| 56ff4df | Eddie Belter | 08 November 2012, 00:39:54 UTC | MC16s 454 test: lower the number of levels when checking classifications b/c it is not deterministic | 08 November 2012, 00:39:54 UTC |
| 5cc44d4 | Chris Miller | 07 November 2012, 22:53:13 UTC | checking for the presence of the variable before trying to split it - a novel idea | 07 November 2012, 22:53:47 UTC |
| 7501659 | Thomas Mooney | 07 November 2012, 22:35:54 UTC | Examine one level deeper (i.e. via the merged results) for the build | 07 November 2012, 22:35:54 UTC |
| 6da4897 | Travis Abbott | 07 November 2012, 22:30:27 UTC | add missing : in phenotype correlation dbsnp info fields | 07 November 2012, 22:30:27 UTC |
| 290654f | Travis Abbott | 07 November 2012, 21:03:06 UTC | update dbsnp info fields in phenotypecorrelation in dbsnp137+, the CLN field has become PM. As an intermediate step on the path to having an annotation_strategy as part of the processing profile, there is now a method that returns the proper info fields for a given dbsnp version. | 07 November 2012, 21:04:31 UTC |
| 608ecf3 | APipe Tester | 07 November 2012, 19:10:10 UTC | Merge remote-tracking branch 'origin/master' | 07 November 2012, 19:10:10 UTC |
| a2590ee | Thomas Mooney | 07 November 2012, 18:20:32 UTC | Skip tiering if there were no qualifying variants. | 07 November 2012, 18:20:32 UTC |
| 19e13b6 | Nathan Nutter | 07 November 2012, 17:00:48 UTC | Merge "Fix how we find Chimerascan for a given version." | 07 November 2012, 17:00:48 UTC |
| f362bfe | Thomas Mooney | 07 November 2012, 15:33:16 UTC | Make annotation build required on validation builds. | 07 November 2012, 15:33:16 UTC |
| c16f0cb | Gabriel Sanderson | 06 November 2012, 23:27:22 UTC | Merge branch 'master' into gb_master | 06 November 2012, 23:27:22 UTC |
| 4de72d5 | Gabriel Sanderson | 06 November 2012, 23:27:06 UTC | If all vcf files are not present, inform the user which builds did and did not have them. | 06 November 2012, 23:27:06 UTC |
| 430aa53 | dmorton | 05 November 2012, 22:44:43 UTC | Fix how we find Chimerascan for a given version. It didn't used to try to find the installation in the typical debian install location. Change-Id: I8ef0f9f0ddc02ef4cb3c01fbacea3ae795b1e8d4 | 06 November 2012, 22:47:59 UTC |
| 9ac0fd8 | Nathaniel Nutter | 06 November 2012, 21:16:55 UTC | work around weird openmpi behavior | 06 November 2012, 21:17:21 UTC |
| 5f80fc0 | apregier | 06 November 2012, 20:54:16 UTC | Merge branch 'fireteam2' into gb_master | 06 November 2012, 20:54:16 UTC |
| 6fb8260 | apregier | 06 November 2012, 20:53:52 UTC | Use Ensembl BiotypeMapper API | 06 November 2012, 20:53:52 UTC |
| a98c349 | dmorton | 06 November 2012, 20:08:41 UTC | Fix how get_vcf_header was being used. | 06 November 2012, 20:08:41 UTC |
| 8030ff5 | dmorton | 06 November 2012, 20:06:57 UTC | Fix mistake in Utility/Vcf get_vcf_header had stupid parameter handling mistake. Added test for get_vcf_header. | 06 November 2012, 20:06:57 UTC |
| 8fbf3d5 | Nathaniel Nutter | 06 November 2012, 16:13:45 UTC | fix invalid call to mkpath mkpath was probably meant to be File::Path's make_path but even more so it should be Genome::Sys->create_directory | 06 November 2012, 16:43:16 UTC |
| d88587d | Scott Smith | 06 November 2012, 16:31:35 UTC | add parens to remove warning | 06 November 2012, 16:31:35 UTC |
| 04f8fda | Scott Smith | 06 November 2012, 16:26:58 UTC | Genome::Sys - pulled snapshot_revision from Genome/Sys/TGI/Extension/Sys.pm, and broke out one method for the TGI-specific part, which shortens directory names. That method is still in the old module but is only called when present. | 06 November 2012, 16:26:58 UTC |
