e756450 | Eddie Belter | 19 September 2012, 20:09:47 UTC | GMT LIMS APIPE: rename fix pidfa params to fir pse params; update class info and help | 19 September 2012, 20:09:47 UTC |
4a94cba | Eddie Belter | 19 September 2012, 20:05:34 UTC | Fix PIDFA params: mv inst data to be param for all | 19 September 2012, 20:05:43 UTC |
0bbb52e | Eddie Belter | 19 September 2012, 18:35:57 UTC | Microarray Extract: update snp id column setting b/c of swithc to switch to 137 | 19 September 2012, 18:38:53 UTC |
215c24c | dmorton | 19 September 2012, 18:36:32 UTC | Clean up MergeAndFixVcfs.t | 19 September 2012, 18:37:29 UTC |
c4792db | Malachi Griffith | 19 September 2012, 18:22:37 UTC | Reorganize clin-seq update-analysis and add archiving checks, somatic-variation model creation, etc. | 19 September 2012, 18:22:37 UTC |
d38a453 | Dave Larson | 19 September 2012, 17:59:16 UTC | added some pod | 19 September 2012, 17:59:26 UTC |
7fa4193 | Christopher C. Harris | 19 September 2012, 17:51:00 UTC | fix capitalizaton | 19 September 2012, 17:52:25 UTC |
829ecc0 | Nathan Dees | 19 September 2012, 17:00:28 UTC | fixed typo in PIs | 19 September 2012, 17:00:28 UTC |
afc82c8 | Nathan Dees | 19 September 2012, 16:56:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:56:32 UTC |
4785d5b | Nathan Dees | 19 September 2012, 16:56:28 UTC | fixed typo in PIs | 19 September 2012, 16:56:28 UTC |
21b1eab | Jason Walker | 19 September 2012, 16:52:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:52:29 UTC |
5cbb89f | Jason Walker | 19 September 2012, 16:52:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 September 2012, 16:52:13 UTC |
d2da2fd | Jason Walker | 19 September 2012, 16:52:09 UTC | Add a filter to limit genes/transcripts by gene biotype. Also increase the default ref-cov RAM to 16GB. | 19 September 2012, 16:52:09 UTC |
421378c | Christopher C. Harris | 19 September 2012, 16:51:44 UTC | commits to make the pipeline handle 2 denovo alleles in one line | 19 September 2012, 16:51:44 UTC |
f4d4c68 | Obi Griffith | 19 September 2012, 00:34:17 UTC | Numerous fixes and updates to importers | 19 September 2012, 00:34:17 UTC |
94eb960 | dmorton | 18 September 2012, 22:53:11 UTC | pp view can show alignment_strategies Plus cleaned up the code a bit. | 18 September 2012, 22:55:02 UTC |
b05f86b | Eddie Belter | 18 September 2012, 22:24:07 UTC | AQID: rm max pses param; overload inst data attr in load_lims test; update whitelist | 18 September 2012, 22:24:19 UTC |
f69a780 | Ben Oberkfell | 18 September 2012, 22:17:41 UTC | Merge branch 'master' of git:/srv/git/genome | 18 September 2012, 22:17:41 UTC |
0ec854d | Ben Oberkfell | 18 September 2012, 22:15:59 UTC | disable this test because it takes too long to run | 18 September 2012, 22:15:59 UTC |
5361554 | Travis Abbott | 18 September 2012, 22:14:56 UTC | specify reference sequence for tigra-sv test | 18 September 2012, 22:15:34 UTC |
af1c4c2 | Chris Miller | 18 September 2012, 22:04:34 UTC | fix to indel VAF reporting | 18 September 2012, 22:07:20 UTC |
57ed03a | Nathaniel Nutter | 18 September 2012, 21:37:49 UTC | update version for release | 18 September 2012, 21:37:59 UTC |
4cdba95 | Thomas Mooney | 18 September 2012, 21:14:56 UTC | Update `genome model instrument-data assign` help text for clarity, typos. | 18 September 2012, 21:14:56 UTC |
c4e00f2 | Nathaniel Nutter | 18 September 2012, 20:43:03 UTC | get_with_lock only gets lock if object does not exist Only try with lock if object does not exist since locking causes a performance hit. It is assumed that if an object is found it is complete. If this is a bad assumption then we need to add a status to SoftwareResults. Please please work. | 18 September 2012, 21:10:04 UTC |
