Timeline



Nov 29, 2019:

2:30 PM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) updated by Nicklas Nordborg
In 5765: […]
2:30 PM Changeset [5765] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
1:49 PM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) updated by Nicklas Nordborg
In 5764: […]
1:49 PM Changeset [5764] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
1:11 PM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) updated by Nicklas Nordborg
In 5763: […]
1:11 PM Changeset [5763] by Nicklas Nordborg
References #1208: Implement wizard for building database of variant …
1:03 PM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) updated by Nicklas Nordborg
Status changed
8:33 AM Ticket #1209 (Add support for storing TMA specimen) created by Nicklas Nordborg
TMA are sometimes created by external projects. We want to track some …
7:40 AM Ticket #1208 (Implement wizard for building database of variant frequencies in ...) created by Nicklas Nordborg
The annotation/filtering step in the variant calling pipeline is using …

Nov 28, 2019:

1:52 PM Ticket #1207 (Replace the "Nothing yet" in the activity log with a quote-of-the-day) closed by Nicklas Nordborg
fixed: In 5762: […]
1:52 PM Changeset [5762] by Nicklas Nordborg
Fixes #1207: Replace the "Nothing yet" in the activity log with a …
9:06 AM Ticket #1207 (Replace the "Nothing yet" in the activity log with a quote-of-the-day) updated by Nicklas Nordborg
In 5761: […]
9:06 AM Changeset [5761] by Nicklas Nordborg
References #1207: Replace the "Nothing yet" in the activity log with a …
8:53 AM Ticket #1207 (Replace the "Nothing yet" in the activity log with a quote-of-the-day) created by Nicklas Nordborg
The "Nothing yet" message in the activity log is a bit boring. We can …

Nov 26, 2019:

1:10 PM Changeset [5760] by Nicklas Nordborg
Merged Reggie 4.24.1 to the trunk.
1:06 PM Milestone Reggie v4.24.1 completed
Bug fixes and enhancements for Reggie 4.24. Revision Log: …
1:05 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.24.1 (diff)
1:05 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.24.1 (diff)
1:04 PM reggie-4.24.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.24.1
1:03 PM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) closed by Nicklas Nordborg
fixed: Closing this for now since we need to release the other bugfixes. If …
1:02 PM Tickets #1196,​1198,​1197 batch updated by Nicklas Nordborg
Milestone changed
The Reggie 4.23.3 milestone was never released separately. Changes was …
12:59 PM Changeset [5759] by Nicklas Nordborg
Tagging Reggie 4.24.1
12:57 PM Changeset [5758] by Nicklas Nordborg
Preparing to release Reggie 4.24.1
9:25 AM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) updated by Nicklas Nordborg
In 5757: […]
9:25 AM Changeset [5757] by Nicklas Nordborg
References #1206: The MIPs aliquot importer should handle some values …
9:03 AM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) updated by Nicklas Nordborg
Summary changed
9:02 AM Ticket #1206 (The MIPs aliquot importer should handle some values as special cases) created by Nicklas Nordborg
Some of the columns in the file used for importing MIPs aliquots …
8:53 AM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) closed by Nicklas Nordborg
fixed
7:56 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5756: […]
7:56 AM Changeset [5756] by olle
Refs #1029. Registration of blood and FFPE blocks updated to set …

Nov 25, 2019:

9:40 AM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) updated by Nicklas Nordborg
In 5755: […]
9:40 AM Changeset [5755] by Nicklas Nordborg
References #1202: Add check for duplicate barcode template in the MIPs …

Nov 22, 2019:

2:04 PM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) updated by Nicklas Nordborg
In 5754: […]
2:04 PM Changeset [5754] by Nicklas Nordborg
References #1202: Add check for duplicate barcode template in the MIPs …
1:46 PM Ticket #1205 (Variant calling fails with "malformed BED entry") closed by Nicklas Nordborg
fixed
1:10 PM Ticket #1205 (Variant calling fails with "malformed BED entry") updated by Nicklas Nordborg
In 5753: […]
1:10 PM Changeset [5753] by Nicklas Nordborg
References #1205: Variant calling fails with "malformed BED entry" …
1:02 PM Ticket #1205 (Variant calling fails with "malformed BED entry") updated by Nicklas Nordborg
In 5752: […]
1:02 PM Changeset [5752] by Nicklas Nordborg
References #1205: Variant calling fails with "malformed BED entry" …
12:52 PM Ticket #1205 (Variant calling fails with "malformed BED entry") created by Nicklas Nordborg
The full error message: […] This seems to happen when a variant is …
11:09 AM Ticket #1204 (Change default flow cell type in MIPs create flow cells wizard) closed by Nicklas Nordborg
fixed: In 5751: […]
11:09 AM Changeset [5751] by Nicklas Nordborg
Fixes #1204: Change default flow cell type in MIPs create flow cells wizard
11:07 AM Ticket #1201 (Incorrect date is displayed for variant calling in the case summary) closed by Nicklas Nordborg
fixed: In 5750: […]
11:07 AM Changeset [5750] by Nicklas Nordborg
Fixes #1201: Incorrect date is displayed for variant calling in the …
11:02 AM Ticket #1203 (Resolve thread deadlocks) closed by Nicklas Nordborg
fixed: In 5749: […]
11:02 AM Changeset [5749] by Nicklas Nordborg
Fixes #1203: Resolve thread deadlocks This should hopefully fix the …
9:56 AM Ticket #1204 (Change default flow cell type in MIPs create flow cells wizard) created by Nicklas Nordborg
The NextSeq is the only sequencer that is used.
9:44 AM Ticket #1203 (Resolve thread deadlocks) created by Nicklas Nordborg
I have had some issues with thread deadlocks during re-installation of …

Nov 21, 2019:

1:19 PM Ticket #1202 (Add check for duplicate barcode template in the MIPs library registration) created by Nicklas Nordborg
In the MIPs library registration wizard it is important that the …
1:13 PM Ticket #1201 (Incorrect date is displayed for variant calling in the case summary) created by Nicklas Nordborg
It seems like the date that is displayed is the same as the date for …
1:09 PM Changeset [5748] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.24
8:40 AM Changeset [5747] by Nicklas Nordborg
Fixes an issue with missing "N" values in the lookup tables for GC …

Nov 20, 2019:

3:03 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5746: […]
3:03 PM Changeset [5746] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …
2:27 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5745: […]
2:27 PM Changeset [5745] by olle
Refs #1029. Updates due to version number change to "1.6.0b7". 1. …
1:46 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5744: […]
1:46 PM Changeset [5744] by olle
Refs #1029. Updates of BASE method calls due to update of BASE version …
8:43 AM Changeset [5743] by Nicklas Nordborg
Preparing for future release Reggie 4.25
8:41 AM Milestone Reggie v4.24 completed
See Reggie extension page for more information.
8:41 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.24 (diff)
8:40 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.24 (diff)
8:39 AM reggie-4.24.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.24
8:37 AM Changeset [5742] by Nicklas Nordborg
Tagging Reggie 4.24
8:36 AM Changeset [5741] by Nicklas Nordborg
Preparing to release Reggie 4.24
8:30 AM Changeset [5740] by Nicklas Nordborg
Merged Reggie 4.23.3 to the trunk.
8:25 AM Milestone Reggie v4.23.3 completed
Bug fixes and enhancements for Reggie 4.23.2. Revision Log: …
8:24 AM Changeset [5739] by Nicklas Nordborg
Tagging Reggie 4.23.3
8:24 AM Changeset [5738] by Nicklas Nordborg
Preparing to release Reggie 4.23.3
7:54 AM Ticket #1198 (Add support for PAD to the "Map external data" wizard) closed by Nicklas Nordborg
fixed
7:54 AM Ticket #1187 (Implement an "External RNA import" wizard) closed by Nicklas Nordborg
fixed
7:54 AM Ticket #1199 (Implement Variant calling pipeline) closed by Nicklas Nordborg
fixed
7:40 AM Tickets #1190,​1186 batch updated by Nicklas Nordborg
Milestone changed
7:39 AM Tickets #1190,​1186 batch updated by Nicklas Nordborg
In 5737: […]
7:39 AM Changeset [5737] by Nicklas Nordborg
References #1186 and #1190. Disabling code related to the SSP plug-in …

Nov 19, 2019:

3:43 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5736: […]
3:43 PM Changeset [5736] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Fixed some …
3:42 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5735: […]
3:42 PM Changeset [5735] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Removed version …
1:41 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
Status changed
12:00 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5734: […]
11:59 AM Changeset [5734] by olle
Refs #1029. Referral form generation wizard for the NordicTrip …
11:50 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5733: […]
11:50 AM Changeset [5733] by olle
Refs #1029. Referral form generation updated to allow projects to use …
11:23 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5732: […]
11:23 AM Changeset [5732] by olle
Refs #1029. Referral form generation updated in generation of referral …
10:59 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
* 2019-11-18 the following changes were decided for referral form …
10:04 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5731: […]
10:04 AM Changeset [5731] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added a variant …

