3d32d95 | Nathaniel Nutter | 01 April 2015, 20:31:47 UTC | Revert "Fix gmt picard typos; remove duplicate method" | 01 April 2015, 20:31:47 UTC |
4a6ffb7 | Susanna Siebert | 01 April 2015, 18:06:23 UTC | Merge pull request #582 from susannasiebert/qc_framework Create qc tool wrappers | 01 April 2015, 18:06:23 UTC |
215f09b | Thomas B. Mooney | 01 April 2015, 15:54:54 UTC | Merge pull request #606 from tmooney/gmt_picard_typos Fix gmt picard typos; remove duplicate method | 01 April 2015, 15:54:54 UTC |
db39485 | Thomas B. Mooney | 01 April 2015, 15:49:13 UTC | Merge pull request #583 from tmooney/AT-750-v3 Add decorators and a "QC" decorator to the Alignment Dispatcher | 01 April 2015, 15:49:13 UTC |
00250a7 | Thomas B. Mooney | 01 April 2015, 15:48:21 UTC | Merge pull request #578 from tmooney/deduplicate_alignment_queue_selection Stop using GENOME_LSF_QUEUE_ALIGNMENT_PROD. | 01 April 2015, 15:48:21 UTC |
9393f43 | Susanna Siebert | 01 April 2015, 15:13:46 UTC | Merge pull request #605 from susannasiebert/model_tests Fix class name | 01 April 2015, 15:13:46 UTC |
c628a80 | Dave Larson | 31 March 2015, 18:48:05 UTC | Merge pull request #603 from ernfrid/bump_bam_readcount change default version of G::M::T::Sam::Readcount to use bam-readcount v... | 31 March 2015, 18:48:05 UTC |
67d7d9b | Thomas B. Mooney | 31 March 2015, 18:06:00 UTC | Merge pull request #597 from tmooney/call_correct_accessor_in_adsp_qc Call Correct Accessor in ADSP QC tools | 31 March 2015, 18:06:00 UTC |
aba1942 | Nathaniel Nutter | 31 March 2015, 16:16:51 UTC | Merge pull request #604 from nnutter/RT-104865 avoid crash when chromosome is missing | 31 March 2015, 16:16:51 UTC |
3f31962 | Nathaniel Nutter | 31 March 2015, 16:16:46 UTC | Merge pull request #600 from nnutter/RT-104836 handle use case where reference sequence is missing | 31 March 2015, 16:16:46 UTC |
fdbcd44 | Thomas Mooney | 31 March 2015, 15:55:12 UTC | Remove incomplete disused "parse_file_into_histogram_hashref". | 31 March 2015, 15:55:12 UTC |
ec2d651 | Susanna Siebert | 31 March 2015, 15:34:26 UTC | Merge remote-tracking branch 'origin/master' into qc_framework | 31 March 2015, 15:34:26 UTC |
2574ab4 | Thomas Mooney | 31 March 2015, 15:23:37 UTC | Check for the method we're really going to call. | 31 March 2015, 15:23:37 UTC |
6c8ad8f | Thomas Mooney | 31 March 2015, 15:23:00 UTC | Fix typo: hashsref => hashref | 31 March 2015, 15:23:00 UTC |
ac0714c | Susanna Siebert | 31 March 2015, 15:16:27 UTC | Explicitly test that there is only one metric_key in the metric_results | 31 March 2015, 15:16:27 UTC |
0063af8 | Susanna Siebert | 31 March 2015, 14:55:27 UTC | Fix doc line for remove_duplicates | 31 March 2015, 14:55:27 UTC |
f4adb57 | Susanna Siebert | 31 March 2015, 14:54:07 UTC | Remove default values from doc line | 31 March 2015, 14:54:07 UTC |
b4f6a12 | Susanna Siebert | 31 March 2015, 14:52:55 UTC | Remove unnecessary dereferencing | 31 March 2015, 14:52:55 UTC |
1b512a6 | Susanna Siebert | 31 March 2015, 14:50:31 UTC | Fix version in test message | 31 March 2015, 14:50:31 UTC |
