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  • 13d610aff7 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obiclean/chimera.go Eric Coissac 2025-02-24 15:25:45 +01:00
  • db284f1d44 Add an experimental chimera detection... Eric Coissac 2025-02-24 15:02:49 +01:00
  • 51b3e83d32 some cleaning Eric Coissac 2025-02-24 11:31:49 +01:00
  • 8671285d02 add the --min-sample-count option to obiclean. Eric Coissac 2025-02-24 08:48:31 +01:00
  • 51d11aa36d Changes to be committed: modified: pkg/obialign/alignment.go modified: pkg/obialign/pairedendalign.go modified: pkg/obioptions/version.go modified: pkg/obitools/obipairing/pairing.go Eric Coissac 2025-02-23 17:37:56 +01:00
  • fb6f857d8c Update the computation of the consensus quality score Eric Coissac 2025-02-23 15:16:31 +01:00
  • d4209b4549 Add a basic test for obiparing Eric Coissac 2025-02-22 09:57:44 +01:00
  • ef05d4975f Upadte the scoring schema of obipairing Eric Coissac 2025-02-21 22:41:34 +01:00
  • 4588bf8b5d Patch the make file to fail on error Eric Coissac 2025-02-19 15:55:07 +01:00
  • 090633850d Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 15:28:42 +01:00
  • 15a058cf63 with all the sample files for tests Eric Coissac 2025-02-19 15:27:38 +01:00
  • 2f5f7634d6 Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:50:10 +01:00
  • 48138b605c Changes to be committed: modified: .github/workflows/obitest.yml modified: Makefile modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:37:05 +01:00
  • aed22c12a6 Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:34:22 +01:00
  • 443a9b3ce3 Changes to be committed: modified: Makefile modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:28:49 +01:00
  • 7e90537379 For run of test using bash in makefile Eric Coissac 2025-02-19 13:58:52 +01:00
  • d3d15acc6c Changes to be committed: modified: obitests/obitools/obicount/test.sh modified: pkg/obioptions/version.go Eric Coissac 2025-02-19 13:54:01 +01:00
  • bd4a0b5ca5 Essais d'une google action pour lancer les tests des obitools Eric Coissac 2025-02-19 13:45:43 +01:00
  • 952f85f312 A first trial of a test for obicount Eric Coissac 2025-02-19 13:17:36 +01:00
  • d70b0a5b42 A first version of obimicroasm... microasm Eric Coissac 2025-02-16 21:47:49 +01:00
  • 4774438644 Changes to be committed: modified: pkg/obiformats/universal_read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/taxonomy_methods.go Eric Coissac 2025-02-12 08:40:38 +01:00
  • 6a8061cc4f Add managment of the taxonomy alias politic Eric Coissac 2025-02-10 14:05:47 +01:00
  • e2563cd8df Patch a bug in registering merged taxa Eric Coissac 2025-02-10 11:42:46 +01:00
  • f2e81adf95 Changes to be committed: modified: .gitignore deleted: xxx.csv Eric Coissac 2025-02-05 19:28:19 +01:00
  • f27e9bc91e patch a bug related to csv and qualities Eric Coissac 2025-02-05 19:27:00 +01:00
  • 773e54965d Patch a bug on compressed output Eric Coissac 2025-02-05 14:18:24 +01:00
  • ceca33998b add extensions fq in directory scanning Eric Coissac 2025-02-04 20:34:58 +01:00
  • b9bee5f426 Changes to be committed: modified: go.mod modified: go.sum modified: pkg/obilua/obilib.go modified: pkg/obilua/obiseq.go modified: pkg/obilua/obiseqslice.go new file: pkg/obilua/obitaxon.go new file: pkg/obilua/obitaxonomy.go modified: pkg/obioptions/version.go Eric Coissac 2025-02-02 16:52:52 +01:00
  • c10df073a7 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitax/iterator.go Eric Coissac 2025-02-01 12:06:19 +01:00
  • d3dac1b21f Make obitag able to use the taxonomic path included in reference database as taxonomy Eric Coissac 2025-01-30 11:50:03 +01:00
  • 0df082da06 Adds possibility to extract a taxonomy from taxonomic path included in sequence files Eric Coissac 2025-01-30 11:18:21 +01:00
  • 2452aef7a9 patch multiple -Z options Eric Coissac 2025-01-29 21:35:28 +01:00
  • 337954592d add the --out option to the obitaxonomy Eric Coissac 2025-01-29 13:22:35 +01:00