| a9626c0 | Scott Smith | 06 November 2012, 16:25:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 November 2012, 16:25:11 UTC |
| dcc026e | Scott Smith | 06 November 2012, 15:51:09 UTC | Genome::Sys - pulled snapshot_revision from Genome/Sys/TGI/Extension/Sys.pm, and broke out one method for the TGI-specific part, which shortens directory names. That method is still in the old module but is only called when present. | 06 November 2012, 15:51:09 UTC |
| 1d8e5cc | Chris Miller | 06 November 2012, 15:23:32 UTC | added option to keep ambiguous calls, added checks to prevent crashing on maf creation when tiering isn't specified | 06 November 2012, 15:23:47 UTC |
| 50fd43c | Chris Miller | 06 November 2012, 15:22:20 UTC | pindel vaf filter obsoleted some code | 06 November 2012, 15:23:47 UTC |
| 9d2291e | Scott Smith | 06 November 2012, 07:18:46 UTC | replaced calls to UR::Time->now with UR::Context->current->now | 06 November 2012, 07:18:46 UTC |
| 9f2aa6b | Scott Smith | 06 November 2012, 06:19:41 UTC | findreplace for all UR::BoolExpr ->specified_value_for_property_name to ->value_for | 06 November 2012, 06:19:41 UTC |
| 3d5c75b | Eddie Belter | 05 November 2012, 23:58:47 UTC | CHANGELOG: Add trimmer info to BWA intermediate alignment results | 06 November 2012, 00:01:05 UTC |
| 26ad9a9 | Feiyu Du | 05 November 2012, 21:01:19 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 November 2012, 21:01:19 UTC |
| 344594e | Feiyu Du | 05 November 2012, 21:01:10 UTC | Increase the mem limit to prevent unnecessary build failures due to mem limit | 05 November 2012, 21:01:10 UTC |
| 56222e1 | Gabriel Sanderson | 05 November 2012, 20:58:59 UTC | Merge branch 'master' into gb_master | 05 November 2012, 20:58:59 UTC |
| 194e007 | Gabriel Sanderson | 05 November 2012, 20:58:33 UTC | Print better error messages when there are duplicate subjects in the input. | 05 November 2012, 20:58:42 UTC |
| 2bed630 | Jim Weible | 05 November 2012, 20:27:46 UTC | compensate for Joinx intersect not sorting (Joinx Union does) | 05 November 2012, 20:27:46 UTC |
| 41c6ae9 | Thomas Mooney | 05 November 2012, 19:11:43 UTC | Add review step to the end of the SomaticValidation pipeline. CHANGELOG: The SomaticValidation pipeline has a new step at the end that compares the variants it found with those variants previously found in the original SomaticVariation run. | 05 November 2012, 19:11:43 UTC |
| 6482b9e | Thomas Mooney | 05 November 2012, 19:09:37 UTC | Refinements to the new variant review at the end of SomaticValidation *Only review tier 1 UHC variants. *Add tiering/annotation for validated variants. *A bit of cleanup | 05 November 2012, 19:09:37 UTC |
| cd7902e | Nathan Dees | 05 November 2012, 18:30:31 UTC | fixed error in purity calculation for wgs analysis type | 05 November 2012, 18:30:31 UTC |
| e47ff53 | Nathan Dees | 05 November 2012, 17:28:10 UTC | fixed a print message | 05 November 2012, 17:28:10 UTC |
| 0d27123 | Nathan Dees | 05 November 2012, 17:25:08 UTC | first pass at a C->T base checker and P-value generator for counting bases before or after C->T mutation | 05 November 2012, 17:25:08 UTC |
| 5560356 | Nathan Dees | 05 November 2012, 17:20:12 UTC | removed dbsingle | 05 November 2012, 17:20:12 UTC |
| cdf05ef | Nathan Dees | 05 November 2012, 16:55:22 UTC | fixed case when type is defined but does not actually indicate INS DEL or SNP | 05 November 2012, 16:55:22 UTC |
| f81a839 | Nathan Dees | 05 November 2012, 16:48:40 UTC | added function to perform p-value for sequence context and print results | 05 November 2012, 16:48:40 UTC |
