Timeline



Sep 29, 2021:

9:34 AM net.sf.basedb.reggie/notes433 edited by Nicklas Nordborg
(diff)
9:10 AM Changeset [6428] by Nicklas Nordborg
Changes for future version Reggie 4.34
9:09 AM Milestone Reggie v4.33 completed
See Reggie extension page for more information.
9:08 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Added link to update notes for Reggie 4.33 (diff)
9:08 AM net.sf.basedb.reggie/notes433 created by Nicklas Nordborg
9:06 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.33 (diff)
9:04 AM reggie-4.33.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.33
9:03 AM Changeset [6427] by Nicklas Nordborg
Tagging Reggie 4.33
9:03 AM Changeset [6426] by Nicklas Nordborg
Preparing to release Reggie 4.33
9:00 AM Ticket #1338 (Sort order in case summary) closed by Nicklas Nordborg
fixed: In 6425: […]
9:00 AM Changeset [6425] by Nicklas Nordborg
Fixes #1338: Sort order in case summary
8:59 AM Ticket #1338 (Sort order in case summary) created by Nicklas Nordborg
Items in the case summary are typically sorted by name. But this has a …

Sep 28, 2021:

9:44 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) closed by Nicklas Nordborg
fixed
9:44 AM Changeset [6424] by Nicklas Nordborg
References #1335: Calculate average read length in FASTQ files after …
8:56 AM Ticket #1337 (Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0) closed by Nicklas Nordborg
fixed: In 6423: […]
8:56 AM Changeset [6423] by Nicklas Nordborg
Fixes #1337: Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0
8:43 AM Ticket #1337 (Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0) created by Nicklas Nordborg
This was initially thought to be a problem with an incorrect value for …
8:32 AM Ticket #1336 (Use the average read length from FASTQ files when calculating ...) closed by Nicklas Nordborg
fixed: In 6422: […]
8:32 AM Changeset [6422] by Nicklas Nordborg
Fixes #1336: Use the average read length from FASTQ files when …

Sep 23, 2021:

12:41 PM Ticket #1336 (Use the average read length from FASTQ files when calculating ...) created by Nicklas Nordborg
See #1335. If the values from the FASTQ files are available, we should …
12:39 PM Changeset [6421] by Nicklas Nordborg
References #1335: Calculate average read length in FASTQ files after …
9:07 AM Changeset [6420] by Nicklas Nordborg
References #1335: Calculate average read length in FASTQ files after …
8:02 AM Changeset [6419] by Nicklas Nordborg
References #1335: Calculate average read length in FASTQ files after …
7:42 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) created by Nicklas Nordborg
In the legacy pipeline we need the average inner distance between R1 …

Sep 20, 2021:

9:57 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.32.1 and Variant Search 1.3 (diff)
9:56 AM Changeset [6418] by Nicklas Nordborg
Changes for future release Variant Search 1.4
9:55 AM Milestone Variant Search v1.3 completed
See Variant Search extension page for …
9:54 AM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.3 (diff)
9:53 AM varsearch-1.3.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.3
9:52 AM Changeset [6417] by Nicklas Nordborg
Tagging Variant search 1.3
9:52 AM Changeset [6416] by Nicklas Nordborg
Preparing to release Variant search 1.3
9:50 AM Changeset [6415] by Nicklas Nordborg
Changes for future release Reggie 4.33
9:49 AM Milestone Reggie v4.32.1 completed
See Reggie extension page for more information.
9:48 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.32.1 (diff)
9:47 AM reggie-4.32.1.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.32.1
9:46 AM Changeset [6414] by Nicklas Nordborg
Tagging Reggie 4.32.1
9:45 AM Changeset [6413] by Nicklas Nordborg
Remove debug flag.
9:44 AM Changeset [6412] by Nicklas Nordborg
Preparing to relase Reggie 4.32.1
9:43 AM Changeset [6411] by Nicklas Nordborg
References #1334: Targeted genotyping should include number of …
9:07 AM Ticket #1334 (Targeted genotyping should include number of variants found in the ...) closed by Nicklas Nordborg
fixed: In 6410: […]
9:07 AM Changeset [6410] by Nicklas Nordborg
Fixes #1334: Targeted genotyping should include number of variants …
9:06 AM Ticket #1334 (Targeted genotyping should include number of variants found in the ...) created by Nicklas Nordborg
8:39 AM Ticket #1332 (Add new translation for CMD library protocol for the showcase report) closed by Nicklas Nordborg
fixed: In 6409: […]
8:39 AM Changeset [6409] by Nicklas Nordborg
Fixes #1332: Add new translation for CMD library protocol for the …
8:34 AM Ticket #1333 (A disabled index still show up as an available column) closed by Nicklas Nordborg
fixed: In 6408: […]
8:34 AM Changeset [6408] by Nicklas Nordborg
Fixes #1333: A disabled index still show up as an available column …
8:21 AM Ticket #1333 (A disabled index still show up as an available column) created by Nicklas Nordborg