  • 8a28c9ae7c add the --download-ncbi option to obitaxonomy Eric Coissac 2025-01-29 12:38:39 +01:00
  • b6b18c0fa1 Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-01-29 11:34:01 +01:00
  • 67e2758d63 Switch to realease number 4.3.0 Eric Coissac 2025-01-29 11:33:30 +01:00
  • 00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. taxonomy Eric Coissac 2025-01-29 10:45:26 +01:00
  • c50a0f409d break the import cyccle Eric Coissac 2025-01-27 17:23:07 +01:00
  • 7c4042df6b introduce obidefault Eric Coissac 2025-01-27 17:12:45 +01:00
  • 0a567f621c small changes Eric Coissac 2025-01-24 18:12:37 +01:00
  • 9acb4a85a8 Refactoring of the default values Eric Coissac 2025-01-24 18:09:59 +01:00
  • 3137c1f841 Adds the ability to read gzip-tar file for the taxonomy dump Eric Coissac 2025-01-24 11:47:59 +01:00
  • ffd67252c3 patch a bug in obimultiplex: change option -t into -s Eric Coissac 2025-01-23 13:50:24 +01:00
  • 757448cb1e debug obigrep taxonomy options Eric Coissac 2025-01-15 20:48:34 +01:00
  • 4ae3336135 obidemerge: set demerge on sample the default Eric Coissac 2025-01-10 17:09:44 +01:00
  • d066bb6878 Changes to be committed: modified: .gitignore modified: cmd/test/main.go modified: pkg/obioptions/version.go Eric Coissac 2025-01-09 07:24:41 +01:00
  • becb995e3d misspellings penality -> pelnalty Eric Coissac 2025-01-09 07:22:23 +01:00
  • c58d9772ac Two small corrections on options Eric Coissac 2025-01-07 11:51:37 +01:00
  • 67c0d00a4d remove the obitag2 command Eric Coissac 2025-01-07 11:50:28 +01:00
  • 4fe0db63ff Patch CSV reader to use the new taxonomy system Eric Coissac 2024-12-20 21:30:00 +01:00
  • ccd3b06532 Merge branch 'master' into taxonomy Eric Coissac 2024-12-20 20:06:57 +01:00
  • 5d0f996625 Patch a small bug on json write Eric Coissac 2024-12-20 19:42:03 +01:00
  • abfa8f357a patch a bug in Taxid parsing Eric Coissac 2024-12-19 13:54:23 +01:00
  • 795df34d1a Changes to be committed: modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitag2/main.go modified: go.mod modified: go.sum modified: pkg/obiformats/ncbitaxdump/read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/attributes.go modified: pkg/obiseq/taxonomy_lca.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obiseq/taxonomy_predicate.go modified: pkg/obitax/inner.go modified: pkg/obitax/lca.go new file: pkg/obitax/taxid.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obigrep/options.go modified: pkg/obitools/obilandmark/obilandmark.go modified: pkg/obitools/obilandmark/options.go modified: pkg/obitools/obirefidx/famlilyindexing.go modified: pkg/obitools/obirefidx/geomindexing.go modified: pkg/obitools/obirefidx/obirefidx.go modified: pkg/obitools/obirefidx/options.go modified: pkg/obitools/obitag/obigeomtag.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitag/options.go modified: pkg/obiutils/strings.go Eric Coissac 2024-12-19 13:36:59 +01:00
  • f2525d7b07 Changes to be committed: modified: pkg/obilua/lua.go modified: pkg/obioptions/version.go Eric Coissac 2024-12-04 11:42:05 +01:00
  • 39dd3e3ce8 Add management of []interface{} to the LUA API. Eric Coissac 2024-12-04 10:58:17 +01:00
  • f41a6fbb60 Patch a small bug on json write Eric Coissac 2024-11-29 18:39:18 +01:00
  • 00b0edc15a refactoring of the file chunck writing Eric Coissac 2024-11-29 18:15:03 +01:00
  • ad2461a656 some minor improvements Eric Coissac 2024-11-27 13:36:06 +01:00
  • 40fb4e9767 reduce the memory impact of obiuniq. Eric Coissac 2024-11-27 13:30:16 +01:00
  • d29a56dcbf Changes to be committed: modified: Release-notes.md modified: pkg/obialign/pairedendalign.go modified: pkg/obilua/obiseq.go modified: pkg/obioptions/version.go modified: pkg/obiseq/biosequence.go modified: pkg/obitools/obipairing/pairing.go Eric Coissac 2024-11-27 09:56:22 +01:00
  • 69ef1758a2 obicsv debug Eric Coissac 2024-11-24 23:38:49 +01:00
