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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
641a6c1 Thomas B. Mooney 15 February 2016, 19:57:44 UTC Merge pull request #1255 from tmooney/remove_old_alignment_accessors Remove Old Alignment Accessors 15 February 2016, 19:57:44 UTC
4df8f38 Thomas B. Mooney 15 February 2016, 14:51:03 UTC Merge pull request #1253 from tmooney/createreport_uses_standard_somvar_accessors SomVar CreateReport uses Build Accessors for BAMs and Reference 15 February 2016, 14:51:03 UTC
9eea86b Chris Miller 12 February 2016, 20:20:22 UTC Merge pull request #1247 from chrisamiller/master typo in docs 12 February 2016, 20:20:22 UTC
bf2cc96 APipe Tester 12 February 2016, 13:16:44 UTC Updated `genome` tab completion. 12 February 2016, 13:16:44 UTC
fe70a5d APipe Tester 12 February 2016, 13:15:11 UTC Updated class browser cache. 12 February 2016, 13:15:11 UTC
9f89d66 Thomas B. Mooney 11 February 2016, 22:28:14 UTC Merge pull request #1252 from tmooney/build_export_improvements Further Refinements to Build Export 11 February 2016, 22:28:14 UTC
d710c88 Thomas B. Mooney 11 February 2016, 20:31:20 UTC Merge pull request #1250 from tmooney/quiet_autoload_warning_in_refalign_summary_report Use GMT:Joinx::SnvConcordanceByQuality in RefAlign Summary Report. 11 February 2016, 20:31:20 UTC
6769e4d Susanna Kiwala 11 February 2016, 18:33:19 UTC Merge pull request #1251 from susannasiebert/epitope_prediction_bugfix2 Add transcript id to the fasta headers to ensure uniqueness 11 February 2016, 18:33:19 UTC
beeb317 Thomas B. Mooney 11 February 2016, 18:21:36 UTC Merge pull request #1246 from tmooney/remove_obsolete_refalign_pp_params Remove Obsolete RefAlign ProcessingProfile Parameters 11 February 2016, 18:21:36 UTC
baac23b Eddie Belter 11 February 2016, 17:13:02 UTC Merge pull request #1243 from ebelter/unarchive-imported-instdata Disk Allocation Unarchive 11 February 2016, 17:13:02 UTC
176611f Thomas Mooney 11 February 2016, 15:11:47 UTC Remove old instrument-data indirect accessors. The "temp hack" was added in bd502ac71a8a613e95af57f429d98b1d948abc76 on 14 July 2008 to the original Genome::Model. It was then migrated to Genome::Model::ShortRead before moving to its most recent location here in Genome::Model::ReferenceAlignment. 11 February 2016, 15:11:47 UTC
f860c3e Thomas Mooney 11 February 2016, 15:03:44 UTC Remove build_subclass_name from RefAlign. The TODO told me to! 11 February 2016, 15:03:44 UTC
219a27c Thomas Mooney 11 February 2016, 15:00:10 UTC Remove "latest_build_bam_file". This can be listed now with latest_build.whole_rmdup_bam_file. 11 February 2016, 15:00:10 UTC
d265030 Thomas Mooney 11 February 2016, 14:54:10 UTC Remove accessors for .map files. Sorry, maq. 11 February 2016, 14:54:10 UTC
c9640a9 Thomas Mooney 11 February 2016, 14:52:03 UTC Remove old accessors for getting allocations owned by events. BAMs are "now" stored in SoftwareResults! 11 February 2016, 14:52:03 UTC
21f1ad8 Susanna Kiwala 11 February 2016, 14:47:15 UTC Merge pull request #1248 from susannasiebert/epitope_prediction_bugfix Pass is_many property as an array ref 11 February 2016, 14:47:15 UTC
457b0ef Susanna Kiwala 11 February 2016, 14:46:49 UTC Move iterator incrementation to a more appropriate place 11 February 2016, 14:46:49 UTC
5dc98c3 Susanna Kiwala 11 February 2016, 14:41:35 UTC Simplify iterator creation 11 February 2016, 14:41:35 UTC
