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  • 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
  • cba355cdde first blackboard Eric Coissac 2024-07-25 18:10:28 -04:00
  • 67665a6b40 Xprize update Eric Coissac 2024-07-25 18:09:03 -04:00
  • 4e4fac491f Fisrt versin of the two levels indexing Eric Coissac 2024-07-12 15:17:48 +02:00
  • 42c5881ddc some cleanning on the new tools Eric Coissac 2024-07-11 10:46:11 +02:00
  • c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished Eric Coissac 2024-07-10 15:21:42 +02:00
  • bd855c4965 Adds CSV as an input format Eric Coissac 2024-07-03 21:04:27 +02:00
  • 5d9ac261ff correct an attribute name Eric Coissac 2024-07-01 17:44:18 +02:00
  • fd663357b5 First version of obicleandb... Eric Coissac 2024-07-01 17:12:42 +02:00
  • 0187a82c5f Patch a bug in obimultiplex loosing sequence with primer dimer Eric Coissac 2024-06-30 17:42:28 +02:00
  • 154753de90 Same bug but for fastq sequence writing only Eric Coissac 2024-06-26 18:46:47 +02:00
  • e40d0bfbe7 Debug fasta and fastq writer when the first sequence is hudge Eric Coissac 2024-06-26 18:39:42 +02:00
  • 1835cb2cf3 remove sonic which only works on AMD64 Eric Coissac 2024-06-24 14:53:18 +02:00
  • c1f03cb1f6 Switch to faster json library go-json and sonic Eric Coissac 2024-06-23 00:36:08 +02:00
  • 93f9dcb95f Reducing memory allocation events Eric Coissac 2024-06-22 22:32:31 +02:00
  • e6b87ecd02 Reduce memory allocation events Eric Coissac 2024-06-22 21:01:53 +02:00
  • 54a138196c Patch a bug in fasta and fastq reading Eric Coissac 2024-06-21 14:28:57 +02:00
  • 818ce87bab Patch some bugs in writing files Eric Coissac 2024-06-19 13:15:30 +02:00
  • 73996bb0b7 Small change in consensus weight Eric Coissac 2024-06-19 09:11:59 +02:00
  • a812fe8b72 debug of obimultiplex Eric Coissac 2024-06-18 23:38:33 +02:00
  • 44533fb61e Bugs in the non stric tag matching algorithm Eric Coissac 2024-06-10 21:19:26 +02:00
  • 2d4813614b Update the release Notes Eric Coissac 2024-06-07 09:11:06 +02:00
  • 3a7661f324 obimultiplex2 in now obimultiplex Eric Coissac 2024-06-07 09:04:37 +02:00
  • bc12b1aaa2 Add a complete documented example of the new obitag format Eric Coissac 2024-06-06 23:44:23 +02:00
  • e47b50de7f Patch a bug in seting of the tag delimiter with an upper case Eric Coissac 2024-06-06 23:25:16 +02:00
  • 1b43fa4247 First complete version of obimultiplex2 Eric Coissac 2024-06-06 23:11:13 +02:00
  • 985c91452a correction of bug and format in obisplit Eric Coissac 2024-06-05 17:18:44 +02:00
  • 87a7219ab4 Adds the reading of the options through the csv formated ngsfilter configuration file Eric Coissac 2024-06-04 22:57:07 +02:00
  • c8ad96f5e6 First fonctionnal version with fixed tag length and strict matching Eric Coissac 2024-06-04 21:46:09 +02:00
  • a0a9fb461c trial on rewriting obimultiplex Eric Coissac 2024-06-04 16:50:07 +02:00
  • 65f5109957 Plenty of small bugs Eric Coissac 2024-06-04 16:49:12 +02:00
  • e843d2aa5c Patch a tricky bug in parsing of json header and save the last sequence from files Eric Coissac 2024-06-04 13:46:23 +02:00
  • aa42df326a Correct a bug in the fastq reader affecting the quality of the last record of each chunk Eric Coissac 2024-06-04 11:57:16 +02:00
  • 411124d1b3 Add automatic rules to manage version number Eric Coissac 2024-06-01 17:26:16 +02:00
  • 38945d0a41 Adds the --template option to obimultiplex Eric Coissac 2024-05-31 11:34:06 +02:00
  • 4487723d14 Adds possibility to provide the ngsfilter configuration as a CSV file Eric Coissac 2024-05-31 11:08:20 +02:00
  • dbeb44bc79 Patch a bug in the quality string writing Eric Coissac 2024-05-31 11:07:25 +02:00
  • 3e1d9a41ec Adds more format checking during fasta parsing Eric Coissac 2024-05-30 18:12:06 +02:00
  • dd9307a4cd Swich to the system min and max functions and remove the version from obiutils Eric Coissac 2024-05-30 08:27:24 +02:00