| 719053f | Nathan Dees | 05 November 2012, 16:47:34 UTC | changed some headings; changed the scale of the differential plot | 05 November 2012, 16:47:34 UTC |
| 837f5ad | Nathan Dees | 05 November 2012, 16:36:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 November 2012, 16:36:17 UTC |
| c07d714 | Nathan Dees | 05 November 2012, 16:36:06 UTC | indented | 05 November 2012, 16:36:06 UTC |
| d6be815 | Nathaniel Nutter | 03 November 2012, 02:11:35 UTC | fix uninitialized warning for exclude_mount_path | 03 November 2012, 02:11:35 UTC |
| 6b17d50 | Nathaniel Nutter | 03 November 2012, 02:11:10 UTC | fix for Oracle conversion error due to "not like" | 03 November 2012, 02:11:10 UTC |
| 13ce279 | Mark Burnett | 02 November 2012, 23:39:26 UTC | Add grow_only option to reallocate command | 02 November 2012, 23:40:03 UTC |
| ae7c05c | Cyriac Kandoth | 02 November 2012, 23:27:50 UTC | Change default method to correlate mut status to quantitative data | 02 November 2012, 23:27:50 UTC |
| a7ad428 | Anthony Brummett | 02 November 2012, 21:50:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 November 2012, 21:50:30 UTC |
| 7883fd7 | Anthony Brummett | 02 November 2012, 21:47:31 UTC | Fix bugs when moving allocations The param exclude_mount_paths was only ever used with one item, and was not getting serialized properly, so we'll only use it as a scalar, Top-level directories in volumes are not writable, so we won't be able to make top-level directories for unarchive_allocation_destination and move_allocation_destination during moves and unarchives. The change just tacks on the additional string to the end of the directory name already being used before moving the name back | 02 November 2012, 21:47:31 UTC |
| a19e1b1 | Adam Coffman | 02 November 2012, 21:31:22 UTC | Add bowtie_version accessor to Merged Alignment Results Also, add a generic method to Merged Alignment results that attempts to discern a scalar property value from its underlying alignment results. | 02 November 2012, 21:31:22 UTC |
| a57dc7d | Cyriac Kandoth | 02 November 2012, 21:03:30 UTC | Fixed: some ncRNA were being classified as UTR | 02 November 2012, 21:03:30 UTC |
| 4997465 | Malachi Griffith | 02 November 2012, 20:47:31 UTC | Cosmetic updates to clinseq comments | 02 November 2012, 20:47:31 UTC |
| d6fa8e2 | Nathan Nutter | 01 November 2012, 19:20:14 UTC | whitespace Change-Id: Ib79e43576f28e3f097e851469d805f160a0a1562 | 02 November 2012, 20:32:15 UTC |
| 0a1b56c | Nathan Nutter | 02 November 2012, 20:31:55 UTC | Merge "whitespace Change-Id: Icc278bcea2c264a6f5dc0e9a27832b90fca4d52b" | 02 November 2012, 20:31:55 UTC |
| 05b466e | APipe Tester | 02 November 2012, 20:08:38 UTC | Merge remote-tracking branch 'origin/master' | 02 November 2012, 20:08:38 UTC |
| 4d55b25 | Nathan Nutter | 02 November 2012, 19:46:06 UTC | Merge "override kilobytes_requested to be more accurate for test usage" | 02 November 2012, 19:46:06 UTC |
| 15bf385 | Nathan Nutter | 02 November 2012, 19:45:57 UTC | Merge "refactor to allow kilobytes_requested to be overridden in tests" | 02 November 2012, 19:45:57 UTC |
| cfd4790 | Nathan Nutter | 02 November 2012, 19:45:49 UTC | Merge "override _staging_disk_usage to be more accurate for test usage" | 02 November 2012, 19:45:49 UTC |
| 83c3daf | Nathan Nutter | 01 November 2012, 15:29:53 UTC | whitespace Change-Id: Icc278bcea2c264a6f5dc0e9a27832b90fca4d52b | 02 November 2012, 19:31:26 UTC |
| 4d37626 | Adam Coffman | 02 November 2012, 19:22:58 UTC | remove hardcoded cpu count directive so it can be specified as a param | 02 November 2012, 19:22:58 UTC |