caa6783 Susanna Kiwala 11 February 2016, 14:41:10 UTC Fix test file 11 February 2016, 14:41:10 UTC
725f6d4 Susanna Kiwala 11 February 2016, 14:36:43 UTC New test file for multiple transcripts 11 February 2016, 14:36:43 UTC
10cda38 Thomas Mooney 10 February 2016, 23:44:04 UTC Use standard SomVar accessors to get BAMs and references. 10 February 2016, 23:44:04 UTC
a7d750b Thomas Mooney 10 February 2016, 23:43:33 UTC Both input builds to SomVar should share a common reference. 10 February 2016, 23:43:33 UTC
6e49272 Thomas Mooney 10 February 2016, 19:34:35 UTC Use GMT:Joinx::SnvConcordanceByQuality. This quiets the warning: Use of inherited AUTOLOAD for non-method Genome::Model::Tools::Joinx::SnvConcordanceByQuality::parse_results_file() is deprecated at .../Genome/Model/ReferenceAlignment/Report/Summary.pm line 220. 10 February 2016, 23:15:27 UTC
040c7d6 Thomas B. Mooney 10 February 2016, 22:11:21 UTC Merge pull request #1242 from tmooney/resurrect_per_iteration_stat Check for directory existence each time before calling mkdir. 10 February 2016, 22:11:21 UTC
97ce67f Eddie Belter 10 February 2016, 22:05:34 UTC Unarchive: check first before adding instdata to AnP 10 February 2016, 22:05:34 UTC
1c1dfc1 Thomas Mooney 10 February 2016, 21:43:00 UTC Paranoidly refuse to unlink things outside our export directory. This shouldn't happen as long as our algorithm is correct, but makes modifications less scary! 10 February 2016, 21:48:59 UTC
9bf6aaa Allison Penner Regier 10 February 2016, 21:45:41 UTC Merge pull request #1231 from apregier/list_hc_files Command to print out all haplotype caller output files 10 February 2016, 21:45:41 UTC
8209da2 Thomas Mooney 10 February 2016, 21:40:45 UTC Handle dangling symlinks ourselves now that follow is disabled. 10 February 2016, 21:40:45 UTC
7003a5b Susanna Kiwala 10 February 2016, 21:40:29 UTC Add an iterator to cover edge case where transcript id is the same 10 February 2016, 21:40:29 UTC
e4ea977 Thomas Mooney 10 February 2016, 21:22:33 UTC Don't follow symlinks. We're explicitly handling them in the $resolve_symlinks function. 10 February 2016, 21:22:33 UTC
0b36a87 Thomas Mooney 10 February 2016, 21:03:05 UTC Only recursively find on directories. 10 February 2016, 21:03:05 UTC
69f539c Thomas Mooney 10 February 2016, 21:00:26 UTC Use abs_path to get the symlink destination. $File::Find::fullname is not always defined. This brings the symlink and the dangling-symlink approach to parity. 10 February 2016, 21:00:26 UTC
3b97b8e Thomas Mooney 10 February 2016, 20:59:18 UTC Friendlier error message when the target directory doesn't exist. Previously this would confusingly report the "Not enough space..." error. 10 February 2016, 20:59:18 UTC
5f960bb Susanna Kiwala 10 February 2016, 19:35:06 UTC Add transcript id to the fasta headers to ensure uniqueness 10 February 2016, 19:38:23 UTC
5264956 Susanna Kiwala 10 February 2016, 18:47:03 UTC Pass is_many property as an array ref 10 February 2016, 18:47:03 UTC
4a09a45 Chris Miller 10 February 2016, 17:45:47 UTC typo in docs 10 February 2016, 17:46:44 UTC
eb74062 Thomas Mooney 10 February 2016, 16:31:42 UTC Remove "read_calibrator_name" and "read_calibrator_params". No processing profiles have these set. 10 February 2016, 16:34:14 UTC
21cff02 Thomas Mooney 10 February 2016, 16:27:42 UTC Remove deprecated "capture_set_name" parameter. These have been using the "target_region_set_name" and "region_of_interest_set_name" inputs for years! 10 February 2016, 16:34:14 UTC