b13f3ec | Susanna Siebert | 31 March 2015, 14:49:22 UTC | Use qq instead of escaping quotes | 31 March 2015, 14:49:22 UTC |
20a151c | Susanna Siebert | 31 March 2015, 13:36:48 UTC | Fix class name | 31 March 2015, 13:36:57 UTC |
813a98d | Nathaniel Nutter | 30 March 2015, 19:29:12 UTC | handle use case where reference sequence is missing | 30 March 2015, 19:57:08 UTC |
bf55aab | Susanna Siebert | 30 March 2015, 19:47:57 UTC | Merge pull request #598 from susannasiebert/alignment_result2 Make a class for merged AlignedBamResults and use it where appropriate | 30 March 2015, 19:47:57 UTC |
d566c76 | Nathaniel Nutter | 30 March 2015, 17:18:11 UTC | avoid crash when chromosome is missing | 30 March 2015, 17:18:11 UTC |
e75a403 | Thomas Mooney | 30 March 2015, 17:09:22 UTC | On refalign, the accessor is called "get_alignments". | 30 March 2015, 17:09:22 UTC |
d8b1051 | Thomas Mooney | 30 March 2015, 17:09:11 UTC | Whitespace. | 30 March 2015, 17:09:11 UTC |
a66b151 | Susanna Siebert | 30 March 2015, 15:08:35 UTC | Make a class for merged AlignedBamResults and use it where appropriate | 30 March 2015, 15:40:57 UTC |
de88b05 | Dave Larson | 30 March 2015, 15:12:52 UTC | change default version of G::M::T::Sam::Readcount to use bam-readcount v0.7 | 30 March 2015, 15:12:52 UTC |
06d184c | Nathaniel Nutter | 28 March 2015, 18:09:22 UTC | Merge pull request #596 from nnutter/master use canonpath to normalize $test_dir | 28 March 2015, 18:09:22 UTC |
f5dde25 | Nathaniel Nutter | 27 March 2015, 22:11:22 UTC | use canonpath to normalize $test_dir Use canonpath to normalize path as something in StreamGraph seemed to do the same. For example, `./WorkflowBuilder` becomes just `WorkflowBuilder` which was breaking the full test suite. | 27 March 2015, 22:11:22 UTC |
17421ed | Allison Penner Regier | 27 March 2015, 18:32:03 UTC | Merge pull request #593 from apregier/shortcut_adaptor Add shortcut to adaptor class | 27 March 2015, 18:32:03 UTC |
f09043c | apregier | 27 March 2015, 17:54:11 UTC | Shortcut delegates to execute | 27 March 2015, 17:54:11 UTC |
1c156a1 | Susanna Siebert | 27 March 2015, 14:36:53 UTC | Make MarkDuplicates a G::M::T::Picard::Base | 27 March 2015, 14:36:53 UTC |
f713990 | Susanna Siebert | 27 March 2015, 14:36:23 UTC | Fix picard class names | 27 March 2015, 14:36:23 UTC |
9a3dc91 | Susanna Siebert | 27 March 2015, 14:35:40 UTC | Consolidate recent Picard changes | 27 March 2015, 14:35:40 UTC |
c44ea31 | Allison Penner Regier | 27 March 2015, 14:34:09 UTC | Merge pull request #546 from apregier/compare_vcf_in_process Compare vcf in process | 27 March 2015, 14:34:09 UTC |
2679d82 | Susanna Siebert | 27 March 2015, 14:33:08 UTC | Put text fields in quotes | 27 March 2015, 14:33:08 UTC |
bfe3ddb | apregier | 27 March 2015, 01:37:22 UTC | Add shortcut to adaptor class There is no reason why this should ever need to run with lots of resources | 27 March 2015, 01:38:22 UTC |
eab32f6 | Thomas B. Mooney | 26 March 2015, 21:37:33 UTC | Merge pull request #586 from tmooney/remove_unused_properties_from_composite_workflow Remove disused properties. | 26 March 2015, 21:37:33 UTC |