Sep 17, 2021:

3:55 PM Ticket #1332 (Add new translation for CMD library protocol for the showcase report) created by Nicklas Nordborg
The CMD library protocol is called CMD TruSeq mRNA v1. This should …
1:59 PM Ticket #1331 (Rename the index for targeted variants) closed by Nicklas Nordborg
fixed: In 6407: […]
1:59 PM Changeset [6407] by Nicklas Nordborg
Fixes #1331: Rename the index for targeted variants
1:58 PM Ticket #1331 (Rename the index for targeted variants) created by Nicklas Nordborg
It will look better with Variants (targeted).
1:57 PM Ticket #1330 (The progress bar in the Index manager is not displaying) closed by Nicklas Nordborg
fixed: In 6406: […]
1:57 PM Changeset [6406] by Nicklas Nordborg
Fixes #1330: The progress bar in the Index manager is not displaying …
1:54 PM Ticket #1330 (The progress bar in the Index manager is not displaying) created by Nicklas Nordborg
There is only vertical bar. It seems like the fix in #1313 broke the …
1:42 PM Ticket #1329 (HaplotypeCaller is "inventing" new variants) closed by Nicklas Nordborg
fixed: In 6405: […]
1:42 PM Changeset [6405] by Nicklas Nordborg
Fixes #1329: HaplotypeCaller? is "inventing" new variants
9:26 AM Ticket #1329 (HaplotypeCaller is "inventing" new variants) created by Nicklas Nordborg
The output from HaplotypeCaller sometimes contain results for more …
9:14 AM Ticket #1328 (Index out of bounds exception) closed by Nicklas Nordborg
fixed: In 6404: […]
9:13 AM Changeset [6404] by Nicklas Nordborg
Fixes #1328: Index out of bounds exception
9:10 AM Ticket #1328 (Index out of bounds exception) created by Nicklas Nordborg
For some VCF files I get an error message when trying to view the …
8:43 AM Ticket #1327 (Incorrect message after submitting targeted genotyping job) closed by Nicklas Nordborg
fixed: In 6403: […]
8:43 AM Changeset [6403] by Nicklas Nordborg
Fixes #1327: Incorrect message after submitting targeted genotyping job
8:21 AM Ticket #1327 (Incorrect message after submitting targeted genotyping job) created by Nicklas Nordborg
The "Targeted genotyping wizard" display an incorrect message after …

Sep 16, 2021:

12:57 PM Changeset [6402] by Nicklas Nordborg
Changes for future release Variant search 1.3
12:56 PM Milestone Variant Search v1.2 completed
See Variant Search extension page for …
12:55 PM PluginDownload edited by Nicklas Nordborg
Released Variant Search 1.2 (diff)
12:54 PM net.sf.basedb.varsearch edited by Nicklas Nordborg
(diff)
12:54 PM net.sf.basedb.varsearch edited by Nicklas Nordborg
Released Variant Search 1.2 (diff)
12:53 PM varsearch-1.2.tar.gz attached to net.sf.basedb.varsearch by Nicklas Nordborg
Variant Search 1.2
12:52 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) closed by Nicklas Nordborg
fixed
12:51 PM Changeset [6401] by Nicklas Nordborg
Tagging Variant search 1.2
12:50 PM Changeset [6400] by Nicklas Nordborg
Preparing to release Variant search 1.2
11:41 AM Changeset [6399] by Nicklas Nordborg
Changes for future release Reggie 4.33
11:39 AM Milestone Reggie v4.32 completed
See Reggie extension page for more information.
11:39 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.32 (diff)
11:37 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.32 (diff)
11:35 AM reggie-4.32.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.32
11:33 AM Changeset [6398] by Nicklas Nordborg
Tagging Reggie 4.32
11:32 AM Ticket #1295 (Registration of specimen handled by external lab) closed by Nicklas Nordborg
fixed
11:30 AM Ticket #1323 (Genotype targeted variants) closed by Nicklas Nordborg
fixed
11:30 AM Changeset [6397] by Nicklas Nordborg
Preparing to release Reggie 4.32
9:28 AM net.sf.basedb.reggie/notes432 edited by Nicklas Nordborg
(diff)
8:39 AM Changeset [6396] by Nicklas Nordborg
References #1323: Genotype targeted variants Remove debug code.
8:39 AM Changeset [6395] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
8:37 AM Changeset [6394] by Nicklas Nordborg
References #1323: Genotype targeted variants Variants with no data is …
8:37 AM Changeset [6393] by Nicklas Nordborg
References #1323: Genotype targeted variants Display information from …

