Timeline
Oct 5, 2021:
- 2:08 PM Ticket #1339 (ReadLengthAvg annotations are -1) updated by
- The items that have -1 need to be updated manually and the results in …
- 1:49 PM Ticket #1339 (ReadLengthAvg annotations are -1) updated by
-
Milestone changed
- 1:48 PM Changeset [6429] by
- Creating bugfix branch for Reggie 4.33
- 1:44 PM Ticket #1339 (ReadLengthAvg annotations are -1) created by
- For the latest sequencing run, there is only one merged item that has …
Sep 29, 2021:
- 9:34 AM net.sf.basedb.reggie/notes433 edited by
- (diff)
- 9:10 AM Changeset [6428] by
- 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
- Added link to update notes for Reggie 4.33 (diff)
- 9:08 AM net.sf.basedb.reggie/notes433 created by
- 9:06 AM net.sf.basedb.reggie edited by
- Released Reggie 4.33 (diff)
- 9:03 AM Changeset [6427] by
- Tagging Reggie 4.33
- 9:03 AM Changeset [6426] by
- Preparing to release Reggie 4.33
- 9:00 AM Ticket #1338 (Sort order in case summary) closed by
- fixed: In 6425: […]
- 9:00 AM Changeset [6425] by
- Fixes #1338: Sort order in case summary
- 8:59 AM Ticket #1338 (Sort order in case summary) created by
- Items in the case summary are typically sorted by name. But this has a …
Sep 28, 2021:
- 10:11 AM Ticket #1337 (Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0) updated by
- This bug may also be related to #1325. The same bug is also present in …
- 9:44 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) closed by
- fixed
- 9:44 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) updated by
- In 6424: […]
- 9:44 AM Changeset [6424] by
- 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
- fixed: In 6423: […]
- 8:56 AM Changeset [6423] by
- Fixes #1337: Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0
- 8:45 AM Ticket #1337 (Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0) updated by
-
Description changed
- 8:43 AM Ticket #1337 (Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0) created by
- 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
- fixed: In 6422: […]
- 8:32 AM Changeset [6422] by
- Fixes #1336: Use the average read length from FASTQ files when …
- 8:28 AM Ticket #1336 (Use the average read length from FASTQ files when calculating ...) updated by
-
Summary changed
Sep 23, 2021:
- 12:41 PM Ticket #1336 (Use the average read length from FASTQ files when calculating ...) created by
- See #1335. If the values from the FASTQ files are available, we should …
- 12:39 PM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) updated by
- In 6421: […]
- 12:39 PM Changeset [6421] by
- References #1335: Calculate average read length in FASTQ files after …
- 9:07 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) updated by
- In 6420: […]
- 9:07 AM Changeset [6420] by
- References #1335: Calculate average read length in FASTQ files after …
- 8:02 AM Ticket #1335 (Calculate average read length in FASTQ files after Trimmomatic) updated by
- In 6419: […]
- 8:02 AM Changeset [6419] by
- 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
- In the legacy pipeline we need the average inner distance between R1 …
Sep 20, 2021:
- 9:57 AM PluginDownload edited by
- Released Reggie 4.32.1 and Variant Search 1.3 (diff)
- 9:56 AM Changeset [6418] by
- Changes for future release Variant Search 1.4
- 9:55 AM Tickets #1328,1330,1331,1333 batch updated by
-
Milestone changed
Milestone renamed - 9:55 AM Milestone Variant Search v1.3 completed
- See Variant Search extension page for …
- 9:54 AM net.sf.basedb.varsearch edited by
- Released Variant Search 1.3 (diff)
- 9:52 AM Changeset [6417] by
- Tagging Variant search 1.3
- 9:52 AM Changeset [6416] by
- Preparing to release Variant search 1.3
- 9:50 AM Changeset [6415] by
- Changes for future release Reggie 4.33
- 9:49 AM Tickets #1329,1332,1334,1327 batch updated by
-
Milestone changed
Milestone renamed - 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
- Released Reggie 4.32.1 (diff)
- 9:46 AM Changeset [6414] by
- Tagging Reggie 4.32.1
- 9:45 AM Changeset [6413] by
- Remove debug flag.
