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e8c55a2b6b
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optimize sequence readers and patch a bug in the format guesser
Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
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2023-10-13 21:52:57 +02:00 |
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ddf0f2cede
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Add the -D (--delta) option to obipcr
Former-commit-id: 753079807faaddb23e03fd6350125bfa67f98c7f
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2023-10-13 17:04:10 +02:00 |
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157c26cdc7
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Patch a bug in the fasta and fastq readers
Former-commit-id: 4998f157a90a6b077124d87d4a5cde0dd075d1ce
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2023-10-13 14:21:27 +02:00 |
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6acce603a1
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Patch a bug in the new version of setDefinition()
Former-commit-id: 9a382d9891e158dd3d445bfb4053691739ca9fdb
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2023-10-05 07:48:47 +02:00 |
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0a8f7afb2a
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Patch sequence writers to remove definition from header when json format is used.
Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
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2023-10-05 07:31:31 +02:00 |
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d23a911080
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Change the way sequence definition are managed. They are now when present stored as an attribute
Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
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2023-10-05 07:21:12 +02:00 |
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5c30ec354f
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Go implementation of fasta and fastq parser
Former-commit-id: 3f4fd355c169afbef2d5fef1f5e407aabb71d031
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2023-09-03 19:16:37 +02:00 |
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6d1ac60c48
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Convert first nucleotide of sequence to lower case in fasta reader
Former-commit-id: 856bb3a39a4f1143a34b1f8b4d8d12b0151c0c3e
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2023-09-01 09:40:02 +02:00 |
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62b57f4ede
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A go implementation of the fasta reader
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
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2023-09-01 09:30:12 +02:00 |
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3f8c0d6a2f
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Replace MakeBioSequence call by NewBioSequence call,
Implements a new file format guesser
Adds some more API doc
Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
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2023-08-30 19:59:46 +02:00 |
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c2533667b2
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Tag a Fatal bug release 4.0.5
Former-commit-id: 10b27c6d3867756d3159ef22eefd75db3fab84d0
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2023-08-29 18:32:00 +02:00 |
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8ebf368a8f
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Patch an extra mutex unlock in biosequence constructor
Former-commit-id: 87a20acb5def1c6832e114726276c638f0ca9efe
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2023-08-29 18:24:02 +02:00 |
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45ea4dacf7
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Every small changes to include into Release 4.0.4
Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
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2023-08-27 17:22:51 +02:00 |
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d437fba535
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Doc change
Former-commit-id: 5cd4547147804f887ad699d4886702545584ba32
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2023-08-27 17:06:36 +02:00 |
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0303244e3c
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Adds doc and unit tests
Former-commit-id: 6f60f97947111b4fc65cc0e72d18770ba6094088
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2023-08-27 16:48:15 +02:00 |
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cd7414d471
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Unit tests for obiutils.Set
Former-commit-id: 352ec0da26184d13f74a34a1ad70ca4edef7e4a6
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2023-08-27 16:40:41 +02:00 |
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bfe6fa630a
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Adds unit tests
Former-commit-id: 33e9d9a8a370afc3d6318c6972de02a957fa3098
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2023-08-27 16:23:09 +02:00 |
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5b7d88ccc6
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Patch a bug in the Dim function
Former-commit-id: 004545e81df4dcf33294fb062de8204692035cdf
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2023-08-27 16:18:10 +02:00 |
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18d3eec24a
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Change the annotation locker to a pointer to mutex to avoid coying mutex
Former-commit-id: d179d8753b593183312bd11184e5d8ebb301138a
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2023-08-27 16:00:35 +02:00 |
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7b7128196a
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small refactoring including doc
Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
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2023-08-27 15:52:28 +02:00 |
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f1025f97b8
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Add a missing prototype
Former-commit-id: 6c5b476f30adba6e0eb41e11e152124090c3f04e
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2023-08-27 15:51:23 +02:00 |
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9bf006af93
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A first prototype for the space of sequences
Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195
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2023-08-27 14:58:55 +02:00 |
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cbd42d5b30
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Implements a parallel version of Kmeans
Former-commit-id: 58ab24b9b274451e00eea0275249234e2c2ea09b
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2023-08-26 01:26:40 +02:00 |
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077f3b5bb5
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first trial of obilandmark
Former-commit-id: 00a50bdbf407b03dfdc385a848a536559f5966a5
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2023-08-25 23:23:23 +02:00 |
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2a11adb346
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Add some doc and switch to the parallel gzip library
Former-commit-id: 2c1187001f989ba3de5895f516d4c8b54d52a4c4
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2023-08-25 14:36:38 +02:00 |
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8a98210103
