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Author SHA1 Message Date
Eric Coissac 51b3e83d32 some cleaning 2025-02-24 11:31:49 +01:00
Eric Coissac 8671285d02 add the --min-sample-count option to obiclean. 2025-02-24 08:48:31 +01:00
Eric Coissac 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
 2025-02-23 17:37:56 +01:00
Eric Coissac fb6f857d8c Update the computation of the consensus quality score 2025-02-23 15:16:31 +01:00
Eric Coissac d4209b4549 Add a basic test for obiparing 2025-02-22 09:57:44 +01:00
Eric Coissac ef05d4975f Upadte the scoring schema of obipairing 2025-02-21 22:41:34 +01:00
Eric Coissac 4588bf8b5d Patch the make file to fail on error 2025-02-19 15:55:07 +01:00
Eric Coissac 090633850d Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 15:28:42 +01:00
Eric Coissac 15a058cf63 with all the sample files for tests 2025-02-19 15:27:38 +01:00
Eric Coissac 2f5f7634d6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:50:10 +01:00
Eric Coissac 48138b605c Changes to be committed: 
modified:   .github/workflows/obitest.yml
	modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:37:05 +01:00
Eric Coissac aed22c12a6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:34:22 +01:00
Eric Coissac 443a9b3ce3 Changes to be committed: 
modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:28:49 +01:00
Eric Coissac 7e90537379 For run of test using bash in makefile 2025-02-19 13:58:52 +01:00
Eric Coissac d3d15acc6c Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
	modified:   pkg/obioptions/version.go
 2025-02-19 13:54:01 +01:00
Eric Coissac bd4a0b5ca5 Essais d'une google action pour lancer les tests des obitools 2025-02-19 13:45:43 +01:00
Eric Coissac 952f85f312 A first trial of a test for obicount 2025-02-19 13:17:36 +01:00
Eric Coissac 4774438644 Changes to be committed: 
modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/taxonomy_methods.go
 2025-02-12 08:40:38 +01:00
Eric Coissac 6a8061cc4f Add managment of the taxonomy alias politic 2025-02-10 14:05:47 +01:00
Eric Coissac e2563cd8df Patch a bug in registering merged taxa 2025-02-10 11:42:46 +01:00
Eric Coissac f2e81adf95 Changes to be committed: 
modified:   .gitignore
	deleted:    xxx.csv
 2025-02-05 19:28:19 +01:00
Eric Coissac f27e9bc91e patch a bug related to csv and qualities 2025-02-05 19:27:00 +01:00
Eric Coissac 773e54965d Patch a bug on compressed output 2025-02-05 14:18:24 +01:00
Eric Coissac ceca33998b add extensions fq in directory scanning 2025-02-04 20:34:58 +01:00
Eric Coissac 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
 2025-02-02 16:52:52 +01:00
Eric Coissac c10df073a7 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitax/iterator.go
 2025-02-01 12:06:19 +01:00
Eric Coissac d3dac1b21f Make obitag able to use the taxonomic path included in reference database as taxonomy 2025-01-30 11:50:03 +01:00
Eric Coissac 0df082da06 Adds possibility to extract a taxonomy from taxonomic path included in sequence files 2025-01-30 11:18:21 +01:00
Eric Coissac 2452aef7a9 patch multiple -Z options 2025-01-29 21:35:28 +01:00
Eric Coissac 337954592d add the --out option to the obitaxonomy 2025-01-29 13:22:35 +01:00
Eric Coissac 8a28c9ae7c add the --download-ncbi option to obitaxonomy 2025-01-29 12:38:39 +01:00
Eric Coissac b6b18c0fa1 Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-01-29 11:34:01 +01:00