| d961609 | Adam Coffman | 02 November 2012, 19:15:58 UTC | update chimerascan result to allow for multiple versions | 02 November 2012, 19:15:58 UTC |
| ad7a859 | APipe Tester | 02 November 2012, 19:12:09 UTC | Merge remote-tracking branch 'origin/master' | 02 November 2012, 19:12:09 UTC |
| 5538baf | Eddie Belter | 02 November 2012, 19:11:43 UTC | Search Queue: add default value to timestamp so command works | 02 November 2012, 19:11:43 UTC |
| 8bcea53 | Nathan Nutter | 02 November 2012, 16:26:08 UTC | refactor to allow kilobytes_requested to be overridden in tests Change-Id: I4a997b562fe651617889a615492563e047d651b5 | 02 November 2012, 16:26:55 UTC |
| dd22424 | Nathan Nutter | 02 November 2012, 16:26:40 UTC | override kilobytes_requested to be more accurate for test usage Change-Id: I258ba743a748136be487c72f2a99d838abfda0a2 | 02 November 2012, 16:26:55 UTC |
| 69d354e | Nathan Nutter | 02 November 2012, 16:25:42 UTC | override _staging_disk_usage to be more accurate for test usage Change-Id: I72911f3215854f69ad6f596cd8e60ba9cfb91288 | 02 November 2012, 16:26:54 UTC |
| e64ee64 | Nathan Nutter | 02 November 2012, 15:43:08 UTC | reallocate on fail (and whitespace) Change-Id: Id53d70df61413922dee4806682ad6621ca2f3c2b | 02 November 2012, 15:45:01 UTC |
| e01e5ba | APipe Tester | 02 November 2012, 14:16:32 UTC | updated jenkins submodule to 0d2f07b | 02 November 2012, 14:16:32 UTC |
| 676b3c6 | Travis Abbott | 01 November 2012, 21:02:21 UTC | update test data to match expected results the previous test data was asserting that the code did the wrong thing (passed files to joinx in incorrect order due to filenames being hashed then iterating over the keys). | 01 November 2012, 21:14:01 UTC |
| df1bd18 | Eddie Belter | 01 November 2012, 20:33:31 UTC | AQID: using skipped as tgi_lims_status for inst data that had no models attempted | 01 November 2012, 20:33:37 UTC |
| c7f3aea | Eddie Belter | 01 November 2012, 18:58:09 UTC | AQID: add better error message for lack of sample/source/taxon. Add test for these failures | 01 November 2012, 20:33:37 UTC |
| a28026f | Travis Abbott | 01 November 2012, 20:22:10 UTC | fix plotting functionality in BurdenTestSummary Mutation diagrams were not being created due to specifying alternate alleles as bases where vcf indices were expected. | 01 November 2012, 20:22:10 UTC |
| 4ca2d7a | Jim Weible | 01 November 2012, 14:09:24 UTC | try to get around terribleness associated with copy number for mouse | 01 November 2012, 15:23:11 UTC |
| 49ddf1b | Thomas Mooney | 01 November 2012, 15:00:46 UTC | Mahalo, jlolofie. | 01 November 2012, 15:00:46 UTC |
| 591b88b | Nathaniel Nutter | 01 November 2012, 14:20:32 UTC | show subject_class in error message | 01 November 2012, 14:20:32 UTC |
| 70efbdc | Thomas Mooney | 01 November 2012, 13:43:30 UTC | Carry forward setting of content_type if it wasn't set initially. | 01 November 2012, 13:44:25 UTC |
| c852712 | Scott Smith | 31 October 2012, 23:32:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/Tools/BioSamtools/ErrorRate.pm | 31 October 2012, 23:32:50 UTC |
| 26b3fd8 | Travis Abbott | 31 October 2012, 21:56:37 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 21:56:37 UTC |
| b567b34 | Travis Abbott | 31 October 2012, 21:55:47 UTC | fix non-deterministic filename ordering in VcfMerge.pm files were being passed to joinx based on the order they appear in a hash. | 31 October 2012, 21:55:47 UTC |
| 7feede4 | Kyung Kim | 31 October 2012, 21:52:14 UTC | per rt#86752, update to remove distinction between euk and bacterial naming .. previously, euk samples were filtered out and not printed to interpro.ace file | 31 October 2012, 21:52:14 UTC |