8be504c Thomas Mooney 10 February 2016, 16:26:51 UTC Remove obsolete "prior_ref_seq" parameter. 10 February 2016, 16:34:13 UTC
2574091 Thomas Mooney 10 February 2016, 16:18:45 UTC Remove things that asked to be removed. They weren't referenced anywhere, so fulfil their destiny. 10 February 2016, 16:34:13 UTC
f454481 Thomas Mooney 10 February 2016, 16:14:34 UTC Remove obsolete parameter "align_dist_threshold". As best I can tell this was used in "AcceptReads" in very early versions of the pipeline. 10 February 2016, 16:34:08 UTC
7bbb7d2 Thomas Mooney 10 February 2016, 16:02:55 UTC Remove special-casing for "maq". This will change the returned value for some old processing profiles, but they don't work any more, anyway. 10 February 2016, 16:02:55 UTC
b539f28 Thomas Mooney 10 February 2016, 16:00:21 UTC Remove maq-related parameter "multi_read_fragment_strategy". 10 February 2016, 16:00:21 UTC
1b14cd3 Thomas B. Mooney 10 February 2016, 14:02:58 UTC Merge pull request #1239 from tmooney/stop_subclassing_refalign_processingprofiles Stop subclassing ReferenceAlignment ProcessingProfiles on sequencing_platform. 10 February 2016, 14:02:58 UTC
84c5a63 APipe Tester 10 February 2016, 13:16:42 UTC Updated `genome` tab completion. 10 February 2016, 13:16:42 UTC
b02631c APipe Tester 10 February 2016, 13:15:11 UTC Updated class browser cache. 10 February 2016, 13:15:11 UTC
4e18ef9 Eddie Belter 09 February 2016, 22:47:44 UTC Merge pull request #1234 from ebelter/import-tweaks InstData Import Fixes and Improvements 09 February 2016, 22:47:44 UTC
15fe3ae Eddie Belter 09 February 2016, 21:25:19 UTC spell check 09 February 2016, 21:25:19 UTC
b272c7c Eddie Belter 09 February 2016, 20:25:21 UTC Spell/grammer check 09 February 2016, 20:25:21 UTC
2e609ae Eddie Belter 09 February 2016, 20:21:18 UTC Merge pull request #1238 from ebelter/instdata-delete-command InstData Delete CLI 09 February 2016, 20:21:18 UTC
6cfafa4 Eddie Belter 09 February 2016, 19:48:35 UTC Unarchive: convert to subtests 09 February 2016, 19:50:19 UTC
5a33a8c Eddie Belter 09 February 2016, 19:36:43 UTC Unarchive: use sub install in test 09 February 2016, 19:36:43 UTC
fd4ae2b Eddie Belter 09 February 2016, 19:36:17 UTC Unarchive: allow imported instrument data 09 February 2016, 19:36:17 UTC
30634f3 Thomas Mooney 09 February 2016, 19:15:48 UTC Check for directory existence each time before calling mkdir. This partially reverts 0a28189020054af452b08c8d496234b1734bf403 from PR #809. 09 February 2016, 19:15:48 UTC
ce9b9be Eddie Belter 09 February 2016, 00:23:03 UTC Unarchive: make and use create allocation function in test 09 February 2016, 19:04:09 UTC
03335f5 Eddie Belter 09 February 2016, 19:03:31 UTC Set no commit in delete test 09 February 2016, 19:03:31 UTC
3cb9770 Anthony Brummett 09 February 2016, 14:28:08 UTC Merge pull request #1241 from brummett/genome-test-env-alloc-cleanup Ensure allocations are cleaned up when genome-test-env exits 09 February 2016, 14:28:08 UTC
3400c40 APipe Tester 09 February 2016, 13:18:00 UTC Updated `gmt` tab completion. 09 February 2016, 13:18:00 UTC
68b02d1 APipe Tester 09 February 2016, 13:17:18 UTC Updated `genome` tab completion. 09 February 2016, 13:17:18 UTC
c0a8cdd APipe Tester 09 February 2016, 13:15:46 UTC Updated class browser cache. 09 February 2016, 13:15:46 UTC
d2e80c6 Eddie Belter 08 February 2016, 23:46:46 UTC InstData: delete command test ensures only imported instdata is deleted 08 February 2016, 23:46:46 UTC
