa765ac | David Morton | 08 September 2012, 02:52:59 UTC | Add 'genome processing-profile view' | 13 September 2012, 21:38:57 UTC |
| fd8ee22 | David Morton | 08 September 2012, 02:52:13 UTC | Add Utility::Text tools | 13 September 2012, 21:38:56 UTC |
| aa3c742 | Malachi Griffith | 07 September 2012, 20:38:48 UTC | Moved CNV global png and single BAM pdf generation code from within ClinSeq Main to a CNV summary module | 13 September 2012, 21:38:56 UTC |
| 79bf7b1 | Ben Oberkfell | 07 September 2012, 19:49:04 UTC | prepare output directory once we have filled up the staging | 13 September 2012, 21:38:56 UTC |
| 6a2f648 | Jason Walker | 07 September 2012, 19:21:08 UTC | Update to use the Cufflinks2 format tracking file | 13 September 2012, 21:38:56 UTC |
| 97d7caf | Justin Lolofie | 07 September 2012, 15:16:33 UTC | unarchive stuff based on path instead of alloc id | 13 September 2012, 21:38:56 UTC |
| 5867e6e | Thomas Mooney | 06 September 2012, 22:49:37 UTC | Get all results associated with a build when finding all allocations. | 13 September 2012, 21:38:56 UTC |
| 950b8e2 | Thomas Mooney | 06 September 2012, 21:55:29 UTC | New method all_results to recursively grab all results associated with a build. | 13 September 2012, 21:38:55 UTC |
| 6198e23 | Malachi Griffith | 06 September 2012, 21:53:27 UTC | Fixed clinseq bug caused by passing a somatic variation instead of a clinseq build object to SummarizeCnvs | 13 September 2012, 21:38:55 UTC |
| 232ff8f | Gabriel Sanderson | 06 September 2012, 21:27:12 UTC | Updated test data | 13 September 2012, 21:38:55 UTC |
| 3fa75f8 | Eddie Belter | 06 September 2012, 20:32:16 UTC | Build Heatbeat: moved out/err file check below process check | 13 September 2012, 21:38:55 UTC |
| c85e3cc | APipe Tester | 06 September 2012, 20:29:56 UTC | updated ur submodule to a3e9a91 | 13 September 2012, 21:38:55 UTC |
| 7c11ad8 | Obi Griffith | 06 September 2012, 20:17:24 UTC | fixed bug in specification of drug primary_name | 13 September 2012, 21:38:54 UTC |
| 0e407d2 | APipe Tester | 06 September 2012, 20:11:05 UTC | updated jenkins submodule to 948b149 | 13 September 2012, 21:38:54 UTC |
| 7c19a17 | Nathaniel Nutter | 06 September 2012, 20:00:55 UTC | remove failing command that is poorly written | 13 September 2012, 21:38:54 UTC |
| accc158 | Eddie Belter | 06 September 2012, 19:32:45 UTC | MC16s Run Status: actually use the given separator when printing | 13 September 2012, 21:38:54 UTC |
| ebf814b | Nathaniel Nutter | 06 September 2012, 19:31:10 UTC | add more error checking around diff | 13 September 2012, 21:38:54 UTC |
| d240fb5 | Nathaniel Nutter | 06 September 2012, 19:18:17 UTC | add diag if diff fails | 13 September 2012, 21:38:54 UTC |
| 3fcebd4 | David Morton | 06 September 2012, 17:24:37 UTC | Remove the supersedes/supercedes param from PP | 13 September 2012, 21:38:53 UTC |
| a630aac | APipe Tester | 06 September 2012, 18:31:06 UTC | updated jenkins submodule to a982dac | 13 September 2012, 21:38:53 UTC |
| 6e7c642 | APipe Tester | 06 September 2012, 18:01:22 UTC | updated jenkins submodule to 545c14e | 13 September 2012, 21:38:53 UTC |
