Timeline



Jan 9, 2024:

2:50 PM PluginDownload edited by Nicklas Nordborg
Updated Reggie and Variant search (diff)
2:28 PM Ticket #1560 (The "Secondary analysis cleanup" wizard display a warning message ...) closed by Nicklas Nordborg
fixed: In 7531: […]
2:28 PM Changeset [7531] by Nicklas Nordborg
Fixes #1560: The "Secondary analysis cleanup" wizard display a warning …
2:05 PM Ticket #1560 (The "Secondary analysis cleanup" wizard display a warning message ...) created by Nicklas Nordborg
9:23 AM Changeset [7530] by Nicklas Nordborg
Changes for future release Reggie 4.52
9:22 AM Changeset [7529] by Nicklas Nordborg
Creating bugfix branch for Reggie 4.51
9:20 AM Milestone Reggie v4.51 completed
See Reggie extension page for more information.
9:20 AM reggie-4.51.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.51
9:19 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.51 (diff)
9:16 AM Changeset [7528] by Nicklas Nordborg
Tagging Reggie 4.51
9:16 AM Changeset [7527] by Nicklas Nordborg
Preparing to release Reggie 4.51
9:14 AM Tickets #1556,​1543 batch updated by Nicklas Nordborg
fixed
8:43 AM Changeset [7526] by Nicklas Nordborg
Changes for future release Variant search 1.11
8:41 AM Milestone Variant Search v1.10 completed
See Variant Search extension page for …
8:41 AM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.10 (diff)
8:39 AM varsearch-1.10.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.10
8:38 AM Changeset [7525] by Nicklas Nordborg
Tagging Variant search 1.10
8:37 AM Changeset [7524] by Nicklas Nordborg
Preparing to relase Variant search 1.10
8:36 AM Changeset [7523] by Nicklas Nordborg
It was not ready for relase
8:35 AM Changeset [7522] by Nicklas Nordborg
Preparing to release Variant search 1.10
8:34 AM Ticket #1549 (Add support for viewing variant details from the WGS variant calling) updated by Nicklas Nordborg
In 7521: […]
8:34 AM Changeset [7521] by Nicklas Nordborg
References #1549: Add support for viewing variant details from the …
8:32 AM Ticket #1549 (Add support for viewing variant details from the WGS variant calling) closed by Nicklas Nordborg
fixed

Jan 8, 2024:

2:55 PM Ticket #1559 (The "View genotypes" dialog should support gzipped VCF files) closed by Nicklas Nordborg
fixed: In 7520: […]
2:55 PM Changeset [7520] by Nicklas Nordborg
Fixes #1559: The "View genotypes" dialog should support gzipped VCF files
2:54 PM Ticket #1559 (The "View genotypes" dialog should support gzipped VCF files) created by Nicklas Nordborg
See #1363 that implemented support for using gzipped VCF files when …
9:18 AM net.sf.basedb.reggie/notes451 created by Nicklas Nordborg
Created update notes for Reggie 4.51

Dec 20, 2023:

8:47 AM Changeset [7519] by Nicklas Nordborg
Container scripts now use Mambaforge instead of Miniconda which gives …

Dec 19, 2023:

2:52 PM Ticket #1558 (Add support for EPIC v2) closed by Nicklas Nordborg
fixed
2:24 PM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7518: […]
2:24 PM Changeset [7518] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Updated reggie-config.xml …
2:14 PM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7517: […]
2:14 PM Changeset [7517] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Use BeadChipPosition from …
1:35 PM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7516: […]
1:35 PM Changeset [7516] by Nicklas Nordborg
References #1558: Add support for EPIC v2 The BeadChipPosition

Dec 18, 2023:

11:55 AM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) closed by Nicklas Nordborg
fixed
11:55 AM Ticket #1554 (Generate counts and plots for SBS signatures) closed by Nicklas Nordborg
fixed
9:48 AM Ticket #1550 (Enabled the "More information" link in the "View variants" dialog) closed by Nicklas Nordborg
fixed
9:48 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
Description changed
9:46 AM Ticket #1556 (Changes to the INCA importer) updated by Nicklas Nordborg
In 7500: References #1556: Changes to the INCA …
9:18 AM Changeset [7515] by Nicklas Nordborg
Changed snpEff reference to GRCh38.mane.1.0.ensembl to match what we …
9:01 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7514: […]
9:01 AM Changeset [7514] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Changes to the beta-value …
8:36 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7513: […]
8:36 AM Changeset [7513] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Export the BeadChipType
8:30 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7512: […]
8:30 AM Changeset [7512] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Updated the container …

Dec 15, 2023:

8:51 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
Description changed
8:09 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
Description changed
7:30 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7511: […]
7:30 AM Changeset [7511] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Use the new configuration …
7:28 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7510: […]
7:28 AM Changeset [7510] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Updated the BeadChipType
7:26 AM Ticket #1558 (Add support for EPIC v2) updated by Nicklas Nordborg
In 7509: […]
7:26 AM Changeset [7509] by Nicklas Nordborg
References #1558: Add support for EPIC v2 Changes to …

Dec 14, 2023:

2:58 PM Ticket #1558 (Add support for EPIC v2) created by Nicklas Nordborg
The EPIC methylation chip has come in a new version. The number of …
2:47 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) updated by Nicklas Nordborg
In 7508: […]
2:47 PM Changeset [7508] by Nicklas Nordborg
References #1557: Add support for setting the "f-score-beta" parameter …
2:37 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) updated by Nicklas Nordborg
In 7507: […]
2:37 PM Changeset [7507] by Nicklas Nordborg
References #1557: Add support for setting the "f-score-beta" parameter …
1:45 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) updated by Nicklas Nordborg
In 7506: […]
1:45 PM Changeset [7506] by Nicklas Nordborg
References #1557: Add support for setting the "f-score-beta" parameter …
1:37 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) updated by Nicklas Nordborg
In 7505: […]
1:37 PM Changeset [7505] by Nicklas Nordborg
References #1557: Add support for setting the "f-score-beta" parameter …
1:35 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) updated by Nicklas Nordborg
In 7504: […]
1:35 PM Changeset [7504] by Nicklas Nordborg
References #1557: Add support for setting the "f-score-beta" parameter …
1:27 PM Ticket #1557 (Add support for setting the "f-score-beta" parameter when filtering ...) created by Nicklas Nordborg
The default value of 1.0 optimizes the precision and sensitivity, but …
8:58 AM Changeset [7503] by Nicklas Nordborg
Changes for future release INCA XML to CSV converter 1.6.
8:57 AM net.sf.basedb.inca edited by Nicklas Nordborg
Released IncaXML2CSV 1.5 (diff)
8:55 AM IncaXml2Csv-1.5.zip attached to net.sf.basedb.inca by Nicklas Nordborg
IncaXml2Csv 1.5 (zip)
8:54 AM Milestone INCA XML to CSV converter 1.5 completed
See IncaXml2Csv extension page for more …
8:54 AM Changeset [7502] by Nicklas Nordborg
Tagging INCA XML to CSV converter 1.5
8:52 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) updated by Nicklas Nordborg
Milestone changed
8:50 AM Changeset [7501] by Nicklas Nordborg
Preparing to release INCA XML to CSV converter 1.4.
8:49 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) closed by Nicklas Nordborg
fixed

Dec 13, 2023:

2:11 PM Ticket #1456 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
THIS IS RELATED TO #1556 AND NOT THIS TICKET In …
2:11 PM Changeset [7500] by Nicklas Nordborg
References #1456: Changes to the INCA importer Headers ending with …
1:27 PM Ticket #1555 (Implement support for INCA data files that are in CSV format) updated by Nicklas Nordborg
In 7499: […]
1:27 PM Changeset [7499] by Nicklas Nordborg
References #1555: Implement support for INCA data files that are in …
12:05 PM Ticket #1556 (Changes to the INCA importer) created by Nicklas Nordborg
The new INCA data have renamed some headers. * Variables ending …
11:51 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) updated by Nicklas Nordborg
In 7498: […]
11:50 AM Changeset [7498] by Nicklas Nordborg
References #1555: Implement support for INCA data files that are in …
11:37 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) updated by Nicklas Nordborg
In 7497: […]
11:36 AM Changeset [7497] by Nicklas Nordborg
References #1555: Implement support for INCA data files that are in …
11:35 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) updated by Nicklas Nordborg
Description changed
11:33 AM Ticket #1555 (Implement support for INCA data files that are in CSV format) created by Nicklas Nordborg
The current converter implementation only works with INCA source data …
9:12 AM Tickets #1543,​1554 batch updated by Nicklas Nordborg
In 7496: […]
9:12 AM Changeset [7496] by Nicklas Nordborg
References #1543 and #1554. Include the SBS counts and PDF plot in the …
9:10 AM Ticket #1551 (Import some information from filtering-stats.txt) updated by Nicklas Nordborg
In 7495: […]
9:10 AM Changeset [7495] by Nicklas Nordborg
References #1551: Import some information from filtering-stats.txt …
9:09 AM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7494: […]
9:09 AM Changeset [7494] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures Added …
8:35 AM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7493: […]
8:35 AM Changeset [7493] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures Added …
8:34 AM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7492: […]
8:34 AM Changeset [7492] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures Added …
7:56 AM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7491: […]
7:56 AM Changeset [7491] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures …
7:49 AM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7490: […]
7:49 AM Changeset [7490] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures Fixed …

Dec 12, 2023:

3:41 PM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7489: […]
3:41 PM Changeset [7489] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures Added …
2:12 PM Ticket #1554 (Generate counts and plots for SBS signatures) updated by Nicklas Nordborg
In 7488: […]
2:12 PM Changeset [7488] by Nicklas Nordborg
References #1554: Generate counts and plots for SBS signatures …
1:52 PM Ticket #1554 (Generate counts and plots for SBS signatures) created by Nicklas Nordborg
The SBS mutational signatures are describer here: …

Dec 11, 2023:

9:56 AM Ticket #1551 (Import some information from filtering-stats.txt) closed by Nicklas Nordborg
fixed
9:41 AM Tickets #1543,​1551 batch updated by Nicklas Nordborg
In 7487: […]
9:41 AM Changeset [7487] by Nicklas Nordborg
References #1543: Release exporter changes due to WGS data Include …
9:23 AM Ticket #1543 (Release exporter changes due to WGS data) updated by Nicklas Nordborg
Description changed
9:15 AM Ticket #1551 (Import some information from filtering-stats.txt) updated by Nicklas Nordborg
In 7486: […]
9:15 AM Changeset [7486] by Nicklas Nordborg
References #1551: Import some information from filtering-stats.txt …
8:47 AM Ticket #1553 (Allow vcf.gz files to be viewed with the tabular view extension) closed by Nicklas Nordborg
fixed: In 7485: […]
8:47 AM Changeset [7485] by Nicklas Nordborg
Fixes #1553: Allow vcf.gz files to be viewed with the tabular view …
8:05 AM Ticket #1553 (Allow vcf.gz files to be viewed with the tabular view extension) created by Nicklas Nordborg
7:48 AM Ticket #1552 (Include the ReferenceBases annotation when running Mutect2) closed by Nicklas Nordborg
fixed
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