7924917 | Thomas Mooney | 18 September 2012, 20:20:42 UTC | Bump the memory request from 1GB to 2GB on GenePrediction::Bacterial. | 18 September 2012, 20:20:42 UTC |
584e2a7 | Jason Walker | 18 September 2012, 20:09:51 UTC | Updates to the DifferentialExpression pipeline to run cuffdiff and cuffcompare | 18 September 2012, 20:09:51 UTC |
d375d2a | Jason Walker | 18 September 2012, 20:08:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 20:08:07 UTC |
41293a0 | Jason Walker | 18 September 2012, 20:07:58 UTC | A command to parse cuffdiff output and run through the Bioconductor R library, SPIA | 18 September 2012, 20:07:58 UTC |
deb840d | Ben Oberkfell | 18 September 2012, 20:05:58 UTC | dont need to use above here | 18 September 2012, 20:05:58 UTC |
b9f0436 | Ben Oberkfell | 18 September 2012, 19:38:20 UTC | must use a fully qualified class name here | 18 September 2012, 19:38:20 UTC |
451d9a6 | apregier | 18 September 2012, 19:14:50 UTC | Merge branch 'updated' into gb_master | 18 September 2012, 19:14:50 UTC |
81fbd02 | apregier | 18 September 2012, 19:13:55 UTC | Deduplicate annotated variant lists in somatic variation | 18 September 2012, 19:14:11 UTC |
b1bb78e | dmorton | 18 September 2012, 18:51:22 UTC | added libconfig-inifiles-perl to genome-shapshot-deps perl | 18 September 2012, 18:51:22 UTC |
212d6be | John Martin | 18 September 2012, 18:35:12 UTC | adding supporting scripts for HMP processing pipeline into repository | 18 September 2012, 18:35:12 UTC |
c1a562b | Nathan Dees | 18 September 2012, 18:08:21 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 18:08:21 UTC |
267a854 | Nathan Dees | 18 September 2012, 18:08:14 UTC | changed grant information | 18 September 2012, 18:08:14 UTC |
1547661 | David Morton | 17 September 2012, 22:10:38 UTC | Show notes and error-log-paths in gmb view | 18 September 2012, 17:56:13 UTC |
61b536d | David Morton | 17 September 2012, 20:13:18 UTC | genome model build view inherits from Viewer | 18 September 2012, 17:56:12 UTC |
c687c61 | David Morton | 17 September 2012, 19:48:46 UTC | Make individual and pp view inherit from Viewer Add default processing-profiles for individual view (for filtering) Cosmetic improvements to individual view | 18 September 2012, 17:56:12 UTC |
96038a6 | David Morton | 17 September 2012, 19:47:57 UTC | Make base class for 'view' type commands. | 18 September 2012, 17:56:12 UTC |
c02af0f | David Morton | 14 September 2012, 18:21:13 UTC | Lean on Strelka to parse strelka params in pp view | 18 September 2012, 17:56:12 UTC |
616e90b | David Morton | 14 September 2012, 18:19:20 UTC | Make Strelka Detector more smart about params Instead of having to specify all params, you only have to specify params that are not default. | 18 September 2012, 17:56:12 UTC |
5979329 | Nathan Dees | 18 September 2012, 16:43:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 16:43:14 UTC |
0733bd0 | Nathan Dees | 18 September 2012, 16:43:11 UTC | changed grant information | 18 September 2012, 16:43:11 UTC |
112993b | Brian Derickson | 18 September 2012, 14:45:24 UTC | added is_archived method to buildl | 18 September 2012, 14:45:24 UTC |
aad0f96 | Malachi Griffith | 18 September 2012, 04:38:50 UTC | Add subroutines to clin-seq analysis-update for somatic-variation models | 18 September 2012, 04:38:50 UTC |
45bba0c | Brian Derickson | 18 September 2012, 01:56:47 UTC | fixed method name | 18 September 2012, 01:56:47 UTC |
848cee1 | Brian Derickson | 17 September 2012, 22:24:05 UTC | added archivable method to builds, which just checks the archivable status of the data directoryallocation | 17 September 2012, 22:24:10 UTC |
0af8596 | Brian Derickson | 17 September 2012, 22:23:40 UTC | attempting to unarchive an allocation that is not archived is no longer a fatal error | 17 September 2012, 22:24:09 UTC |