76f1a76 | Thomas B. Mooney | 26 March 2015, 21:37:15 UTC | Merge pull request #585 from tmooney/dont_log_rollbacks_on_build_requested Don't log rollbacks on build requested | 26 March 2015, 21:37:15 UTC |
098ef67 | Susanna Siebert | 26 March 2015, 20:57:30 UTC | Merge remote-tracking branch 'origin/master' into qc_framework | 26 March 2015, 20:57:30 UTC |
6900b8f | Susanna Siebert | 26 March 2015, 20:56:03 UTC | Merge remote-tracking branch 'origin/master' into qc_framework | 26 March 2015, 20:56:03 UTC |
5ccc6a2 | Ian Ferguson | 26 March 2015, 20:55:18 UTC | Merge pull request #573 from iferguson90/picard-class-fix Picard classnames | 26 March 2015, 20:55:18 UTC |
df7702f | Eddie Belter | 26 March 2015, 19:41:21 UTC | Merge pull request #590 from ebelter/instdata2 InstData Import: give default value to resolved instdata properties | 26 March 2015, 19:41:21 UTC |
2352f4c | Eddie Belter | 26 March 2015, 19:40:57 UTC | Merge pull request #584 from ebelter/instdata-description InstData Import: pass description on to created instdasta | 26 March 2015, 19:40:57 UTC |
a828d62 | apregier | 26 March 2015, 19:39:08 UTC | Simplify by passing arguments straight through | 26 March 2015, 19:39:08 UTC |
ab60abc | Nathaniel Nutter | 26 March 2015, 19:37:44 UTC | Merge pull request #591 from nnutter/master make StreamGraph.t independent of current working directory | 26 March 2015, 19:37:44 UTC |
8b314a0 | Avinash Ramu | 26 March 2015, 19:27:44 UTC | Merge pull request #547 from gatoravi/clinseq_update_analysis clinseq: update defaults in update-analysis | 26 March 2015, 19:27:44 UTC |
cdbf64b | Ian Ferguson | 26 March 2015, 18:48:32 UTC | Use an HTTP request instead of a socket | 26 March 2015, 18:48:32 UTC |
9ab9c24 | Avinash Ramu | 26 March 2015, 16:27:35 UTC | pull in snapshot changes from master | 26 March 2015, 16:27:35 UTC |
801ac9d | Susanna Siebert | 26 March 2015, 15:51:58 UTC | Fix package name for MarkDuplicates in Picard 1.123 | 26 March 2015, 15:51:58 UTC |
46a7998 | Avinash Ramu | 26 March 2015, 15:36:17 UTC | Merge remote-tracking branch 'origin' into clinseq_update_analysis | 26 March 2015, 15:36:17 UTC |
e34a533 | Avinash Ramu | 26 March 2015, 15:33:39 UTC | update db snapshot | 26 March 2015, 15:33:39 UTC |
ad3ab9b | Thomas Mooney | 26 March 2015, 13:29:14 UTC | Replace caller with Carp::shortmess. | 26 March 2015, 13:29:14 UTC |
edc004b | APipe Tester | 26 March 2015, 12:16:55 UTC | Updated `genome` tab completion. | 26 March 2015, 12:16:55 UTC |
66f9153 | APipe Tester | 26 March 2015, 12:15:07 UTC | Updated class browser cache. | 26 March 2015, 12:15:07 UTC |
05f3b91 | Ian Ferguson | 25 March 2015, 20:17:42 UTC | Collect call info and send it to my workstation | 25 March 2015, 20:17:42 UTC |
0b9c64d | Ian Ferguson | 25 March 2015, 19:57:14 UTC | Don't die when supplied with an undef Picard vers. | 25 March 2015, 19:57:14 UTC |
1393ae4 | Nathaniel Nutter | 25 March 2015, 19:30:21 UTC | make StreamGraph.t independent of current working directory | 25 March 2015, 19:30:21 UTC |
