181 Commits

Author	SHA1	Message	Date
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	241f2286f2	remove the slice pool management	2024-09-24 16:31:30 +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	1b1cd41fd3	Add some code refactoring from the blackboard branch	2024-08-02 12:35:46 +02:00
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	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	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	44533fb61e	Bugs in the non stric tag matching algorithm ... Former-commit-id: efad98d6521322209ce22bc58fab54c7bddd19ec	2024-06-10 21:19:26 +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	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	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	65f5109957	Plenty of small bugs ... Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8	2024-06-04 16:49:12 +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	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	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	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
Eric Coissac	0a2ea962db	obitag bug ... Former-commit-id: e6f8750d8db74c0b175c4a93d5b58bd84f293d52	2024-04-03 16:28:06 +02:00
Eric Coissac	3d1d9f32df	Make obiconsensus using the count of the sequences ... Former-commit-id: 7fc5292aeb225843a86cd85591a5405e35125e3d	2024-04-03 12:58:32 +02:00
Eric Coissac	bf41d16e67	Patch a bug in obitag on the identification of the best match ... Former-commit-id: e551b3b83e79a517dd5409ea8112fb005c39c2ee	2024-04-03 12:30:40 +02:00
Eric Coissac	b428c48353	Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning ... Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f	2024-03-18 19:11:41 +01:00
Eric Coissac	aa07ef2127	adds a obisplit_nfrg attribute ... Former-commit-id: b8d32ba8f32a77457747f6a4616432feb5313396	2024-03-13 10:41:53 +01:00
Eric Coissac	65933ca031	A working version of obiscript ... Former-commit-id: 6652ac7dfe681e6c92a2946c34a8248bd62996b0	2024-03-08 21:39:05 +01:00
Eric Coissac	b40015deb7	first preliminary version of obiscript. ... Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90	2024-03-06 12:56:44 -03:00