bf4e3af | Justin Lolofie | 17 September 2012, 21:46:54 UTC | total disk usage and archive info | 17 September 2012, 21:46:54 UTC |
b6c09d0 | Travis Abbott | 17 September 2012, 21:09:15 UTC | correctly output genes with null p-values in burden test | 17 September 2012, 21:09:15 UTC |
5492c2c | Travis Abbott | 17 September 2012, 21:03:21 UTC | convert VEP annotation priority from hash to array | 17 September 2012, 21:04:06 UTC |
7b51721 | Thomas Mooney | 17 September 2012, 21:00:55 UTC | Strip the trailing L off of certain cell types. | 17 September 2012, 21:03:50 UTC |
e319a6d | Dave Larson | 17 September 2012, 21:01:00 UTC | added back in unfiltered qqplots | 17 September 2012, 21:01:08 UTC |
f20b2f7 | Dave Larson | 17 September 2012, 18:12:57 UTC | made vcf-report output files available via build | 17 September 2012, 21:01:07 UTC |
6207893 | Dave Larson | 17 September 2012, 16:30:19 UTC | add in the removal of rare variants from the qqplots | 17 September 2012, 21:01:07 UTC |
be8f0ef | Malachi Griffith | 17 September 2012, 20:54:21 UTC | Bring clin-seq ad hoc druggable genes heatmap code under version control | 17 September 2012, 20:54:21 UTC |
7796fca | Malachi Griffith | 17 September 2012, 20:53:38 UTC | Continued development of clin-seq update-analysis | 17 September 2012, 20:53:38 UTC |
b9cbce6 | Travis Abbott | 17 September 2012, 20:50:38 UTC | add VEP support to gmt graph mutation-diagram | 17 September 2012, 20:51:10 UTC |
c355e87 | Thomas Mooney | 17 September 2012, 20:08:53 UTC | Avoid spurious indication the calculated property wasn't specified. Update the LIMS whitelist to reflect two new lines. | 17 September 2012, 20:08:53 UTC |
fcc285d | Thomas Mooney | 17 September 2012, 19:15:59 UTC | Declare the calculated property as calculated so it doesn't get default magic. | 17 September 2012, 19:15:59 UTC |
a9815aa | Dan Koboldt | 17 September 2012, 19:12:38 UTC | Updates to perform FET on rare deleterious table | 17 September 2012, 19:12:38 UTC |
357366c | Dan Koboldt | 17 September 2012, 19:12:20 UTC | Directory for Beagle tools | 17 September 2012, 19:12:20 UTC |
3859094 | Nathan Dees | 17 September 2012, 18:39:08 UTC | changed it to music in the license section | 17 September 2012, 18:39:08 UTC |
e68ff77 | Thomas Mooney | 17 September 2012, 17:55:31 UTC | Speed up view by pre-loading data in fewer queries. | 17 September 2012, 17:55:31 UTC |
6cd527a | Eddie Belter | 17 September 2012, 16:43:36 UTC | MC16s: update entire run email | 17 September 2012, 16:43:36 UTC |
89f1ed1 | Eddie Belter | 17 September 2012, 16:35:18 UTC | MC16s Run Status: update pp doc | 17 September 2012, 16:35:18 UTC |
7ea23c3 | Dan Koboldt | 17 September 2012, 15:44:28 UTC | Updates to human genetics analysis tools | 17 September 2012, 15:44:28 UTC |
25ab32e | Dan Koboldt | 17 September 2012, 15:42:45 UTC | New tools for human genetics analysis | 17 September 2012, 15:42:45 UTC |
6363cf2 | apregier | 17 September 2012, 15:33:40 UTC | Merge branch 'updated' into gb_master | 17 September 2012, 15:33:40 UTC |
ad9fdab | apregier | 17 September 2012, 15:32:08 UTC | CHANGELOG Default human dbsnp build is 137 | 17 September 2012, 15:33:25 UTC |
748b4af | APipe Tester | 17 September 2012, 15:15:12 UTC | updated ur submodule to 8376d66 | 17 September 2012, 15:15:12 UTC |
81e9d0f | Justin Lolofie | 17 September 2012, 14:58:43 UTC | better error msg better ret value | 17 September 2012, 14:58:43 UTC |
2483b85 | APipe Tester | 17 September 2012, 13:55:21 UTC | updated ur submodule to c3d459b | 17 September 2012, 13:55:21 UTC |
43d0567 | Obi Griffith | 16 September 2012, 23:05:10 UTC | Improved usage example for Entrez Importer | 16 September 2012, 23:05:10 UTC |