Eric Coissac 67e2758d63 Switch to realease number 4.3.0 2025-01-29 11:33:30 +01:00
Eric Coissac 00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. 2025-01-29 10:45:26 +01:00
Eric Coissac c50a0f409d break the import cyccle 2025-01-27 17:23:07 +01:00
Eric Coissac 7c4042df6b introduce obidefault 2025-01-27 17:12:45 +01:00
Eric Coissac 0a567f621c small changes 2025-01-24 18:12:37 +01:00
Eric Coissac 9acb4a85a8 Refactoring of the default values 2025-01-24 18:09:59 +01:00
Eric Coissac 3137c1f841 Adds the ability to read gzip-tar file for the taxonomy dump 2025-01-24 11:47:59 +01:00
Eric Coissac ffd67252c3 patch a bug in obimultiplex: change option -t into -s 2025-01-23 13:50:24 +01:00
Eric Coissac 757448cb1e debug obigrep taxonomy options 2025-01-15 20:48:34 +01:00
Eric Coissac 4ae3336135 obidemerge: set demerge on sample the default 2025-01-10 17:09:44 +01:00
Eric Coissac d066bb6878 Changes to be committed: 
modified:   .gitignore
	modified:   cmd/test/main.go
	modified:   pkg/obioptions/version.go
 2025-01-09 07:24:41 +01:00
Eric Coissac becb995e3d misspellings penality -> pelnalty 2025-01-09 07:22:23 +01:00
Eric Coissac c58d9772ac Two small corrections on options 2025-01-07 11:51:37 +01:00
Eric Coissac 67c0d00a4d remove the obitag2 command 2025-01-07 11:50:28 +01:00
Eric Coissac 4fe0db63ff Patch CSV reader to use the new taxonomy system 2024-12-20 21:30:00 +01:00
Eric Coissac ccd3b06532 Merge branch 'master' into taxonomy 2024-12-20 20:06:57 +01:00
Eric Coissac 5d0f996625 Patch a small bug on json write 2024-12-20 19:42:03 +01:00
Eric Coissac abfa8f357a patch a bug in Taxid parsing 2024-12-19 13:54:23 +01:00
Eric Coissac 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
 2024-12-19 13:36:59 +01:00
Eric Coissac f2525d7b07 Changes to be committed: 
modified:   pkg/obilua/lua.go
	modified:   pkg/obioptions/version.go
 2024-12-04 11:42:05 +01:00
Eric Coissac 39dd3e3ce8 Add management of []interface{} to the LUA API. 2024-12-04 10:58:17 +01:00
Eric Coissac f41a6fbb60 Patch a small bug on json write 2024-11-29 18:39:18 +01:00
Eric Coissac 00b0edc15a refactoring of the file chunck writing 2024-11-29 18:15:03 +01:00
Eric Coissac ad2461a656 some minor improvements 2024-11-27 13:36:06 +01:00
Eric Coissac 40fb4e9767 reduce the memory impact of obiuniq. 2024-11-27 13:30:16 +01:00
Eric Coissac 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
 2024-11-27 09:56:22 +01:00
Eric Coissac 69ef1758a2 obicsv debug 2024-11-24 23:38:49 +01:00
Eric Coissac 3d06978808 a functional new version of obifind 2024-11-24 19:33:24 +01:00
Eric Coissac 7884a74f9c Patch a bug in obitagpcr 2024-11-18 21:10:47 +01:00
Eric Coissac 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
 2024-11-16 10:01:49 +01:00
Eric Coissac f3d8707c08 Add default taxonomy 2024-11-16 10:01:07 +01:00
Eric Coissac 7633fc4d23 update documentation 2024-11-16 06:00:27 +01:00
Eric Coissac f5d79d0bc4 update api documentation 2024-11-16 05:59:41 +01:00
Eric Coissac 03f4e88a17 Fisrt functional version 2024-11-14 19:10:23 +01:00
Eric Coissac 9471fedfa1 Fisrt step in the obitax rewriting 2024-11-08 09:48:16 +01:00
Eric Coissac 4b65bfce84 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obitagpcr/pcrtag.go
 2024-11-04 14:30:17 +01:00