| 0dcc1a1 | Scott Smith | 31 October 2012, 21:39:02 UTC | replaced calls to the old get_class_object with newer __meta__ | 31 October 2012, 21:39:02 UTC |
| fde012b | Eddie Belter | 31 October 2012, 19:59:31 UTC | AQID: Add tgi lims failed message when an inst data fails | 31 October 2012, 19:59:38 UTC |
| a9e2d2f | apregier | 31 October 2012, 19:44:35 UTC | Merge branch 'music' into gb_master | 31 October 2012, 19:44:35 UTC |
| 3deb4fe | apregier | 31 October 2012, 19:08:43 UTC | Assign dbsnp to AQID somatic variation models again | 31 October 2012, 19:44:17 UTC |
| 0945fca | apregier | 31 October 2012, 18:40:51 UTC | Add options to run only certain parts of play music | 31 October 2012, 19:44:17 UTC |
| 7750cb2 | Ian Ferguson | 31 October 2012, 19:38:02 UTC | Fixes for GMT::BioSamtools::ErrorRate Rearranged some code in ErrorRate and fixed an issue with single- vs paired-end reads. | 31 October 2012, 19:38:02 UTC |
| 0820b28 | Ian Ferguson | 31 October 2012, 19:25:45 UTC | Added support for bwa-0.6.2. Updated AlignmentResult and IntermediateAlignmentResult modules for bwa. Index files and log formats have changed with 0.6.2. | 31 October 2012, 19:25:45 UTC |
| 92510be | Travis Abbott | 31 October 2012, 19:05:36 UTC | more phenocorr updates for music output format change rename clinical correlation outputs -> tsv instead of csv, P-val in headers becomes Pval | 31 October 2012, 19:05:36 UTC |
| 73474a2 | Cyriac Kandoth | 31 October 2012, 18:56:01 UTC | Change output files names to .tsv to reflect tab-separation | 31 October 2012, 18:56:01 UTC |
| 1ab7a28 | Scott Smith | 31 October 2012, 18:51:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 18:51:02 UTC |
| 1dc56f9 | Scott Smith | 31 October 2012, 18:50:56 UTC | replaced calls to get_rule_for_params to define_boolexpr, since the former is deprecated and will not run outside of TGI | 31 October 2012, 18:50:56 UTC |
| 215030f | Travis Abbott | 31 October 2012, 18:44:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 18:44:17 UTC |
| 2457ed7 | Travis Abbott | 31 October 2012, 18:43:42 UTC | update phenocorr to cope with new music format | 31 October 2012, 18:43:42 UTC |
| 61ea612 | Mark Burnett | 31 October 2012, 18:21:29 UTC | Remove test for removed command | 31 October 2012, 18:21:29 UTC |
| 2e28de2 | Travis Abbott | 31 October 2012, 18:12:05 UTC | update to cope with new music output format | 31 October 2012, 18:12:05 UTC |
| 62a7991 | Travis Abbott | 31 October 2012, 17:43:19 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 17:43:19 UTC |
| de71cd7 | Travis Abbott | 31 October 2012, 17:42:36 UTC | point tigra-sv to /usr/bin, update test SvCalls test data | 31 October 2012, 17:42:36 UTC |
| 6bad744 | Nathaniel Nutter | 31 October 2012, 17:00:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 17:00:35 UTC |
| 8af8344 | Cyriac Kandoth | 31 October 2012, 16:57:00 UTC | Fix typos and other minor tweaks to formatting | 31 October 2012, 16:57:00 UTC |
| 3ae908c | Nathaniel Nutter | 31 October 2012, 16:55:33 UTC | Merge branch 'lockless_allocation_refactor' CHANGELOG: Allocations can now be created without requiring a lock on the volume. We expect this will decrease average allocation creation times from ~15-20 seconds down to ~3 seconds and will also provide a more consistent creation time. (The locking version has spikes as high several minutes.) Despite thoroughly testing these changes it is quite possible that unexpected issue may occur. If you notice any issues during allocation creation please let us know. | 31 October 2012, 16:55:33 UTC |