97ed2d2 | Obi Griffith | 16 September 2012, 23:02:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 September 2012, 23:02:30 UTC |
376da72 | Dave Larson | 14 September 2012, 22:27:27 UTC | remove some unnecessary includes and include attribution | 14 September 2012, 22:27:27 UTC |
0c280d3 | Dave Larson | 14 September 2012, 22:25:16 UTC | simple module to filter clinical correlation results by MAF | 14 September 2012, 22:25:24 UTC |
a0e48c3 | Ian Ferguson | 14 September 2012, 22:09:50 UTC | Updated location of C utility for ErrorRate.pm | 14 September 2012, 22:10:11 UTC |
2cd7cde | Justin Lolofie | 14 September 2012, 21:43:22 UTC | unarchive allocations for a build | 14 September 2012, 21:43:22 UTC |
e8e7219 | Eddie Belter | 14 September 2012, 21:21:52 UTC | AQID: update test count for validation | 14 September 2012, 21:38:35 UTC |
4810163 | Eddie Belter | 14 September 2012, 21:17:52 UTC | AQID: make validation test PSE free | 14 September 2012, 21:38:35 UTC |
bba93e0 | Eddie Belter | 14 September 2012, 21:17:28 UTC | AQID: override GSC::PSE::get in mc16s test | 14 September 2012, 21:38:35 UTC |
975dd9f | Eddie Belter | 14 September 2012, 21:04:02 UTC | AQID: add call to GSC::PSE class to avoid editing the whitelist during refactoring | 14 September 2012, 21:38:34 UTC |
6ff5242 | Eddie Belter | 14 September 2012, 19:07:55 UTC | AQID: stop preloading or wahtever | 14 September 2012, 21:38:34 UTC |
b0150a1 | Obi Griffith | 14 September 2012, 20:41:02 UTC | Updated all importers to use consistent default location for intermediate TSV files | 14 September 2012, 20:41:02 UTC |
d892f2a | Kyung Kim | 14 September 2012, 20:20:48 UTC | Update to filter out reads that become 10 or less bases after clipping since such reads will fail further processing down the stream | 14 September 2012, 20:20:48 UTC |
e21fde3 | Obi Griffith | 14 September 2012, 20:16:13 UTC | Created new generic category for Druggable Genome lists | 14 September 2012, 20:16:13 UTC |
3ae2e57 | Jim Weible | 14 September 2012, 19:08:51 UTC | tool to removed paired reads from a namesorted bam | 14 September 2012, 19:08:59 UTC |
13fa38c | Jim Weible | 14 September 2012, 19:07:49 UTC | clarify help text | 14 September 2012, 19:08:59 UTC |
44334aa | Eddie Belter | 14 September 2012, 18:57:29 UTC | AQID: rm PSEParam from white list | 14 September 2012, 18:57:37 UTC |
84436c4 | Eddie Belter | 14 September 2012, 18:57:14 UTC | AQID: rm instrument_data_type | 14 September 2012, 18:57:36 UTC |
a60e6d6 | Eddie Belter | 14 September 2012, 18:52:19 UTC | AQID: update whitelist | 14 September 2012, 18:57:36 UTC |
bd392da | Eddie Belter | 14 September 2012, 18:48:47 UTC | AQID: rm root ref seq method | 14 September 2012, 18:57:36 UTC |
8c49968 | Nathan Dees | 14 September 2012, 18:55:15 UTC | updated the call to bam-readcount with --variant-file | 14 September 2012, 18:55:15 UTC |
8f9a89d | Eddie Belter | 14 September 2012, 18:42:55 UTC | AQID: fix indent | 14 September 2012, 18:43:02 UTC |
d3ea947 | Brian Derickson | 14 September 2012, 18:41:35 UTC | added a few new abbreviations | 14 September 2012, 18:41:35 UTC |
0926894 | Ian Ferguson | 14 September 2012, 18:22:00 UTC | Updated archive_path for raw sra download format in ID/Imported.pm Updated _archive_file_name and archive_path handling of 'raw sra download' formatted instrument data. It now attempts to output the path to a directory if we happen to find a directory structure instead of a single .sra file. | 14 September 2012, 18:25:21 UTC |
b6f2efb | Travis Abbott | 14 September 2012, 17:33:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 September 2012, 17:33:18 UTC |
a2e10da | Travis Abbott | 14 September 2012, 17:31:56 UTC | submodules -> latest | 14 September 2012, 17:32:59 UTC |