Eric Coissac fc75974c68 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obitagpcr/options.go
 2024-11-04 13:25:52 +01:00
Eric Coissac 422f11cceb Changes to be committed: 
modified:   pkg/obitools/obitagpcr/pcrtag.go
 2024-10-29 16:53:10 +01:00
Eric Coissac 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
 2024-10-28 21:51:21 +01:00
Eric Coissac 3e00d39d47 In obimultiplex, patch a bug when no tag are associated to a primer. 2024-10-22 14:12:20 +02:00
Eric Coissac 9e8a7fd9be Patch a bug in fastq reader 2024-10-20 16:07:43 +02:00
Eric Coissac 74280e4704 Merge branch 'no-pools' 2024-09-24 16:38:23 +02:00
Eric Coissac 7255c71576 commit version 2024-09-24 16:36:59 +02:00
Eric Coissac 241f2286f2 remove the slice pool management 2024-09-24 16:31:30 +02:00
Eric Coissac b37fc39ead switch to go version 1.23.1 2024-09-24 15:55:01 +02:00
Eric Coissac 2b4a633c30 EndGapFree alignments 2024-09-24 15:52:12 +02:00
Eric Coissac 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
Eric Coissac 65ae82622e correction of several small bugs 2024-09-03 06:08:07 -03:00
Eric Coissac 373464cb06 On development genome skim tools 2024-08-30 11:17:33 +02:00
Eric Coissac cd330db672 Add option to obimicrosat to control microsat length and orientation 2024-08-30 11:16:43 +02:00
Eric Coissac 31bfc88eb9 Patch a bug on writing to stdout, and add clearer error on openning data files 2024-08-13 09:45:28 +02:00
Eric Coissac bdb96dda94 Adds the obimicrosat command 2024-08-05 15:31:20 +02:00
Eric Coissac 3f57935328 Adjust the size of the genbank and embl buffer size 2024-08-05 11:32:37 +02:00
Eric Coissac 886b5d9a96 Optimize memory for readers and writers 2024-08-05 10:48:28 +02:00
Eric Coissac f83032e643 Tag version 2024-08-02 14:30:53 +02:00
Eric Coissac c0c18030c8 Adds information on the new github address 2024-08-02 14:26:20 +02:00
Eric Coissac 242f4d8f56 Realease notes 2024-08-02 13:50:33 +02:00
Eric Coissac 1b1cd41fd3 Add some code refactoring from the blackboard branch 2024-08-02 12:35:46 +02:00
Eric Coissac bc1aaaf7d9 New install script updated for github 2024-07-29 14:35:21 +02:00
Eric Coissac 2247c3bc0a obitag xprize version 
Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d
 2024-07-25 18:11:11 -04:00
Eric Coissac 67665a6b40 Xprize update 
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
 2024-07-25 18:09:03 -04:00
Eric Coissac 4e4fac491f Fisrt versin of the two levels indexing 
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
 2024-07-12 15:17:48 +02:00
Eric Coissac 42c5881ddc some cleanning on the new tools 
Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
 2024-07-11 10:46:11 +02:00
Eric Coissac c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished 
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
 2024-07-10 15:21:42 +02:00
Eric Coissac bd855c4965 Adds CSV as an input format 
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
 2024-07-03 21:04:27 +02:00
Eric Coissac 5d9ac261ff correct an attribute name 
Former-commit-id: 2bc540dc3863aef4f8745666047c2a7d94405343
 2024-07-01 17:44:18 +02:00
Eric Coissac fd663357b5 First version of obicleandb... 
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
 2024-07-01 17:12:42 +02:00
Eric Coissac 0187a82c5f Patch a bug in obimultiplex loosing sequence with primer dimer 
Former-commit-id: ea14e1aa2e4670c19fe8ee7ec61565bd21cc25b0
 2024-06-30 17:42:28 +02:00