| c3b82bf | Kyung Kim | 13 September 2012, 20:26:41 UTC | Bug fix so empty fasta file is not created for blast when blast output from prev staged, pooled and split. This was possible when number of reads in pooled file is a multiple of number of reads to split | 13 September 2012, 21:39:09 UTC |
| 2278a74 | Nathan Dees | 13 September 2012, 19:50:04 UTC | added doc sub for authors | 13 September 2012, 21:39:09 UTC |
| 65bac01 | Eddie Belter | 13 September 2012, 19:28:23 UTC | AQID: use is_rna on sample instead of internal method | 13 September 2012, 21:39:09 UTC |
| 92b064b | Eddie Belter | 13 September 2012, 19:25:39 UTC | Sample: add is_rna to class def; update tests | 13 September 2012, 21:39:09 UTC |
| 7571255 | Kyung Kim | 13 September 2012, 19:21:20 UTC | Update to work for velvet versions deployed in usr/bin | 13 September 2012, 21:39:09 UTC |
| 1e46278 | Travis Abbott | 13 September 2012, 19:16:28 UTC | verify that clinical data, vcf, and pop group have same samples phenotype correlation now checks that the intersection of samples in the clinical data, multisample vcf, and population group is non-empty before doing anything serious. | 13 September 2012, 21:39:08 UTC |
| 31675b3 | Travis Abbott | 13 September 2012, 18:13:23 UTC | add sample_names accessor to clinical data object | 13 September 2012, 21:39:08 UTC |
| e54db12 | Eddie Belter | 13 September 2012, 16:41:27 UTC | AQID de novo, gm, mc16s tests: rm refs to pses! | 13 September 2012, 21:39:08 UTC |
| b60fad6 | Eddie Belter | 13 September 2012, 16:31:23 UTC | AQID: QIDFGM no longer required to process inst data | 13 September 2012, 21:39:08 UTC |
| f678817 | Eddie Belter | 12 September 2012, 21:39:02 UTC | AQID: Rm all PSE refs except those needed for the transition period | 13 September 2012, 21:39:08 UTC |
| 2067478 | Eddie Belter | 12 September 2012, 20:38:47 UTC | AQID: made execute completely inst data centric | 13 September 2012, 21:39:08 UTC |
| cc561e6 | Eddie Belter | 12 September 2012, 20:12:22 UTC | AQID: load_pses is now _load_instrument_data; made execute more isnt data centric | 13 September 2012, 21:39:08 UTC |
| 57c6446 | Eddie Belter | 12 September 2012, 19:56:55 UTC | AQID: make load_pses more inst data centric | 13 September 2012, 21:39:08 UTC |
| 5400661 | Eddie Belter | 12 September 2012, 19:15:59 UTC | AQID: rm max_pses_to_check param | 13 September 2012, 21:39:07 UTC |
| 3b02e78 | Eddie Belter | 12 September 2012, 17:21:06 UTC | AQID: rm pse_id use from one test | 13 September 2012, 21:39:07 UTC |
| b2a4e49 | Eddie Belter | 12 September 2012, 16:49:44 UTC | AQID: rm pse_id option | 13 September 2012, 21:39:07 UTC |
| a86a852 | Eddie Belter | 12 September 2012, 16:38:51 UTC | AQID: consolidate default pp for de novo | 13 September 2012, 21:39:07 UTC |
| 0513aad | Eddie Belter | 12 September 2012, 16:35:57 UTC | AQID: consolidate default pp for ref align | 13 September 2012, 21:39:07 UTC |
| 7e2d385 | Eddie Belter | 11 September 2012, 22:52:23 UTC | AQID: Made separate method for setting tgi lims status to failed | 13 September 2012, 21:39:07 UTC |
| 4586282 | Eddie Belter | 11 September 2012, 22:12:04 UTC | AQID: getting pp and ref seqs in one place | 13 September 2012, 21:39:07 UTC |
| 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 |
