Timeline



Apr 14, 2023:

11:46 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7114: […]
11:46 AM Changeset [7114] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
9:34 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7113: […]
9:34 AM Changeset [7113] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
9:24 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7112: […]
9:24 AM Changeset [7112] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Making …
7:20 AM net.sf.basedb.meludi edited by olle
Updated version of README file to 1.6.0. (diff)

Apr 13, 2023:

1:31 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7111: […]
1:31 PM Changeset [7111] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Use …
11:08 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7110: […]
11:08 AM Changeset [7110] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline All …
10:46 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7109: […]
10:46 AM Changeset [7109] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
10:39 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7108: […]
10:39 AM Changeset [7108] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Apr 12, 2023:

1:46 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7107: […]
1:45 PM Changeset [7107] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
11:27 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7106: […]
11:27 AM Changeset [7106] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Apr 11, 2023:

1:35 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7105: […]
1:35 PM Changeset [7105] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
1:20 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7104: […]
1:20 PM Changeset [7104] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
1:16 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7103: […]
1:16 PM Changeset [7103] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
11:34 AM Ticket #1475 (Validation of laterality fails with error if it is missing in the JSON ...) created by Nicklas Nordborg
Normally, the laterality is allowed to be missing in a JSON file since …

Apr 6, 2023:

1:42 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7102: […]
1:42 PM Changeset [7102] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Remove …
1:14 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7101: […]
1:14 PM Changeset [7101] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
12:54 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7100: […]
12:54 PM Changeset [7100] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Better …
12:44 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7099: […]
12:44 PM Changeset [7099] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
8:58 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7098: […]
8:58 AM Changeset [7098] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …

Apr 5, 2023:

8:49 AM Changeset [7097] by Nicklas Nordborg
Merge Reggie 4.45.2 to the trunk.
8:47 AM Milestone Reggie v4.45.2 completed
Bug fixes and enhancements for Reggie 4.45.1. Revision Log: …
8:46 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.45.2 (diff)
8:45 AM reggie-4.45.2.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.45.2
8:44 AM Changeset [7096] by Nicklas Nordborg
Tagging Reggie 4.45.2
8:43 AM Changeset [7095] by Nicklas Nordborg
Preparing to release Reggie 4.45.2
8:40 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) updated by Nicklas Nordborg
The dates can't be used and the code has been removed in #1474 [7094].
8:40 AM Ticket #1474 (Stop importing of "Arrival date" from JSON files) closed by Nicklas Nordborg
fixed: In 7094: […]
8:40 AM Changeset [7094] by Nicklas Nordborg
Fixes #1474: Stop importing of "Arrival date" from JSON files Also …
8:32 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7093: […]
8:32 AM Changeset [7093] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Apr 4, 2023:

2:23 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7092: […]
2:23 PM Changeset [7092] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline First …
11:01 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7091: […]
11:01 AM Changeset [7091] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
10:56 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7090: […]
10:56 AM Changeset [7090] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
8:36 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7089: […]
8:36 AM Changeset [7089] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Copy …

Apr 3, 2023:

2:12 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7088: […]
2:12 PM Changeset [7088] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
1:55 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7087: […]
1:55 PM Changeset [7087] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline The …

Mar 31, 2023:

1:28 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7086: […]
1:28 PM Changeset [7086] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
1:24 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7085: […]
1:24 PM Changeset [7085] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Mar 28, 2023:

2:00 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7084: […]
2:00 PM Changeset [7084] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline …
1:20 PM Ticket #1462 (Re-enable importing of sampling and RNA later date in the JSON importer) closed by Nicklas Nordborg
wontfix: The dates in the JSON doesn't represent the events. The information …
1:18 PM Ticket #1474 (Stop importing of "Arrival date" from JSON files) created by Nicklas Nordborg
This date doesn't represent the same event as it used to.
8:51 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7083: […]
8:51 AM Changeset [7083] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
8:37 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7082: […]
8:37 AM Changeset [7082] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …
7:45 AM Ticket #1473 (Implement alignment for the DNA WGS pipeline) updated by Nicklas Nordborg
In 7081: […]
7:45 AM Changeset [7081] by Nicklas Nordborg
References #1473: Implement alignment for the DNA WGS pipeline Added …

Mar 27, 2023:

3:57 PM Ticket #1473 (Implement alignment for the DNA WGS pipeline) created by Nicklas Nordborg
See #1464 for background. The first alignment step is done separately …
1:42 PM Ticket #1472 (Use the new service logging implementation) updated by Nicklas Nordborg
In 7080: […]
1:42 PM Changeset [7080] by Nicklas Nordborg
References #1472: Use the new service logging implementation Updated …
1:16 PM Ticket #1472 (Use the new service logging implementation) updated by Nicklas Nordborg
In 7079: […]
1:16 PM Changeset [7079] by Nicklas Nordborg
References #1472: Use the new service logging implementation Updated …
1:05 PM Ticket #1472 (Use the new service logging implementation) updated by Nicklas Nordborg
In 7078: […]
1:05 PM Changeset [7078] by Nicklas Nordborg
References #1472: Use the new service logging implementation Updated …
10:58 AM Ticket #1472 (Use the new service logging implementation) updated by Nicklas Nordborg
In 7077: […]
10:58 AM Changeset [7077] by Nicklas Nordborg
References #1472: Use the new service logging implementation Updated …
9:31 AM Ticket #1472 (Use the new service logging implementation) updated by Nicklas Nordborg
In 7076: […]
9:31 AM Changeset [7076] by Nicklas Nordborg
References #1472: Use the new service logging implementation Updated …
8:51 AM Ticket #1472 (Use the new service logging implementation) created by Nicklas Nordborg
See ​https://base.thep.lu.se/ticket/2295
8:50 AM Ticket #1466 (Switch to BASE 3.19.8 and use the new service logging implementation) updated by Nicklas Nordborg
In 7075: […]
8:50 AM Changeset [7075] by Nicklas Nordborg
References #1466: Switch to BASE 3.19.8 and use the new service …

Mar 24, 2023:

2:52 PM Ticket #1467 (Switch to BASE 3.19.8 and use the new service logging implementation) updated by Nicklas Nordborg
In 7074: […]
2:52 PM Changeset [7074] by Nicklas Nordborg
References #1467: Switch to BASE 3.19.8 and use the new service …

Mar 21, 2023:

2:06 PM Ticket #1470 (Use multiple threads when loading existing VCF files in the genotype ...) updated by Nicklas Nordborg
In 7073: […]
2:06 PM Changeset [7073] by Nicklas Nordborg
References #1470: Use multiple threads when loading existing VCF files …
1:29 PM Ticket #1471 (Switch to BASE 3.19.8) closed by Nicklas Nordborg
fixed: In 7072: […]
1:29 PM Changeset [7072] by Nicklas Nordborg
Fixes #1471: Switch to BASE 3.19.8
1:27 PM Ticket #1471 (Switch to BASE 3.19.8) created by Nicklas Nordborg
So that we can use the performance improvements in …
9:03 AM Ticket #1470 (Use multiple threads when loading existing VCF files in the genotype ...) updated by Nicklas Nordborg
In [7071] Referenes #1470: Use multiple threads when loading existing …

Mar 20, 2023:

8:55 AM Changeset [7071] by Nicklas Nordborg
Referenes #1470: Use multiple threads when loading existing VCF files …

Mar 17, 2023:

9:15 AM Changeset [7070] by Nicklas Nordborg
Merge Reggie 4.45.1 to the trunk
8:59 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.45.1 (diff)
8:59 AM reggie-4.45.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.45.1
8:57 AM Changeset [7069] by Nicklas Nordborg
Tagging Reggie 4.45.1
8:57 AM Changeset [7068] by Nicklas Nordborg
Preparing to release Reggie 4.45.1
8:56 AM Ticket #1469 (Update VarDict to version 1.8.3) closed by Nicklas Nordborg
fixed: In 7067: […]
8:56 AM Changeset [7067] by Nicklas Nordborg
Fixes #1469: Update VarDict to version 1.8.3
8:50 AM Milestone Reggie v4.45.1 completed
7:54 AM Changeset [7066] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.45
7:54 AM Changeset [7065] by Nicklas Nordborg
Incorrect path
7:53 AM Changeset [7064] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.45
7:52 AM Ticket #1470 (Use multiple threads when loading existing VCF files in the genotype ...) created by Nicklas Nordborg
This could save some time when running this wizard.
7:51 AM Ticket #1469 (Update VarDict to version 1.8.3) created by Nicklas Nordborg
The Variant calling script crashed due to a bug in VarDict: […] …
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