a8beaf0 Eddie Belter 08 February 2016, 21:23:11 UTC Fix removes input files role test 08 February 2016, 21:23:11 UTC
05ad1b3 Eddie Belter 08 February 2016, 21:16:56 UTC Have split by read group have the remoes input files role 08 February 2016, 21:16:56 UTC
9389309 Eddie Belter 08 February 2016, 21:15:00 UTC Update path propeties to be FilePath data type 08 February 2016, 21:15:00 UTC
ece2f54 Thomas B. Mooney 08 February 2016, 20:56:32 UTC Merge pull request #1219 from tmooney/export_symlink_handling_copies_files_not_allocations Don't copy entire allocations in place of symlinks. 08 February 2016, 20:56:32 UTC
4280271 Jason Walker 08 February 2016, 18:58:53 UTC Merge pull request #1233 from jasonwalker80/picard_130_filter_sam_reads Update Picard FilterSamReads to use Base class 08 February 2016, 18:58:53 UTC
341d666 Thomas Mooney 04 February 2016, 22:31:35 UTC Workaround for multiple equivalent class names. 08 February 2016, 15:41:14 UTC
deadb1f Thomas Mooney 04 February 2016, 15:12:54 UTC Stop subclassing processing-profiles on sequencing platform. We'll need to wait for old snapshots to fall out of use before editing the class of existing profiles and removing the subclasses altogether. 08 February 2016, 15:41:14 UTC
6687ce8 Thomas B. Mooney 08 February 2016, 14:32:20 UTC Merge pull request #1237 from tmooney/remove_refalign_maq_references Remove lingering references to maq-generated files in ReferenceAlignment. 08 February 2016, 14:32:20 UTC
4a75166 Thomas B. Mooney 08 February 2016, 14:32:07 UTC Merge pull request #1236 from tmooney/eliminate_duplicating_id_property_declarations Remove explicit _id properties that Model.pm will generate for us. 08 February 2016, 14:32:07 UTC
7fad2c5 Thomas B. Mooney 08 February 2016, 14:31:51 UTC Merge pull request #1235 from tmooney/modernize_refalign_inputs Modernize input listing for ReferenceAlignment. 08 February 2016, 14:31:51 UTC
db46b7e Anthony Brummett 05 February 2016, 22:22:19 UTC Ensure allocations are cleaned up when genome-test-env exits Looks like UR_DBI_NO_COMMIT was still true when the allocation removal ran, so calling delete() on allocations did not remove the files. 05 February 2016, 22:22:19 UTC
d9d8ba9 Jason Walker 05 February 2016, 17:28:04 UTC Use File::Spec->join for file paths. 05 February 2016, 17:28:04 UTC
0673c58 Thomas B. Mooney 04 February 2016, 22:23:06 UTC Merge pull request #1232 from tmooney/commit_between_intervals_in_haplotypecaller Commit after each interval of the HaplotypeCaller runs. 04 February 2016, 22:23:06 UTC
3b0ce41 Eddie Belter 04 February 2016, 20:39:31 UTC Move use ur role to after use genome to get to compile 04 February 2016, 20:39:35 UTC
63d34f5 Eddie Belter 04 February 2016, 20:33:23 UTC Update expected status message 04 February 2016, 20:33:23 UTC
4ef67ac APipe Tester 04 February 2016, 20:17:14 UTC updated graphite submodule to 5141125 04 February 2016, 20:17:14 UTC
3d68f4c APipe Tester 04 February 2016, 13:16:24 UTC Updated `genome` tab completion. 04 February 2016, 13:16:24 UTC
e5bf3c8 Eddie Belter 03 February 2016, 23:39:42 UTC InstData: rm remove command, use CRUD built in delete and only allow imported instrument data to be deleted 03 February 2016, 23:39:42 UTC
9a976e9 Thomas Mooney 03 February 2016, 23:31:50 UTC Update tests to account for stricter class-checking. 03 February 2016, 23:31:50 UTC