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A small bug in logging and API documentation
Former-commit-id: 1ab4534581987586741db13d3453db52973524fe
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2023-08-14 15:21:30 +02:00 |
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845c76abeb
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documentation updates
Former-commit-id: 39653082c9cd026299f6fcabef7446d569704e1f
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2023-08-14 15:20:02 +02:00 |
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70a77c9ec6
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Adds doc
Former-commit-id: e720718686da480e1abd4302ebff145aeee5eb4a
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2023-08-14 10:04:16 +02:00 |
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fd4c7c2572
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Adds some docs
Former-commit-id: 7e96983ed707b2a574425799c32c32243f4876cf
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2023-08-14 00:12:17 +02:00 |
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be47ec909c
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add the --skip-empty option
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
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2023-07-17 14:24:02 +02:00 |
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b44fcfb2a0
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Correct a bug related to the renaming of the forward_mismatch and reverse_mismatch to forward_error and reverse_error
Former-commit-id: c0d6cfda0d8e50364616fd79313c5711ed7bb43e
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2023-06-08 16:40:03 +02:00 |
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1cedc0765d
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update release note and the install script
Former-commit-id: 11db481e26f3f5099b9ea8b2d66658d47f2992b1
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2023-06-07 17:54:02 +02:00 |
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d46f6b06c5
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several small changes
Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96
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2023-06-07 17:50:10 +02:00 |
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49fa1a76cb
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correction in obitag to save partially indexed reference db
Former-commit-id: ba1e5ce42ac77b143d20fd8903a6e157d83c09f5
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2023-06-07 17:48:38 +02:00 |
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63dc67f344
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add debuging log
Former-commit-id: 7543d12838463bd9d9bcb365e5e6772b51daa5ec
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2023-06-07 17:47:58 +02:00 |
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e29dacc1ba
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change default of output options and add the actual printing of the column sequence
Former-commit-id: bc3adf7ddecca3683def980ffc8a8bd63410ab3a
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2023-06-07 17:47:06 +02:00 |
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7f08f58336
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several correction in obitag and adds the --save-db option
Former-commit-id: b3a15b1a1b3971388a8749faaba519028f6e976c
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2023-06-07 17:45:11 +02:00 |
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8895381c92
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Correct a bug when sequence length is shorter than kmer size in debruijngraph
Former-commit-id: 56cd670d24065d8774abdcbf685ff4a13e7c4132
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2023-06-07 17:43:32 +02:00 |
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68a290d564
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Update install_obitools.sh
Former-commit-id: c0a6d779f1a4e94548f3c30f2ba4ba8e8878f16f
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2023-06-06 10:13:13 +02:00 |
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3e27c1f432
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Update install_obitools.sh
Former-commit-id: 31f640c6ef2e7fc5faa472b773f8cdd9a9cdb309
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2023-06-06 10:11:37 +02:00 |
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19e43e8916
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Update install_obitools.sh
Former-commit-id: 47a81f78f528c08abf8d4098f1c5b9052c6b3759
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2023-06-06 10:02:24 +02:00 |
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c6b59c0c80
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Update install_obitools.sh to print on stderr
Former-commit-id: 830b4b12b2462bc73ad7a97718741c0f68899034
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2023-06-06 09:21:16 +02:00 |
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f6628a1ba2
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Update install script
Former-commit-id: 0dc6b22490fe6228e0099bd96fb1c53ee2754f03
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2023-05-23 10:09:42 +02:00 |
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670876d3a4
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adds info
Former-commit-id: 89de557379f688ae23bfdb48b1a8ce35f57b6091
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2023-05-05 14:15:05 +02:00 |
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e9574bae07
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Small change to increase efficiency (a little)
Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb
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2023-05-05 13:33:15 +02:00 |
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3778ae9266
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Correction a a bug and transfert of the new matching rules from obirefidx to obitag
Former-commit-id: a28540f72a504ad4e7e8a8b6f7609116913445b4
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2023-05-05 07:37:19 +02:00 |
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88a9e38952
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Took better advantage of taxonomy structure and LCA upperbound base on common word. Accelleration by a factor two of obirefidx compared to previous version.
Former-commit-id: 35f40498d642058e9dbff20128d11303a314018d
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2023-05-04 09:32:47 +02:00 |
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870cb1aabb
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New refdb indexing algorithm
Former-commit-id: 7ae480cec5d277a08620a2e666b5c9b69bb6cd73
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2023-05-03 15:32:31 +02:00 |
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e8bd130ffc
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Tagging of the 4.0.3 version.
Former-commit-id: 347d9d3340d722846e69569a8eccad40344ae00d
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2023-05-02 11:02:58 +02:00 |
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bffcab1096
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Complete release notes and change obiannotate options accordingly
Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
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2023-05-02 11:01:26 +02:00 |
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