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812 Commits 13 Branches 41 Tags
f727ae930f3508ca80581b6647ee83109cc89e5b
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26 Commits
Author SHA1 Message Date
Eric Coissac 438893d910 refactor: improve FASTQ error messages with explicit filenames 
The options system now tracks explicit file paths via a new accessor and functional option. This filename is threaded through the FASTQ parser chain to replace generic source references in fatal error messages, providing clearer, file-specific diagnostics without altering core parsing logic or test suites.
 2026-08-19 16:47:36 +02:00
Eric Coissac 43b285587e Debug on taxonomy extraction and CSV conversion 2025-07-07 15:29:40 +02:00
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 8448783499 Make sequence files recognized as a taxonomy 2025-03-14 14:22:22 +01:00
Eric Coissac 7c4042df6b introduce obidefault 2025-01-27 17:12:45 +01:00
Eric Coissac 40fb4e9767 reduce the memory impact of obiuniq. 2024-11-27 13:30:16 +01:00
Eric Coissac 1b1cd41fd3 Add some code refactoring from the blackboard branch 2024-08-02 12:35:46 +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 3d1d9f32df Make obiconsensus using the count of the sequences 
Former-commit-id: 7fc5292aeb225843a86cd85591a5405e35125e3d
 2024-04-03 12:58:32 +02:00
coissac 1542ce4c63 Work on EMBL and Genbank parser efficienct 
Former-commit-id: 309cc9ce4eea4c8085d7d4451a66a81710532f07
 2024-02-20 13:23:07 +01:00
coissac 8d77cc4133 Change path of the obitools pkg 
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
 2023-11-29 12:14:37 +01:00
coissac 61c30f9b6a Patch rev complement and first implementation of --auto in obicsv 
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
 2023-11-07 09:37:07 +02:00
coissac 62b57f4ede A go implementation of the fasta reader 
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
 2023-09-01 09:30:12 +02:00
coissac be47ec909c add the --skip-empty option 
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
 2023-07-17 14:24:02 +02:00
coissac a33e471b39 First attempt for obiconsensus... The graph traversing algorithm is too simple 
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
 2023-03-27 19:51:10 +07:00
coissac d88de15cdc Refactoring codes for removing buffer size options. An some other changes... 
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
 2023-03-07 11:12:13 +07:00
coissac 072b85e155 change the model for representing paired reads and extend its usage to other commands 2023-02-23 23:35:58 +01:00
coissac 56722895e4 Adds to every obitools the ability to save in gzip compressed files 2023-02-18 12:06:52 +01:00
coissac 9554a32490 Add capacity to obidistribute to save gzipped files 2023-02-17 12:52:19 +01:00
coissac 2975042982 Adds the possiblility to append to files to obidistribute 2023-02-16 16:13:13 +01:00
coissac 2d375df94f move the worker class to the obiseq package 2023-01-22 22:39:13 +01:00
coissac eaf65fbcce Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools 2022-02-24 07:08:40 +01:00
coissac 2e7c1834b0 Big change iin the data model, and a first version of obiuniq 2022-02-21 19:00:23 +01:00
coissac 3586ecc483 second version of obidistribute and a first buggy version of obiuniq 2022-02-15 00:47:02 +01:00
coissac b9b9c0f179 Patch module name from oa2 to obitools 2022-01-13 23:43:01 +01:00
coissac f53bf1b804 First commit 2022-01-13 23:27:39 +01:00