Timeline



Nov 28, 2023:

2:12 PM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7467: […]
2:12 PM Changeset [7467] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data File …
2:09 PM Ticket #1546 (Add support for file items on different file servers) updated by Nicklas Nordborg
In 7466: […]
2:09 PM Changeset [7466] by Nicklas Nordborg
References #1546: Add support for file items on different file servers …
2:03 PM Ticket #1452 (Release importer changes due to new subtypes from Reggie) updated by Nicklas Nordborg
In 7465: […]
2:03 PM Changeset [7465] by Nicklas Nordborg
References #1452: Release importer changes due to new subtypes from …
1:27 PM Ticket #1546 (Add support for file items on different file servers) updated by Nicklas Nordborg
In 7464: […]
1:27 PM Changeset [7464] by Nicklas Nordborg
References #1546: Add support for file items on different file servers …
11:39 AM Ticket #1546 (Add support for file items on different file servers) created by Nicklas Nordborg
The release importer currently assume that all files items are located …
11:37 AM Ticket #1545 (Add support for items with multiple parent items) closed by Nicklas Nordborg
fixed: In 7463: […]
11:37 AM Changeset [7463] by Nicklas Nordborg
Fixes #1545: Add support for items with multiple parent items
9:12 AM Ticket #1545 (Add support for items with multiple parent items) created by Nicklas Nordborg
In Reggie 4.51 the release exporter will include CopyNumber items …
9:10 AM Ticket #1452 (Release importer changes due to new subtypes from Reggie) updated by Nicklas Nordborg
In 7462: […]
9:10 AM Changeset [7462] by Nicklas Nordborg
References #1452: Release importer changes due to new subtypes from …
8:39 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7461: […]
8:39 AM Changeset [7461] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added …
8:34 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
Description changed
8:32 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7460: […]
8:32 AM Changeset [7460] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added more …
8:03 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7459: […]
8:03 AM Changeset [7459] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added …

Nov 27, 2023:

1:52 PM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
Description changed
1:51 PM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7458: […]
1:51 PM Changeset [7458] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added more …
11:11 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7457: […]
11:11 AM Changeset [7457] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added a …
8:26 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7456: […]
8:26 AM Changeset [7456] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data The export …

Nov 24, 2023:

12:08 PM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7455: […]
12:08 PM Changeset [7455] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added …
9:19 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
In 7454: […]
9:19 AM Changeset [7454] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Added …

Nov 22, 2023:

8:41 AM Changeset [7453] by Nicklas Nordborg
Merge Reggie 4.50.1 to the trunk
8:38 AM Milestone Reggie v4.50.1 completed
Bug fixes and enhancements for Reggie 4.50. Revision Log: …
8:38 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.50.1 (diff)
8:36 AM reggie-4.50.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.50.1
8:34 AM Ticket #1542 (The WGS Start variant calling wizard select software with ...) closed by Nicklas Nordborg
fixed: Fixed in [7449]
8:34 AM Ticket #1544 (Include operator information in the Confirm variant calling of normals) closed by Nicklas Nordborg
fixed: Fixed in [7450]
8:33 AM Changeset [7452] by Nicklas Nordborg
Tagging Reggie 4.50.1
8:32 AM Changeset [7451] by Nicklas Nordborg
Preparing to release Reggie 4.50.1
8:10 AM Changeset [7450] by Nicklas Nordborg
Fixes #1544: Include operator information in the Confirm variant …
8:02 AM Ticket #1544 (Include operator information in the Confirm variant calling of normals) created by Nicklas Nordborg

Nov 21, 2023:

3:22 PM Changeset [7449] by Nicklas Nordborg
Fixes #1542: The WGS Start variant calling wizard select software with …
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8:06 AM Ticket #1543 (Release exporter changes due to WGS data) created by Nicklas Nordborg
We should include some WGS data in the next release. The starting …

Nov 20, 2023:

6:11 PM Ticket #1542 (The WGS Start variant calling wizard select software with ...) created by Nicklas Nordborg
It should use Pipeline=DNA/Paired/VariantCall The workaround is to …
2:29 PM Ticket #1541 (Variant calling (RNA) section in Case summary display "No variant ...) closed by Nicklas Nordborg
fixed: In 7448: […]
2:29 PM Changeset [7448] by Nicklas Nordborg
Fixes #1541: Variant calling (RNA) section in Case summary display "No …
2:23 PM Changeset [7447] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.50
2:21 PM Ticket #1541 (Variant calling (RNA) section in Case summary display "No variant ...) created by Nicklas Nordborg
7:56 AM Changeset [7446] by Nicklas Nordborg
Changes for future release Reggie 4.51
7:55 AM Milestone Reggie v4.50 completed
See Reggie extension page for more information.
7:54 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.50 (diff)
7:54 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.50 (diff)
7:51 AM reggie-4.50.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.50
7:49 AM Changeset [7445] by Nicklas Nordborg
Tagging Reggie 4.50
7:49 AM Changeset [7444] by Nicklas Nordborg
Preparing to release Reggie 4.50
7:44 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7443: […]
7:44 AM Changeset [7443] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Use …
7:41 AM net.sf.basedb.reggie/notes450 created by Nicklas Nordborg
Added update notes for Reggie 4.50
7:32 AM Tickets #1536,​1537 batch updated by Nicklas Nordborg
fixed

Nov 17, 2023:

11:23 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7442: […]
11:23 AM Changeset [7442] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added a …

Nov 16, 2023:

2:33 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7441: […]
2:33 PM Changeset [7441] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Updated …
1:49 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7440: […]
1:49 PM Changeset [7440] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Display …
1:27 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7439: […]
1:27 PM Changeset [7439] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …
7:56 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7438: […]
7:56 AM Changeset [7438] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …

Nov 15, 2023:

1:18 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7437: […]
1:18 PM Changeset [7437] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …
11:55 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7436: […]
11:55 AM Changeset [7436] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Started to …
9:43 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7435: […]
9:43 AM Changeset [7435] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added …
9:07 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7434: […]
9:07 AM Changeset [7434] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Limit the …
8:28 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7433: […]
8:28 AM Changeset [7433] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Use unique …
8:11 AM Milestone Reggie v4.49.5 completed
Bug fixes and enhancements for Reggie 4.49.4. Revision Log: …
8:05 AM Changeset [7432] by Nicklas Nordborg
Merge Reggie 4.49.5 to the trunk (second try)
8:04 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49.5 (second try) (diff)
8:03 AM reggie-4.49.5.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.49.5
8:02 AM Changeset [7431] by Nicklas Nordborg
Tagging Reggie 4.49.5 (second try)
8:01 AM Ticket #1540 (ASCAT fails when a solution can't be found) closed by Nicklas Nordborg
fixed: In 7430: […]
8:01 AM Changeset [7430] by Nicklas Nordborg
Fixes #1540: ASCAT fails when a solution can't be found
7:50 AM Ticket #1540 (ASCAT fails when a solution can't be found) reopened by Nicklas Nordborg
It seems like the fix in [7418] for creating a better message …
7:47 AM Changeset [7429] by Nicklas Nordborg
Removing Reggie 4.49.5 since #1540 was not fixed.

Nov 14, 2023:

2:47 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7428: […]
2:47 PM Changeset [7428] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added a …
1:01 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7427: […]
1:01 PM Changeset [7427] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS The dialog …
1:00 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7426: […]
1:00 PM Changeset [7426] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Display …
12:46 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7425: […]
12:46 PM Changeset [7425] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS We need …
11:20 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7424: […]
11:20 AM Changeset [7424] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …
8:32 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7423: […]
8:32 AM Changeset [7423] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added a …
8:03 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7422: […]
8:02 AM Changeset [7422] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added …
7:45 AM Changeset [7421] by Nicklas Nordborg
Merge Reggie 4.49.5 to the trunk.
7:42 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49.5 (diff)
7:37 AM Changeset [7420] by Nicklas Nordborg
Tagging Reggie 4.49.5
7:37 AM Changeset [7419] by Nicklas Nordborg
Preparing to release Reggie 4.49.5

Nov 13, 2023:

1:59 PM Ticket #1540 (ASCAT fails when a solution can't be found) closed by Nicklas Nordborg
fixed: In 7418: […]
1:59 PM Changeset [7418] by Nicklas Nordborg
Fixes #1540: ASCAT fails when a solution can't be found Updated the …
1:27 PM Ticket #1540 (ASCAT fails when a solution can't be found) updated by Nicklas Nordborg
In 7417: […]
1:27 PM Changeset [7417] by Nicklas Nordborg
References #1540: ASCAT fails when a solution can't be found This …
12:58 PM Ticket #1540 (ASCAT fails when a solution can't be found) created by Nicklas Nordborg
In the stacktrace we can find the following: […]
9:16 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7416: […]
9:16 AM Changeset [7416] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Renaming …
7:41 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7415: […]
7:41 AM Changeset [7415] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …

Nov 10, 2023:

2:01 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7414: […]
2:01 PM Changeset [7414] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added …
1:25 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7413: […]
1:25 PM Changeset [7413] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS It is nice …
8:53 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7412: […]
8:53 AM Changeset [7412] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Files …
8:44 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7411: […]
8:44 AM Changeset [7411] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS …
8:05 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7410: […]
8:05 AM Changeset [7410] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Some …

Nov 8, 2023:

2:56 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7409: […]
2:56 PM Changeset [7409] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added …
2:23 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7408: […]
2:23 PM Changeset [7408] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added the …
1:32 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7407: […]
1:32 PM Changeset [7407] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added the …
11:10 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7406: […]
11:10 AM Changeset [7406] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Started to …
8:04 AM Changeset [7405] by Nicklas Nordborg
Merge Reggie 4.49.4 to the trunk.
7:59 AM Milestone Reggie v4.49.4 completed
Bug fixes and enhancements for Reggie 4.49.3. Revision Log: …
7:59 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.49.4 (diff)
7:58 AM reggie-4.49.4.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.49.4
7:56 AM Changeset [7404] by Nicklas Nordborg
Tagging Reggie 4.49.4
7:55 AM Changeset [7403] by Nicklas Nordborg
Preparing to release Reggie 4.49.4

Nov 7, 2023:

2:32 PM Ticket #1535 (Generate more metrics from ASCAT) closed by Nicklas Nordborg
fixed: In 7402: […]
2:32 PM Changeset [7402] by Nicklas Nordborg
Fixes #1535: Generate more metrics from ASCAT Added three more …
1:40 PM Ticket #1539 (Change default values for ASCAT analysis) closed by Nicklas Nordborg
fixed: In 7401: […]
1:40 PM Changeset [7401] by Nicklas Nordborg
Fixes #1539: Change default values for ASCAT analysis
1:23 PM Ticket #1539 (Change default values for ASCAT analysis) created by Nicklas Nordborg
The following parameters should have new defaults: * Imbalance test: …
1:21 PM Ticket #1535 (Generate more metrics from ASCAT) updated by Nicklas Nordborg
Description changed
1:19 PM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7400: […]
1:19 PM Changeset [7400] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Started to …
8:37 AM Ticket #1538 (Re-factor the code that show the "auto-processing is disabled" warning ...) closed by Nicklas Nordborg
fixed: In 7399: […]
8:37 AM Changeset [7399] by Nicklas Nordborg
Fixes #1538: Re-factor the code that show the "auto-processing is …
8:36 AM Ticket #1538 (Re-factor the code that show the "auto-processing is disabled" warning ...) created by Nicklas Nordborg
Several steps in the secondary analysis can be disabled for …
7:55 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7398: […]
7:54 AM Changeset [7398] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added an …
7:53 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
Status, Milestone changed

Nov 6, 2023:

2:40 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7397: […]
2:40 PM Changeset [7397] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …
1:47 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7396: […]
1:47 PM Changeset [7396] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …
1:08 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7395: […]
1:08 PM Changeset [7395] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals A …
8:35 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7394: […]
8:35 AM Changeset [7394] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals It …
7:44 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7393: […]
7:44 AM Changeset [7393] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …

Nov 3, 2023:

11:51 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7392: […]
11:51 AM Changeset [7392] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …
9:05 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7391: […]
9:05 AM Changeset [7391] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …

Nov 2, 2023:

2:57 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7390: […]
2:57 PM Changeset [7390] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …

Nov 1, 2023:

2:39 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7389: […]
2:39 PM Changeset [7389] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …

Oct 31, 2023:

2:56 PM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7388: […]
2:56 PM Changeset [7388] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …
11:06 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) updated by Nicklas Nordborg
In 7387: […]
11:06 AM Changeset [7387] by Nicklas Nordborg
References #1537: Implement a wizard for creating panel-of-normals …

Oct 30, 2023:

11:22 AM Ticket #1536 (Implement variant calling for paired WGS) updated by Nicklas Nordborg
In 7386: […]
11:22 AM Changeset [7386] by Nicklas Nordborg
References #1536: Implement variant calling for paired WGS Added a …
9:54 AM Ticket #1537 (Implement a wizard for creating panel-of-normals) created by Nicklas Nordborg
This is part of the WGS variant calling pipeline (see #1536). We …
9:03 AM Ticket #1536 (Implement variant calling for paired WGS) created by Nicklas Nordborg
The plan is to use GATK Mutect2 …
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