- 9:44 AM Changeset [6412] by
- Preparing to relase Reggie 4.32.1
- 9:43 AM Ticket #1334 (Targeted genotyping should include number of variants found in the ...) updated by
- In 6411: […]
- 9:43 AM Changeset [6411] by
- 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
- fixed: In 6410: […]
- 9:07 AM Changeset [6410] by
- 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
- 8:39 AM Ticket #1332 (Add new translation for CMD library protocol for the showcase report) closed by
- fixed: In 6409: […]
- 8:39 AM Changeset [6409] by
- 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
- fixed: In 6408: […]
- 8:34 AM Changeset [6408] by
- 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
Sep 17, 2021:
- 3:55 PM Ticket #1332 (Add new translation for CMD library protocol for the showcase report) created by
-
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
- fixed: In 6407: […]
- 1:59 PM Changeset [6407] by
- Fixes #1331: Rename the index for targeted variants
- 1:58 PM Ticket #1331 (Rename the index for targeted variants) created by
- It will look better with Variants (targeted).
- 1:57 PM Ticket #1330 (The progress bar in the Index manager is not displaying) closed by
- fixed: In 6406: […]
- 1:57 PM Changeset [6406] by
- 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
- 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
- fixed: In 6405: […]
- 1:42 PM Changeset [6405] by
- Fixes #1329: HaplotypeCaller is "inventing" new variants
- 10:02 AM Ticket #1329 (HaplotypeCaller is "inventing" new variants) updated by
-
I think it should be possible to use
grep "\(^#\|TYPE\=\)"to filter … - 9:26 AM Ticket #1329 (HaplotypeCaller is "inventing" new variants) created by
- The output from HaplotypeCaller sometimes contain results for more …
- 9:14 AM Ticket #1328 (Index out of bounds exception) closed by
- fixed: In 6404: […]
- 9:13 AM Changeset [6404] by
- Fixes #1328: Index out of bounds exception
- 9:10 AM Ticket #1328 (Index out of bounds exception) created by
- 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
- fixed: In 6403: […]
- 8:43 AM Changeset [6403] by
- Fixes #1327: Incorrect message after submitting targeted genotyping job
- 8:21 AM Ticket #1327 (Incorrect message after submitting targeted genotyping job) created by
- The "Targeted genotyping wizard" display an incorrect message after …
Sep 16, 2021:
- 12:57 PM Changeset [6402] by
- 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
- Released Variant Search 1.2 (diff)
- 12:54 PM net.sf.basedb.varsearch edited by
- (diff)
- 12:54 PM net.sf.basedb.varsearch edited by
- Released Variant Search 1.2 (diff)
- 12:52 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) closed by
- fixed
- 12:51 PM Changeset [6401] by
- Tagging Variant search 1.2
- 12:50 PM Changeset [6400] by
- Preparing to release Variant search 1.2
- 11:41 AM Changeset [6399] by
- 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
- Released Reggie 4.32 (diff)
- 11:37 AM net.sf.basedb.reggie edited by
- Released Reggie 4.32 (diff)
- 11:33 AM Changeset [6398] by
- Tagging Reggie 4.32
- 11:32 AM Ticket #1295 (Registration of specimen handled by external lab) closed by
- fixed
- 11:30 AM Ticket #1323 (Genotype targeted variants) closed by
- fixed
- 11:30 AM Changeset [6397] by
- Preparing to release Reggie 4.32
- 9:28 AM net.sf.basedb.reggie/notes432 edited by
- (diff)
- 8:39 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6396: […]
- 8:39 AM Changeset [6396] by
- References #1323: Genotype targeted variants Remove debug code.
