19 Commits

Author	SHA1	Message	Date
Eric Coissac	6ee8750635	Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting ... Replace SplitInTwo calls with LeftSplitInTwo or RightSplitInTwo depending on the intended split direction. In fastseq_json_header.go, extract rank from suffix without splitting; in biosequenceslice.go and taxid.go, use LeftSplitInTwo to split from the left; add RightSplitInTwo utility function for splitting from the right.	2026-03-12 18:41:28 +01:00
Eric Coissac	6cb7a5a352	Changes to be committed: ... modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitaxonomy/main.go modified: pkg/obiformats/csvtaxdump_read.go modified: pkg/obiformats/ecopcr_read.go modified: pkg/obiformats/ncbitaxdump_read.go modified: pkg/obiformats/ncbitaxdump_readtar.go modified: pkg/obiformats/newick_write.go modified: pkg/obiformats/options.go modified: pkg/obiformats/taxonomy_read.go modified: pkg/obiformats/universal_read.go modified: pkg/obiiter/extract_taxonomy.go modified: pkg/obioptions/options.go modified: pkg/obioptions/version.go new file: pkg/obiphylo/tree.go modified: pkg/obiseq/biosequenceslice.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonset.go modified: pkg/obitools/obiconvert/sequence_reader.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitaxonomy/obitaxonomy.go modified: pkg/obitools/obitaxonomy/options.go deleted: sample/.DS_Store	2025-06-04 09:48:10 +02:00
Eric Coissac	5a3705b6bb	Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.	2025-03-25 16:44:46 +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	00b0edc15a	refactoring of the file chunck writing	2024-11-29 18:15:03 +01:00
Eric Coissac	241f2286f2	remove the slice pool management	2024-09-24 16:31:30 +02:00
Eric Coissac	4e4fac491f	Fisrt versin of the two levels indexing ... Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69	2024-07-12 15:17:48 +02:00
Eric Coissac	3c48bafab0	patch a low level bug in EnsureCapacity ... Former-commit-id: 2d50dc6923e7cfca9b864fb885577c1d1f936fc1	2024-01-16 20:51:45 +01:00
Eric Coissac	2caaa62485	Implements the kmeans++ algo to select the landmarks in the geometric method ... Former-commit-id: 732404a0dc6d7276e4e479dd2481aa4bd42d4ce5	2023-12-11 16:07:03 +01:00
Eric Coissac	8d77cc4133	Change path of the obitools pkg ... Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65	2023-11-29 12:14:37 +01:00
Eric Coissac	61c30f9b6a	Patch rev complement and first implementation of --auto in obicsv ... Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764	2023-11-07 09:37:07 +02:00
Eric Coissac	62b57f4ede	A go implementation of the fasta reader ... Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa	2023-09-01 09:30:12 +02:00
Eric Coissac	988ae79989	Optimize memory allocation of the apat algorithms ... Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede	2023-03-28 19:37:05 +07:00
Eric Coissac	072b85e155	change the model for representing paired reads and extend its usage to other commands	2023-02-23 23:35:58 +01:00
Eric Coissac	cfddc78161	Patch an aligment bug on obipairing	2023-01-25 13:22:56 +01:00
Eric Coissac	62968aaa26	patch the Taxid method	2022-08-23 11:06:51 +02:00
Eric Coissac	2e7c1834b0	Big change iin the data model, and a first version of obiuniq	2022-02-21 19:00:23 +01:00
Eric Coissac	64676db3f4	Connect the command line options to the algorithm of obipairing	2022-01-16 17:30:30 +01:00
Eric Coissac	576a9f4d2d	A global version of a Slice pool	2022-01-16 00:21:42 +01:00