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6cb7a5a352
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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
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2025-06-04 09:48:10 +02:00 |
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3424d3057f
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Changes to be committed:
modified: pkg/obiformats/ngsfilter_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiutils/mimetypes.go
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2025-05-14 14:53:25 +02:00 |
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2d52322876
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Patch a bug in the obi2 annotation parser on map indexed by integers
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2025-03-27 14:54:13 +01:00 |
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5a3705b6bb
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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
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2025-03-25 16:44:46 +01:00 |
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8448783499
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Make sequence files recognized as a taxonomy
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2025-03-14 14:22:22 +01:00 |
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3a1cf4fe97
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Accelerate the speed of very long fasta sequences, and more generaly of every format
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2025-03-12 13:29:41 +01:00 |
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0339e4dffa
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Patch size limite of the filetype guesser
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2025-03-08 07:34:02 +01:00 |
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0067152c2b
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Patch the production of the ratio file
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2025-02-27 10:19:39 +01:00 |
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4774438644
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Changes to be committed:
modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
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2025-02-12 08:40:38 +01:00 |
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6a8061cc4f
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Add managment of the taxonomy alias politic
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2025-02-10 14:05:47 +01:00 |
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0df082da06
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Adds possibility to extract a taxonomy from taxonomic path included in sequence files
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2025-01-30 11:18:21 +01:00 |
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7c4042df6b
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introduce obidefault
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2025-01-27 17:12:45 +01:00 |
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9acb4a85a8
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Refactoring of the default values
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2025-01-24 18:09:59 +01:00 |
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3137c1f841
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Adds the ability to read gzip-tar file for the taxonomy dump
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2025-01-24 11:47:59 +01:00 |
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4fe0db63ff
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Patch CSV reader to use the new taxonomy system
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2024-12-20 21:30:00 +01:00 |
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ccd3b06532
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Merge branch 'master' into taxonomy
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2024-12-20 20:06:57 +01:00 |
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5d0f996625
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Patch a small bug on json write
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2024-12-20 19:42:03 +01:00 |
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795df34d1a
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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
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2024-12-19 13:36:59 +01:00 |
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f41a6fbb60
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Patch a small bug on json write
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2024-11-29 18:39:18 +01:00 |
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00b0edc15a
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refactoring of the file chunck writing
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2024-11-29 18:15:03 +01:00 |
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40fb4e9767
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reduce the memory impact of obiuniq.
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2024-11-27 13:30:16 +01:00 |
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3d06978808
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a functional new version of obifind
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2024-11-24 19:33:24 +01:00 |
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7633fc4d23
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update documentation
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2024-11-16 06:00:27 +01:00 |
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03f4e88a17
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Fisrt functional version
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2024-11-14 19:10:23 +01:00 |
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3e00d39d47
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In obimultiplex, patch a bug when no tag are associated to a primer.
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2024-10-22 14:12:20 +02:00 |
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9e8a7fd9be
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Patch a bug in fastq reader
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2024-10-20 16:07:43 +02:00 |
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05bf2bfd6c
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Add option related to agrep match on obigrep and obiannotate
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2024-09-09 16:52:13 +02:00 |
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65ae82622e
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correction of several small bugs
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2024-09-03 06:08:07 -03:00 |
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31bfc88eb9
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Patch a bug on writing to stdout, and add clearer error on openning data files
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2024-08-13 09:45:28 +02:00 |
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3f57935328
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Adjust the size of the genbank and embl buffer size
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2024-08-05 11:32:37 +02:00 |
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886b5d9a96
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Optimize memory for readers and writers
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2024-08-05 10:48:28 +02:00 |
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1b1cd41fd3
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Add some code refactoring from the blackboard branch
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2024-08-02 12:35:46 +02:00 |
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67665a6b40
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Xprize update
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
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2024-07-25 18:09:03 -04:00 |
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bd855c4965
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Adds CSV as an input format
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
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2024-07-03 21:04:27 +02:00 |
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154753de90
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Same bug but for fastq sequence writing only
Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
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2024-06-26 18:46:47 +02:00 |
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e40d0bfbe7
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Debug fasta and fastq writer when the first sequence is hudge
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
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2024-06-26 18:39:42 +02:00 |
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c1f03cb1f6
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Switch to faster json library go-json and sonic
Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
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2024-06-23 00:36:08 +02:00 |
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93f9dcb95f
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Reducing memory allocation events
Former-commit-id: c94e79ba116464504580fc397270ead154063971
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2024-06-22 22:32:31 +02:00 |
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e6b87ecd02
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Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
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2024-06-22 21:01:53 +02:00 |
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54a138196c
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Patch a bug in fasta and fastq reading
Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
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2024-06-21 14:28:57 +02:00 |
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818ce87bab
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Patch some bugs in writing files
Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
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2024-06-19 13:15:30 +02:00 |
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a812fe8b72
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debug of obimultiplex
Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
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2024-06-18 23:38:33 +02:00 |
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1b43fa4247
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First complete version of obimultiplex2
Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
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2024-06-06 23:11:13 +02:00 |
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87a7219ab4
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Adds the reading of the options through the csv formated ngsfilter configuration file
Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238
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2024-06-04 22:57:07 +02:00 |
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65f5109957
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Plenty of small bugs
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
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2024-06-04 16:49:12 +02:00 |
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e843d2aa5c
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Patch a tricky bug in parsing of json header and save the last sequence from files
Former-commit-id: bfe3d0e9eb8e65113699d535bd1d9a5fe0d3ce1d
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2024-06-04 13:46:23 +02:00 |
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aa42df326a
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Correct a bug in the fastq reader affecting the quality of the last record of each chunk
Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
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2024-06-04 11:57:16 +02:00 |
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4487723d14
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Adds possibility to provide the ngsfilter configuration as a CSV file
Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
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2024-05-31 11:08:20 +02:00 |
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3e1d9a41ec
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Adds more format checking during fasta parsing
Former-commit-id: fbc3d9c923936287a591f01f9401b710b584aa14
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2024-05-30 18:12:06 +02:00 |
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dd9307a4cd
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Swich to the system min and max functions and remove the version from obiutils
Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
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2024-05-30 08:27:24 +02:00 |
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