- 8:39 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6395: […]
- 8:39 AM Changeset [6395] by
- References #1324: Implement support for indexing VCF files from the …
- 8:38 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6394: […]
- 8:37 AM Changeset [6394] by
- References #1323: Genotype targeted variants Variants with no data is …
- 8:37 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6393: […]
- 8:37 AM Changeset [6393] by
- References #1323: Genotype targeted variants Display information from …
Sep 15, 2021:
- 1:53 PM Ticket #1323 (Genotype targeted variants) updated by
- In 6392: […]
- 1:53 PM Changeset [6392] by
- References #1323: Genotype targeted variants Default configuration …
- 11:17 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6391: […]
- 11:17 AM Changeset [6391] by
- References #1323: Genotype targeted variants Add link to a dialog in …
- 9:22 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6390: […]
- 9:22 AM Changeset [6390] by
- References #1323: Genotype targeted variants The link to the dialog …
- 9:17 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6389: […]
- 9:17 AM Changeset [6389] by
- References #1323: Genotype targeted variants Updating @since …
- 9:14 AM Ticket #1323 (Genotype targeted variants) updated by
-
Milestone changed
- 9:14 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6388: […]
- 9:14 AM Changeset [6388] by
- References #1323: Genotype targeted variants Added …
- 8:30 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6387: […]
- 8:30 AM Changeset [6387] by
- References #1323: Genotype targeted variants Merge all changes to the …
- 8:27 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6386: […]
- 8:27 AM Changeset [6386] by
- References #1323: Genotype targeted variants Genotype VCF files …
- 8:27 AM Changeset [6385] by
- 8:22 AM Tickets #1323,1326 batch updated by
- In 6384: […]
- 8:22 AM Changeset [6384] by
- References #1323: Genotype targeted variants Ignore some effects from …
- 8:19 AM Ticket #1326 (Some SnpEff effects should be ignored) closed by
- fixed: In 6383: […]
- 8:18 AM Changeset [6383] by
- Fixes #1326: Some SnpEff effects should be ignored
- 8:16 AM Ticket #1326 (Some SnpEff effects should be ignored) created by
- The ANN field that is created by SnpEff can be a large table with …
Sep 14, 2021:
- 2:46 PM Ticket #1323 (Genotype targeted variants) updated by
- In 6382: […]
- 2:46 PM Changeset [6382] by
- References #1323: Genotype targeted variants Skip 'p.?' when …
- 2:11 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6381: […]
- 2:11 PM Changeset [6381] by
- References #1324: Implement support for indexing VCF files from the …
- 8:51 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6380: […]
- 8:51 AM Changeset [6380] by
- References #1324: Implement support for indexing VCF files from the …
- 8:33 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6379: […]
- 8:33 AM Changeset [6379] by
- References #1324: Implement support for indexing VCF files from the …
Sep 10, 2021:
- 2:48 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) updated by
-
Description changed
- 2:11 PM net.sf.basedb.reggie/notes432 edited by
- (diff)
- 2:09 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) closed by
- fixed: In 6378: […]
- 2:09 PM Changeset [6378] by
- Fixes #1325: Calculating the average fragment size needs fixing due to …
- 2:06 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) updated by
-
Description changed
- 2:05 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) updated by
-
Description changed
- 2:03 PM Ticket #1325 (Calculating the average fragment size needs fixing due to Hisat bug) created by
- It seems that Hisat 2.1 has a bug that in some cases output a negative …
Sep 8, 2021:
- 1:30 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6377: […]
- 1:30 PM Changeset [6377] by
- References #1324: Implement support for indexing VCF files from the …
Sep 7, 2021:
- 2:24 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6376: […]
- 2:24 PM Changeset [6376] by
- References #1324: Implement support for indexing VCF files from the …
- 12:21 PM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6375: […]
- 12:21 PM Changeset [6375] by
- References #1324: Implement support for indexing VCF files from the …
- 11:23 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6374: […]
- 11:23 AM Changeset [6374] by
- References #1324: Implement support for indexing VCF files from the …
- 11:23 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6373: […]
- 11:23 AM Changeset [6373] by
- References #1324: Implement support for indexing VCF files from the …
- 9:16 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6372: […]
- 9:16 AM Changeset [6372] by
- References #1324: Implement support for indexing VCF files from the …
- 8:58 AM Ticket #1324 (Implement support for indexing VCF files from the targeted genotyping) updated by
- In 6371: […]
- 8:58 AM Changeset [6371] by
- 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
- See Reggie ticket #1323. The VCF files should be more or less …
- 8:43 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6370: […]
- 8:43 AM Changeset [6370] by
- References #1323: Genotype targeted variants Added auto-confirm …
- 8:43 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6369: […]
- 8:43 AM Changeset [6369] by
- References #1323: Genotype targeted variants Added auto-confirm …
Sep 6, 2021:
- 2:42 PM Ticket #1323 (Genotype targeted variants) updated by
- In 6368: […]
- 2:42 PM Changeset [6368] by
- References #1323: Genotype targeted variants The "View variant" …
- 9:43 AM Ticket #1323 (Genotype targeted variants) updated by
- In 6367: […]
- 9:43 AM Changeset [6367] by
- References #1323: Genotype targeted variants Change to GATK version …
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