 coissac
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dedf125f6e
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Patch a bug in Subsequence and adds few unit tests.
Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383
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2023-11-08 10:16:34 +02:00 |
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coissac
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8f96517f3c
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small changes
Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e
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2023-11-07 21:20:45 +02:00 |
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coissac
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aa0443e484
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correction to release notes
Former-commit-id: 424819230f26bccd6f5ef26684f50e9ff477a7de
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2023-11-07 12:20:40 +02:00 |
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coissac
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f991886155
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Force json encoding to ascii
Former-commit-id: b35110f3fed5fedfc03380863ece5c95a2b9d6a7
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2023-11-07 12:10:14 +02:00 |
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coissac
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185b974d13
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Adds a JSON output format
Former-commit-id: 26f07460772c0f735bf705d473f892878d3e57f0
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2023-11-07 11:56:49 +02:00 |
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coissac
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61c30f9b6a
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Patch rev complement and first implementation of --auto in obicsv
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
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2023-11-07 09:37:07 +02:00 |
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coissac
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6a6a6f6f2c
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Correctly handle empty files
Former-commit-id: d166aa352ce4bf32739ddc2f7d1c9967918822fd
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2023-10-16 15:34:06 +02:00 |
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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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60c187404d
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Restore old obisort and add LCA functionnality to obiannotate.
Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
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2023-05-02 10:43:22 +02:00 |
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coissac
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e9dcacbf24
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Correction of one base deletion in the consensus
Former-commit-id: 6aabd8bfdb5263a2285718cb2eca27628c0e717c
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2023-04-19 09:12:12 +02:00 |
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coissac
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450e54f4aa
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Rename forward and reverse mitmatches tags
Former-commit-id: faa0f41bf725da3c416326572cc90701704092da
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2023-04-18 12:08:13 +02:00 |
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coissac
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9bac7f387a
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Patch a bug in the help messages
Former-commit-id: 61ffea65db66215c072139540ec19c11c52efbbc
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2023-04-17 11:32:10 +02:00 |
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coissac
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71023423e6
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Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
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2023-04-07 17:45:22 +02:00 |
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coissac
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dbf69b7da5
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Patch a bug in obiseq.GetSlice
Former-commit-id: ab1a49c3d9bf19585e36842ecc15fa17afbcbf57
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2023-04-07 17:44:11 +02:00 |
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coissac
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74babcec55
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adds the contains function to the language
Former-commit-id: 5fb3629b56aa0180c388333e4bfbbd199edf4cf2
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2023-04-07 16:54:57 +02:00 |
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coissac
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d70bb45f3f
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Small change in parallelisation tuning
Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
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2023-04-05 14:15:47 +02:00 |
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coissac
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2e7fc9a589
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Release 4.0.2
Former-commit-id: e516cce018691172afae26147282b4b9702f44c2
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2023-03-31 15:56:37 +02:00 |
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coissac
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3f69fa41d6
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Patch a bug for multiple amplicon per sequence.
Former-commit-id: b252d2de8e1a85d65c2951aa1958ee038e35741d
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2023-03-31 15:10:25 +02:00 |
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coissac
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84b3e4d097
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Reduce memomry inprint of obipcr
Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
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2023-03-31 10:53:53 +02:00 |
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coissac
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2c9bca5c8a
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realease-notes
Former-commit-id: 0f8e6959e3c8dea279b76bf6668b743151a9ada7
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2023-03-29 11:16:25 +07:00 |
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coissac
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e7b9ba3f30
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Limit allocation during genbank parsing
Former-commit-id: eee3c1fa7ffb79943109ee32dbf21e78bf11b14f
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2023-03-28 22:42:58 +07:00 |
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coissac
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446ba06c63
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edited .gitignore
Former-commit-id: 7090da08a2acd8d73d3c9e3aced387862bcc9822
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2023-03-28 21:31:31 +07:00 |
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coissac
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0746c95f4f
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Update the package dependencies
Former-commit-id: e3fecfd65ec03f3a354338f16c52c130ea25c7f9
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2023-03-28 21:30:25 +07:00 |
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coissac
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4bf041be62
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Add some option to the obiconsensus command
Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028
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2023-03-28 21:23:27 +07:00 |
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coissac
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e863dc456a
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Add an option --pprof
Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
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2023-03-28 20:07:26 +07:00 |
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coissac
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988ae79989
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Optimize memory allocation of the apat algorithms
Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
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2023-03-28 19:37:05 +07:00 |
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coissac
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21819cd41e
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Add some geometry data to the GML edges
Former-commit-id: 81022c8b6916819e5351026ebabe9641856cc06d
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2023-03-28 11:43:46 +07:00 |
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coissac
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bc82422bc5
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Reduce redundante call to bytes.ToLower and substitute the last call by an home made version doing the conversion in place
Former-commit-id: d9ea22f649d97be352f8dbb37acc1495df830118
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2023-03-28 11:43:04 +07:00 |
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coissac
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e8a8f746d3
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few bug in the graph algorithm
Former-commit-id: b61bdd9f671e2f5e90d32c1beac1ed84efa5e05c
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2023-03-27 22:43:45 +07:00 |
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coissac
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245230ae12
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A small correction
Former-commit-id: 2616ea6bc0e288312326bfb2542e24da22876965
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2023-03-27 19:51:38 +07:00 |
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coissac
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a33e471b39
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First attempt for obiconsensus... The graph traversing algorithm is too simple
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
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2023-03-27 19:51:10 +07:00 |
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coissac
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d5e84ec676
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rename goutils to obiutils
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
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2023-03-24 10:25:12 +07:00 |
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coissac
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42aae88520
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complete the correction related to the tag detection
Former-commit-id: 98326fb0f27788de672cdbd686b32b4dc2615038
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2023-03-23 11:52:08 +07:00 |
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coissac
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57474214e7
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Patch excessive log in obimultiplex and an error in detecting the tag.
Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
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2023-03-23 11:40:24 +07:00 |
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coissac
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98eac2360c
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adds a rule to update packages and push the corresponding updates module files
Former-commit-id: 1ffa805e74571f9d970dcb185f187dd586c1a190
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2023-03-21 22:02:18 +07:00 |
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coissac
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7ed567fbad
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Make the --help or -h options working when mandatory options are declared
Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
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2023-03-21 22:01:20 +07:00 |
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coissac
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d09011fac2
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Finalyse the obimultiplex with indels
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
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2023-03-21 22:01:02 +07:00 |
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coissac
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27d6c60e25
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Add the possibility to look for patterns allowing indels.
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
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2023-03-20 15:28:24 +07:00 |
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coissac
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5fbe52368c
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Patch the empty batch bug
Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e
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2023-03-07 20:16:06 +07:00 |
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coissac
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1e7756ec91
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Add comment on release notes
Former-commit-id: 79bc0a68e46c92cfac60d1cf25604a1bcba0ba34
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2023-03-07 17:36:35 +07:00 |
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coissac
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9a48614a9b
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Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4
Former-commit-id: 45c52be778d3d5c61db438c18c38a85171be86cd
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2023-03-07 17:34:34 +07:00 |
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coissac
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b3922c3896
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Produce less weird crash on non existing files
Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
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2023-03-07 17:34:25 +07:00 |
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coissac
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42cf8cea73
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Update README.md
Former-commit-id: c2d9f79cceb8f059f65a417bea5041fc2abc362b
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2023-03-07 05:50:19 +01:00 |
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coissac
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7b4249b775
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Update README.md
Former-commit-id: 544600322dd3c4465bf02d99ea76c802529b9aed
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2023-03-07 05:48:50 +01:00 |
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coissac
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fbfed52508
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Tag realease 4.0.1 in release notes
Former-commit-id: 55d009baf1b975c2da397a93406d132c8a52cdd6
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2023-03-07 11:15:06 +07:00 |
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coissac
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bb0282b6a1
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Progress on the development
Former-commit-id: a8aa6fd60480d4453838d6846a08c84dd5a2f1d9
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2023-03-07 11:13:25 +07:00 |
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coissac
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d4b185b716
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Adds some new dependencies
Former-commit-id: 2f31ea6f852651e1ffca1d9ce78b17bddd26f2bb
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2023-03-07 11:12:39 +07:00 |
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coissac
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d88de15cdc
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Refactoring codes for removing buffer size options. An some other changes...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
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2023-03-07 11:12:13 +07:00 |
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coissac
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9811e440b8
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Takes into account the option parsing errors
Former-commit-id: d0b3ed0b96a72f79f887df8fbc325427e63d7a73
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2023-03-07 11:06:08 +07:00 |
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coissac
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6b52dc0700
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Correct the Makefile for a default rule
Former-commit-id: 7ac32f3f9778842fecd65cdd796b81f61b7fa41f
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2023-03-02 20:48:55 +07:00 |
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coissac
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b9bf88d4df
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Adds some new columns to the ratio file.
Former-commit-id: 1b2d6116622b754670e86b683077aceac2db4ce7
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2023-02-25 15:56:23 +01:00 |
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