ea96bf9 | Eddie Belter | 25 March 2015, 18:30:35 UTC | InstData Import: give default value to resolved instdata properties | 25 March 2015, 18:30:35 UTC |
c3b5255 | Eddie Belter | 25 March 2015, 17:13:02 UTC | InstData Import: spell cprrect | 25 March 2015, 17:13:02 UTC |
d2781f2 | Susanna Siebert | 25 March 2015, 17:10:57 UTC | Merge pull request #587 from susannasiebert/alignment_result Filter out G::ID::AlignmentResult | 25 March 2015, 17:10:57 UTC |
cb14972 | Thomas B. Mooney | 25 March 2015, 17:00:04 UTC | Merge pull request #581 from tmooney/optional_tag_during_add_menu_item Optionally add tag(s) when associating menu item(s) to the AnP. | 25 March 2015, 17:00:04 UTC |
3f560c5 | Susanna Siebert | 25 March 2015, 14:19:12 UTC | Remove breakpoint | 25 March 2015, 14:19:12 UTC |
7ebe5b9 | Susanna Siebert | 25 March 2015, 14:18:14 UTC | Move Picard-specific cmd_line subroutine to Picard.pm | 25 March 2015, 14:18:14 UTC |
091467d | Susanna Siebert | 25 March 2015, 14:16:00 UTC | Use temp file path instead of __FILE__ | 25 March 2015, 14:16:00 UTC |
3017e52 | Susanna Siebert | 25 March 2015, 13:41:30 UTC | Filter out G::ID::AlignmentResult Since per-lane alignments are now G::ID::AlignedBamResult they need to be explicitly filtered out | 25 March 2015, 13:41:30 UTC |
a9a456b | Thomas B. Mooney | 25 March 2015, 13:29:12 UTC | Merge pull request #579 from tmooney/merge_error_message_on_deleted_object Don't call error_message on a deleted object. | 25 March 2015, 13:29:12 UTC |
321cd84 | Thomas Mooney | 25 March 2015, 13:26:52 UTC | Remove disused properties. | 25 March 2015, 13:26:52 UTC |
ea3c493 | Thomas Mooney | 25 March 2015, 13:09:25 UTC | Remove old comments. * We already do have a note. * This isn't especially TGI-specific. | 25 March 2015, 13:09:25 UTC |
e941937 | Thomas Mooney | 25 March 2015, 13:04:16 UTC | Remove the caller check; make the "real" property _build_requested | 25 March 2015, 13:04:16 UTC |
ca7d3e5 | Thomas Mooney | 24 March 2015, 23:06:08 UTC | Test that QC decorator modifies workflow properly. | 24 March 2015, 23:06:08 UTC |
a3d938b | Thomas Mooney | 24 March 2015, 22:45:48 UTC | Basic test for decorator delegation. | 24 March 2015, 22:49:06 UTC |
a6a8363 | Thomas Mooney | 11 March 2015, 21:38:16 UTC | Add a test of decorators. | 24 March 2015, 22:30:01 UTC |
b022316 | Thomas Mooney | 11 March 2015, 21:37:17 UTC | Extract _test_strategy to perform the create/execute/diff cycle. | 24 March 2015, 22:30:01 UTC |
3399449 | Thomas Mooney | 11 March 2015, 21:35:49 UTC | Create $package variable for easier reuse. | 24 March 2015, 22:30:01 UTC |
2be018e | Thomas B. Mooney | 24 March 2015, 22:02:39 UTC | Merge pull request #577 from tmooney/more_consistent_bases_warnings Don't Warn about Each Missing ".bases" File if We Didn't Make Any | 24 March 2015, 22:02:39 UTC |
97fbed8 | Thomas Mooney | 24 March 2015, 21:39:46 UTC | Also unlock if our change was rolled back. | 24 March 2015, 21:39:46 UTC |
b7ce6a3 | Thomas Mooney | 24 March 2015, 21:38:24 UTC | When rolling back, don't lock or record a note. * We don't need to lock, since we're not changing the value. * We don't need to record a note, since the note of the original change will be removed. | 24 March 2015, 21:38:24 UTC |