Sep 15, 2021:

1:53 PM Changeset [6392] by Nicklas Nordborg
References #1323: Genotype targeted variants Default configuration …
11:17 AM Changeset [6391] by Nicklas Nordborg
References #1323: Genotype targeted variants Add link to a dialog in …
9:22 AM Changeset [6390] by Nicklas Nordborg
References #1323: Genotype targeted variants The link to the dialog …
9:17 AM Changeset [6389] by Nicklas Nordborg
References #1323: Genotype targeted variants Updating @since …
9:14 AM Changeset [6388] by Nicklas Nordborg
References #1323: Genotype targeted variants Added …
8:30 AM Changeset [6387] by Nicklas Nordborg
References #1323: Genotype targeted variants Merge all changes to the …
8:27 AM Changeset [6386] by Nicklas Nordborg
References #1323: Genotype targeted variants Genotype VCF files …
8:27 AM Changeset [6385] by Nicklas Nordborg
8:22 AM Changeset [6384] by Nicklas Nordborg
References #1323: Genotype targeted variants Ignore some effects from …
8:19 AM Ticket #1326 (Some SnpEff effects should be ignored) closed by Nicklas Nordborg
fixed: In 6383: […]
8:18 AM Changeset [6383] by Nicklas Nordborg
Fixes #1326: Some SnpEff? effects should be ignored
8:16 AM Ticket #1326 (Some SnpEff effects should be ignored) created by Nicklas Nordborg
The ANN field that is created by SnpEff can be a large table with …

Sep 14, 2021:

2:46 PM Changeset [6382] by Nicklas Nordborg
References #1323: Genotype targeted variants Skip 'p.?' when …
2:11 PM Changeset [6381] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
8:51 AM Changeset [6380] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
8:33 AM Changeset [6379] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …

Sep 10, 2021:

2:11 PM net.sf.basedb.reggie/notes432 edited by Nicklas Nordborg
(diff)
2:09 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) closed by Nicklas Nordborg
fixed: In 6378: […]
2:09 PM Changeset [6378] by Nicklas Nordborg
Fixes #1325: Calculating the average fragment size needs fixing due to …
2:03 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) created by Nicklas Nordborg
It seems that Hisat 2.1 has a bug that in some cases output a negative …

Sep 8, 2021:

1:30 PM Changeset [6377] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …

Sep 7, 2021:

2:24 PM Changeset [6376] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
12:21 PM Changeset [6375] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
11:23 AM Changeset [6374] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
11:23 AM Changeset [6373] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
9:16 AM Changeset [6372] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
8:58 AM Changeset [6371] by Nicklas Nordborg
References #1324: Implement support for indexing VCF files from the …
8:55 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) created by Nicklas Nordborg
See Reggie ticket #1323. The VCF files should be more or less …
8:43 AM Changeset [6370] by Nicklas Nordborg
References #1323: Genotype targeted variants Added auto-confirm …
8:43 AM Changeset [6369] by Nicklas Nordborg
References #1323: Genotype targeted variants Added auto-confirm …

Sep 6, 2021:

2:42 PM Changeset [6368] by Nicklas Nordborg
References #1323: Genotype targeted variants The "View variant" …
9:43 AM Changeset [6367] by Nicklas Nordborg
References #1323: Genotype targeted variants Change to GATK version …

Sep 2, 2021:

12:36 PM Changeset [6366] by Nicklas Nordborg
References #1323: Genotype targeted variants Updated the dialog for …
9:55 AM Changeset [6365] by Nicklas Nordborg
References #1323: Genotype targeted variants Added TargetedGenotype

Aug 31, 2021:

1:48 PM Changeset [6364] by Nicklas Nordborg
References #1323: Genotype targeted variants Implemented steps for …

Aug 30, 2021:

1:47 PM Changeset [6363] by Nicklas Nordborg
References #1323: Genotype targeted variants Added …
11:01 AM Changeset [6362] by Nicklas Nordborg
References #1323: Genotype targeted variants Auto-confirmation after …
9:34 AM Changeset [6361] by Nicklas Nordborg
References #1323: Genotype targeted variants Result VCF files are now …
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