230bebb Thomas Mooney 03 February 2016, 23:24:38 UTC Remove lingering references to maq-generated files. Support for running maq in the pipeline has been gone for many years. 03 February 2016, 23:24:38 UTC
2a4ac6c Thomas Mooney 03 February 2016, 23:09:01 UTC Remove explicit _id properties that Model.pm will generate for us. The generated version points at the bridge table and so does not require the manually-generated "add_" methods either. 03 February 2016, 23:09:01 UTC
4205edd Thomas Mooney 03 February 2016, 23:00:44 UTC Modernize input listing for ReferenceAlignment. This removes support for programmatically defining a build with a name or ID. (Programmers can easily get the object!) The command line resolution based on name or ID should still be in place. 03 February 2016, 23:05:26 UTC
1e774c2 Eddie Belter 03 February 2016, 22:33:33 UTC Convert verify not imported test to subtests 03 February 2016, 22:35:09 UTC
fde6522 Eddie Belter 03 February 2016, 22:24:38 UTC Verify Not Imported: die if source file is in the working directory 03 February 2016, 22:24:38 UTC
458c052 Eddie Belter 03 February 2016, 21:53:00 UTC Recursively set log directory 03 February 2016, 21:53:00 UTC
ade498f David Morton 03 February 2016, 21:36:16 UTC Merge pull request #1226 from davidlmorton/ptero_lsf_execs Use pre/post-exec scripts for ptero LSF jobs 03 February 2016, 21:36:16 UTC
854e7d8 Jason Walker 03 February 2016, 21:13:09 UTC _java_class returns a list of class parts that will be assembled by the base class. 03 February 2016, 21:13:09 UTC
1a22487 Jason Walker 03 February 2016, 17:56:12 UTC Update the FilterSamReads picard command to use the Base picard class. Also an integration test since the old test only covered the command creation logic. 03 February 2016, 17:56:12 UTC
669a3db Jason Walker 03 February 2016, 17:51:06 UTC A few typos and comment changes. 03 February 2016, 17:51:06 UTC
c42830d Thomas Mooney 03 February 2016, 17:01:21 UTC Commit after each interval of the HaplotypeCaller runs. 03 February 2016, 17:01:21 UTC
74aed4d Jason Walker 03 February 2016, 15:14:42 UTC Merge pull request #1230 from jasonwalker80/picard_130_genotype_concordance Support Picard v1.130 Changes 03 February 2016, 15:14:42 UTC
21d1264 David Morton 03 February 2016, 01:12:10 UTC Update test data 03 February 2016, 01:12:10 UTC
e72391a David Morton 03 February 2016, 01:00:36 UTC Be really careful about pre/post-exec scripts 03 February 2016, 01:00:36 UTC
2e08768 Thomas B. Mooney 02 February 2016, 23:28:00 UTC Merge pull request #1229 from tmooney/remove_disused_subclassing_by_sequencing_platform Remove disused method for subclassing by sequencing_platform. 02 February 2016, 23:28:00 UTC
b734e0e Eddie Belter 02 February 2016, 23:27:17 UTC Symlink source files during verify 02 February 2016, 23:27:17 UTC
60290d1 Eddie Belter 02 February 2016, 23:26:38 UTC Import InstData: update sra 02 February 2016, 23:26:38 UTC
4ab784b Eddie Belter 02 February 2016, 23:02:27 UTC Update builder with working_directory input property 02 February 2016, 23:02:27 UTC
0d3da14 Thomas B. Mooney 02 February 2016, 22:50:27 UTC Merge pull request #1228 from tmooney/remove_processing_profile_execute_build_support Remove ProcessingProfile-based _execute_build support 02 February 2016, 22:50:27 UTC
50965a7 Eddie Belter 02 February 2016, 22:45:03 UTC Add removes input files role for clean up after execute 02 February 2016, 22:45:03 UTC
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