47caba6 | apregier | 24 March 2015, 20:39:50 UTC | igv xml file has urls that will be different for each run | 24 March 2015, 20:39:50 UTC |
3ef7af6 | Eddie Belter | 24 March 2015, 20:16:38 UTC | InstData Import: pass description on to created instdasta | 24 March 2015, 20:16:38 UTC |
b6ceff1 | APipe Tester | 24 March 2015, 19:19:53 UTC | updated workflow submodule to 0b9e071 | 24 March 2015, 19:19:53 UTC |
ecffc88 | Thomas Mooney | 23 March 2015, 14:35:41 UTC | Override QC in the test so we don't really try to run it. | 24 March 2015, 19:19:34 UTC |
4895569 | Thomas Mooney | 23 March 2015, 14:25:58 UTC | Provide a way to programmatically pass the users hash. | 24 March 2015, 19:19:33 UTC |
4efdf7e | Ian Ferguson | 24 March 2015, 19:15:34 UTC | Add Picard version to Bwamem.t | 24 March 2015, 19:15:34 UTC |
afb33c8 | Ian Ferguson | 24 March 2015, 19:03:43 UTC | Die when explicitly given an undef Picard version | 24 March 2015, 19:03:43 UTC |
26e5059 | Thomas Mooney | 23 March 2015, 22:17:29 UTC | Stop using GENOME_LSF_QUEUE_ALIGNMENT_PROD. * Since the queues are controlled by environment variables, the user can select between the multiple alignment queues by controlling their environment. * Leave the old environment variable in as non-required for now (so as to not break everyone's configurations when we deploy the new snapshot). | 24 March 2015, 17:56:35 UTC |
284f752 | Susanna Siebert | 24 March 2015, 17:07:39 UTC | Another typo fix | 24 March 2015, 17:07:39 UTC |
f1d20a8 | Susanna Siebert | 24 March 2015, 17:06:36 UTC | Fix typo | 24 March 2015, 17:06:36 UTC |
cad4a6e | Susanna Siebert | 24 March 2015, 17:01:01 UTC | Override nondeterministic subroutine | 24 March 2015, 17:01:01 UTC |
b045a2c | APipe Tester | 24 March 2015, 16:25:08 UTC | updated workflow submodule to 297de2d | 24 March 2015, 16:25:08 UTC |
c7abe9c | Thomas Mooney | 19 March 2015, 21:57:35 UTC | Add testcase for QC decorator. | 24 March 2015, 16:12:29 UTC |
27af3ad | Thomas Mooney | 19 March 2015, 20:59:12 UTC | A QC decorator. | 24 March 2015, 16:12:29 UTC |
8bbe0ee | Thomas Mooney | 19 March 2015, 20:37:49 UTC | Process decorations (if any). | 24 March 2015, 16:12:28 UTC |
45694e1 | Thomas Mooney | 11 March 2015, 20:16:46 UTC | Also make the result available as an output. | 24 March 2015, 16:12:28 UTC |
215e9ee | Thomas Mooney | 10 March 2015, 19:21:53 UTC | Add factory and base class for decorators. | 24 March 2015, 16:12:26 UTC |
5e3e655 | Thomas Mooney | 10 March 2015, 19:16:18 UTC | Add optional decorators to alignment strategy | 24 March 2015, 16:12:25 UTC |
b35517b | Susanna Siebert | 23 March 2015, 20:20:02 UTC | Enforce minimum Picard version | 24 March 2015, 16:00:00 UTC |
6ab3dcf | Susanna Siebert | 23 March 2015, 20:07:51 UTC | New qc tool for Picard CollectWgsMetrics | 24 March 2015, 16:00:00 UTC |
cc709e6 | Susanna Siebert | 23 March 2015, 20:07:30 UTC | New wrapper for Picard CollectWgsMetrics | 24 March 2015, 16:00:00 UTC |