Nov 18, 2019:

2:12 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5730: […]
2:12 PM Changeset [5730] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added a dialog …
1:43 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5729: […]
1:43 PM Changeset [5729] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added support …

Nov 15, 2019:

11:32 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5728: […]
11:32 AM Changeset [5728] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Implemented …
8:24 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
Design update for the NordicTrip referral form generation: * …

Nov 14, 2019:

4:14 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5727: […]
4:14 PM Changeset [5727] by olle
Refs #1029. Referral form generation updated to add suffix ".b1" and …
4:03 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5726: […]
4:03 PM Changeset [5726] by olle
Refs #1029. Referral form generation for project NordicTrip updated …

Nov 13, 2019:

1:32 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5725: […]
1:32 PM Changeset [5725] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added …
11:09 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5724: […]
11:09 AM Changeset [5724] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline …
9:07 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5723: […]
9:07 AM Changeset [5723] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline …
8:56 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5722: […]
8:56 AM Changeset [5722] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Updated the …
8:53 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5721: […]
8:53 AM Changeset [5721] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Renamed the raw …
8:17 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5720: […]
8:17 AM Changeset [5720] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Checked the …

Nov 12, 2019:

1:06 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5719: […]
1:06 PM Changeset [5719] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added …
12:56 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5718: […]
12:56 PM Changeset [5718] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Helper script …
12:54 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5717: […]
12:54 PM Changeset [5717] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Re-factored the …
11:12 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5716: […]
11:12 AM Changeset [5716] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Implemented …
10:45 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5715: […]
10:45 AM Changeset [5715] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Implemented …
9:31 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5714: […]
9:31 AM Changeset [5714] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Implemented a …
9:01 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5713: […]
9:01 AM Changeset [5713] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added options in …

Nov 11, 2019:

1:58 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5712: […]
1:58 PM Changeset [5712] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added helper …
1:55 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5711: […]
1:55 PM Changeset [5711] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Implemented …

Nov 8, 2019:

3:48 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5710: […]
3:48 PM Changeset [5710] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Changed the …
3:41 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5709: […]
3:41 PM Changeset [5709] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added python …
7:18 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5708: […]
7:18 AM Changeset [5708] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …

Nov 7, 2019:

4:39 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5707: […]
4:38 PM Changeset [5707] by olle
Refs #1029. Updates due to version number change to "1.6.0b6". 1. …
9:27 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5706: […]
9:27 AM Changeset [5706] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Defined …

Nov 6, 2019:

1:46 PM Ticket #1200 (Release exporter changes due to Variant calling pipeline) created by Nicklas Nordborg
When the Variant calling pipeline has been fully implemented (#1199), …
1:12 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5705: […]
1:12 PM Changeset [5705] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Moving the 't' …
11:46 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5704: […]
11:46 AM Changeset [5704] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline All programs …
11:32 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5703: […]
11:32 AM Changeset [5703] by olle
Refs #1029. Referral form generation updated in generation of referral …
11:01 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
Design update for the NordicTrip referral form generation: * …
9:38 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5702: […]
9:38 AM Changeset [5702] by olle
Refs #1029. Referral form generation updated in generation of referral …

Nov 5, 2019:

3:17 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5701: […]
3:17 PM Changeset [5701] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Reorganised some …
2:37 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5700: […]
2:37 PM Changeset [5700] by olle
Refs #1029. Referral form generation updated to support generation of …
8:34 AM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5699: […]
8:34 AM Changeset [5699] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added filtering …

Nov 4, 2019:

1:53 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5698: […]
1:53 PM Changeset [5698] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added wrapper …
1:50 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5697: […]
1:50 PM Changeset [5697] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Improve error …
1:22 PM Ticket #1199 (Implement Variant calling pipeline) updated by Nicklas Nordborg
In 5696: […]
1:22 PM Changeset [5696] by Nicklas Nordborg
References #1199: Implement Variant calling pipeline Added second …
1:08 PM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
In 5695: […]
1:08 PM Changeset [5695] by olle
Refs #1029. Referral form generation updated to store a start info …
11:58 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
Design update for the NordicTrip project: * 2019-10-28 it was …

Nov 1, 2019:

11:12 AM Ticket #1029 (MeLuDI should be adapted to support the SCAN-B-rec project) updated by olle
Design discussion: * Some design choices for referral form …
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