  • 3d06978808 a functional new version of obifind Eric Coissac 2024-11-24 19:33:24 +01:00
  • 7884a74f9c Patch a bug in obitagpcr Eric Coissac 2024-11-18 21:10:47 +01:00
  • 36327c79c8 Changes to be committed: modified: .gitignore new file: pkg/obitax/default_taxonomy.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonnode.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonset.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obifind/iterator.go modified: pkg/obitools/obifind/options.go Eric Coissac 2024-11-16 10:01:49 +01:00
  • f3d8707c08 Add default taxonomy Eric Coissac 2024-11-16 10:01:07 +01:00
  • 7633fc4d23 update documentation Eric Coissac 2024-11-16 06:00:27 +01:00
  • f5d79d0bc4 update api documentation Eric Coissac 2024-11-16 05:59:41 +01:00
  • 03f4e88a17 Fisrt functional version Eric Coissac 2024-11-14 19:10:23 +01:00
  • 9471fedfa1 Fisrt step in the obitax rewriting Eric Coissac 2024-11-08 09:48:16 +01:00
  • 4b65bfce84 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/pcrtag.go Eric Coissac 2024-11-04 14:30:17 +01:00
  • fc75974c68 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/options.go Eric Coissac 2024-11-04 13:25:52 +01:00
  • 422f11cceb Changes to be committed: modified: pkg/obitools/obitagpcr/pcrtag.go Eric Coissac 2024-10-29 16:53:10 +01:00
  • fefc360f80 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/pcrtag.go modified: pkg/obiutils/abs.go new file: pkg/obiutils/abs_test.go Eric Coissac 2024-10-28 21:51:21 +01:00
  • 3e00d39d47 In obimultiplex, patch a bug when no tag are associated to a primer. Eric Coissac 2024-10-22 14:12:20 +02:00
  • 9e8a7fd9be Patch a bug in fastq reader Eric Coissac 2024-10-20 16:07:43 +02:00
  • 74280e4704 Merge branch 'no-pools' Eric Coissac 2024-09-24 16:38:23 +02:00
  • 7255c71576 commit version Eric Coissac 2024-09-24 16:36:59 +02:00
  • 241f2286f2 remove the slice pool management Eric Coissac 2024-09-24 16:31:30 +02:00
  • b37fc39ead switch to go version 1.23.1 Eric Coissac 2024-09-24 15:55:01 +02:00
  • 2b4a633c30 EndGapFree alignments Eric Coissac 2024-09-24 15:52:12 +02:00
  • 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate Eric Coissac 2024-09-09 16:52:13 +02:00
  • 65ae82622e correction of several small bugs Eric Coissac 2024-09-03 06:08:07 -03:00
  • 373464cb06 On development genome skim tools Eric Coissac 2024-08-30 11:17:33 +02:00
  • cd330db672 Add option to obimicrosat to control microsat length and orientation Eric Coissac 2024-08-30 11:16:43 +02:00
  • 31bfc88eb9 Patch a bug on writing to stdout, and add clearer error on openning data files Eric Coissac 2024-08-13 09:45:28 +02:00
  • bdb96dda94 Adds the obimicrosat command Eric Coissac 2024-08-05 15:31:20 +02:00
  • 3f57935328 Adjust the size of the genbank and embl buffer size Eric Coissac 2024-08-05 11:32:37 +02:00
  • 886b5d9a96 Optimize memory for readers and writers Eric Coissac 2024-08-05 10:48:28 +02:00
  • f83032e643 Tag version Eric Coissac 2024-08-02 14:30:53 +02:00
  • c0c18030c8 Adds information on the new github address Release_4.3.0 Eric Coissac 2024-08-02 14:26:20 +02:00
  • 242f4d8f56 Realease notes Eric Coissac 2024-08-02 13:50:33 +02:00
  • 1b1cd41fd3 Add some code refactoring from the blackboard branch Eric Coissac 2024-08-02 12:35:46 +02:00
  • 6a2f867ae1 Factorize code between fasta and fastq writers blackboard Eric Coissac 2024-08-01 17:22:46 +02:00
  • 776b8f75b7 Muspelling chunck -> chunk Eric Coissac 2024-08-01 16:43:23 +02:00
  • 882cc82f23 Write results as a csv file Eric Coissac 2024-08-01 16:41:50 +02:00
  • f36b39bfa3 First functional version of a blackboard and a blackboard based obicount Eric Coissac 2024-07-31 23:16:45 +02:00
  • bc1aaaf7d9 New install script updated for github Eric Coissac 2024-07-29 14:35:21 +02:00
  • dfe2fc3d43 Last changes on blackboard Eric Coissac 2024-07-29 11:25:54 +02:00
  • 2247c3bc0a obitag xprize version Eric Coissac 2024-07-25 18:11:11 -04:00