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Author SHA1 Message Date
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
Eric Coissac 154753de90 Same bug but for fastq sequence writing only 
Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
 2024-06-26 18:46:47 +02:00
Eric Coissac e40d0bfbe7 Debug fasta and fastq writer when the first sequence is hudge 
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
 2024-06-26 18:39:42 +02:00
Eric Coissac 1835cb2cf3 remove sonic which only works on AMD64 
Former-commit-id: 5073957b4706b68896006ee0f7bc30e49ff72c3b
 2024-06-24 14:53:18 +02:00
Eric Coissac c1f03cb1f6 Switch to faster json library go-json and sonic 
Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
 2024-06-23 00:36:08 +02:00
Eric Coissac 93f9dcb95f Reducing memory allocation events 
Former-commit-id: c94e79ba116464504580fc397270ead154063971
 2024-06-22 22:32:31 +02:00
Eric Coissac e6b87ecd02 Reduce memory allocation events 
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
 2024-06-22 21:01:53 +02:00
Eric Coissac 54a138196c Patch a bug in fasta and fastq reading 
Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
 2024-06-21 14:28:57 +02:00
Eric Coissac 818ce87bab Patch some bugs in writing files 
Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
 2024-06-19 13:15:30 +02:00
Eric Coissac 73996bb0b7 Small change in consensus weight 
Former-commit-id: 58bcc67044b82e4e1d9e0e52be336ae02ab248e9
 2024-06-19 09:11:59 +02:00
Eric Coissac a812fe8b72 debug of obimultiplex 
Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
 2024-06-18 23:38:33 +02:00
Eric Coissac 44533fb61e Bugs in the non stric tag matching algorithm 
Former-commit-id: efad98d6521322209ce22bc58fab54c7bddd19ec
 2024-06-10 21:19:26 +02:00
Eric Coissac 2d4813614b Update the release Notes 
Former-commit-id: 5611fb13809c5cc45a515be5d62aac61e6fc51ad
 2024-06-07 09:11:06 +02:00
Eric Coissac 3a7661f324 obimultiplex2 in now obimultiplex 
Former-commit-id: ee6f5e15a3f1729dfc2806d039c842c9c3bdd343
 2024-06-07 09:04:37 +02:00
Eric Coissac bc12b1aaa2 Add a complete documented example of the new obitag format 
Former-commit-id: 748a2357cc29aefd3bdee55c85c06eab31fb9fe1
 2024-06-06 23:44:23 +02:00
Eric Coissac e47b50de7f Patch a bug in seting of the tag delimiter with an upper case 
Former-commit-id: a3962400b7ab91b25102c4c7c35cd824bf7ceaf0
 2024-06-06 23:25:16 +02:00
Eric Coissac 1b43fa4247 First complete version of obimultiplex2 
Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
 2024-06-06 23:11:13 +02:00
Eric Coissac 985c91452a correction of bug and format in obisplit 
Former-commit-id: d600713a5f48c8d682971be9b8a09a1c021be28c
 2024-06-05 17:18:44 +02:00
Eric Coissac 87a7219ab4 Adds the reading of the options through the csv formated ngsfilter configuration file 
Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238
 2024-06-04 22:57:07 +02:00
Eric Coissac c8ad96f5e6 First fonctionnal version with fixed tag length and strict matching 
Former-commit-id: 5affee2c7c66dd1da5b17c2d1ea64f44db76df50
 2024-06-04 21:46:09 +02:00
Eric Coissac a0a9fb461c trial on rewriting obimultiplex 
Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
 2024-06-04 16:50:07 +02:00
Eric Coissac 65f5109957 Plenty of small bugs 
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
 2024-06-04 16:49:12 +02:00
Eric Coissac e843d2aa5c Patch a tricky bug in parsing of json header and save the last sequence from files 
Former-commit-id: bfe3d0e9eb8e65113699d535bd1d9a5fe0d3ce1d
 2024-06-04 13:46:23 +02:00
Eric Coissac aa42df326a Correct a bug in the fastq reader affecting the quality of the last record of each chunk 
Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
 2024-06-04 11:57:16 +02:00
Eric Coissac 411124d1b3 Add automatic rules to manage version number 
Former-commit-id: f4fcc1927f4169025c1d8cc88c5f3abcdc76037c
 2024-06-01 17:26:16 +02:00
Eric Coissac 38945d0a41 Adds the --template option to obimultiplex 
Former-commit-id: 349e9f278abd6a6c258f31d99ea04853a79c62de
 2024-05-31 11:34:06 +02:00
Eric Coissac 4487723d14 Adds possibility to provide the ngsfilter configuration as a CSV file 
Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
 2024-05-31 11:08:20 +02:00
Eric Coissac dbeb44bc79 Patch a bug in the quality string writing 
Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
 2024-05-31 11:07:25 +02:00
Eric Coissac 3e1d9a41ec Adds more format checking during fasta parsing 
Former-commit-id: fbc3d9c923936287a591f01f9401b710b584aa14
 2024-05-30 18:12:06 +02:00
Eric Coissac dd9307a4cd Swich to the system min and max functions and remove the version from obiutils 
Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
 2024-05-30 08:27:24 +02:00
Eric Coissac 98b3bc2a8c Patch a bug on the reading of each last sequence of a chunck in the fasta reader 
Former-commit-id: eacf64112582befa4751f66352999a28abf349f7
 2024-05-27 10:17:17 +02:00
Eric Coissac d249902073 A lot of changes and debug... A complete first 
version of the recipy in the Cookbook about
avaluating primers


Former-commit-id: 6c816f5546b3f472f6930d112abe3da04d2d5a55
 2024-05-26 12:56:29 +02:00
Eric Coissac 55ce36f329 Update of obipcr and homogenization of logging 
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
 2024-05-16 15:18:30 +02:00
Eric Coissac 61be8a55b1 Merge obiminion and obiconsensus 
Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c
 2024-05-14 17:53:32 +02:00
Eric Coissac 7fcb0538a3 Cleaning of obiminion 
Former-commit-id: 75148afd70e5006cc6855bcddc86506b099761a1
 2024-05-14 11:45:46 +02:00
Eric Coissac 017030bcce Add obiminion first version 
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
 2024-05-14 08:16:12 +02:00
Eric Coissac 9e63013bc2 Correction on obiformat of bug leading to partial parsing and add godocs 
Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
 2024-05-07 10:54:12 +02:00
Eric Coissac 5b98393a68 Refactor sequence file reading 
Former-commit-id: 3dcb96e68da648d72bb585da047e3496427d7851
 2024-05-01 00:50:23 +02:00
Eric Coissac 33d4d63acd Adds a warning on max-cpu = 1 
Former-commit-id: ed02328d7d0e36b7c6b77ea776c0bde7c0eb64f3
 2024-04-30 13:27:19 +02:00
Eric Coissac d30d736e48 Simplify the workers code by removing dupplicates 
Former-commit-id: 638fcf8d88dd93755d1ec89c8fe92f6ed3f733df
 2024-04-30 12:22:22 +02:00
Eric Coissac f37477b26c Progress bar are automagically disabled if stderr is redirected 
Former-commit-id: 20a3a22db7dcf530b9e9cad9090b46f22db0d078
 2024-04-22 12:23:59 +02:00
Eric Coissac 8f08959ebb Make the --no-progressbar option effective on graph building progress too. 
Former-commit-id: 3fabecfc9de69ad406d6840c8f821c16eebaef46
 2024-04-22 12:01:43 +02:00