|
|
d46f6b06c5
|
several small changes
Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96
|
2023-06-07 17:50:10 +02:00 |
|
|
|
63dc67f344
|
add debuging log
Former-commit-id: 7543d12838463bd9d9bcb365e5e6772b51daa5ec
|
2023-06-07 17:47:58 +02:00 |
|
|
|
e29dacc1ba
|
change default of output options and add the actual printing of the column sequence
Former-commit-id: bc3adf7ddecca3683def980ffc8a8bd63410ab3a
|
2023-06-07 17:47:06 +02:00 |
|
|
|
7f08f58336
|
several correction in obitag and adds the --save-db option
Former-commit-id: b3a15b1a1b3971388a8749faaba519028f6e976c
|
2023-06-07 17:45:11 +02:00 |
|
|
|
8895381c92
|
Correct a bug when sequence length is shorter than kmer size in debruijngraph
Former-commit-id: 56cd670d24065d8774abdcbf685ff4a13e7c4132
|
2023-06-07 17:43:32 +02:00 |
|
|
|
e9574bae07
|
Small change to increase efficiency (a little)
Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb
|
2023-05-05 13:33:15 +02:00 |
|
|
|
3778ae9266
|
Correction a a bug and transfert of the new matching rules from obirefidx to obitag
Former-commit-id: a28540f72a504ad4e7e8a8b6f7609116913445b4
|
2023-05-05 07:37:19 +02:00 |
|
|
|
88a9e38952
|
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
|
2023-05-04 09:32:47 +02:00 |
|
|
|
870cb1aabb
|
New refdb indexing algorithm
Former-commit-id: 7ae480cec5d277a08620a2e666b5c9b69bb6cd73
|
2023-05-03 15:32:31 +02:00 |
|
|
|
bffcab1096
|
Complete release notes and change obiannotate options accordingly
Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
|
2023-05-02 11:01:26 +02:00 |
|
|
|
60c187404d
|
Restore old obisort and add LCA functionnality to obiannotate.
Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
|
2023-05-02 10:43:22 +02:00 |
|
|
|
e9dcacbf24
|
Correction of one base deletion in the consensus
Former-commit-id: 6aabd8bfdb5263a2285718cb2eca27628c0e717c
|
2023-04-19 09:12:12 +02:00 |
|
|
|
450e54f4aa
|
Rename forward and reverse mitmatches tags
Former-commit-id: faa0f41bf725da3c416326572cc90701704092da
|
2023-04-18 12:08:13 +02:00 |
|
|
|
9bac7f387a
|
Patch a bug in the help messages
Former-commit-id: 61ffea65db66215c072139540ec19c11c52efbbc
|
2023-04-17 11:32:10 +02:00 |
|
|
|
71023423e6
|
Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
|
2023-04-07 17:45:22 +02:00 |
|
|
|
dbf69b7da5
|
Patch a bug in obiseq.GetSlice
Former-commit-id: ab1a49c3d9bf19585e36842ecc15fa17afbcbf57
|
2023-04-07 17:44:11 +02:00 |
|
|
|
74babcec55
|
adds the contains function to the language
Former-commit-id: 5fb3629b56aa0180c388333e4bfbbd199edf4cf2
|
2023-04-07 16:54:57 +02:00 |
|
|
|
d70bb45f3f
|
Small change in parallelisation tuning
Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
|
2023-04-05 14:15:47 +02:00 |
|
|
|
3f69fa41d6
|
Patch a bug for multiple amplicon per sequence.
Former-commit-id: b252d2de8e1a85d65c2951aa1958ee038e35741d
|
2023-03-31 15:10:25 +02:00 |
|
|
|
84b3e4d097
|
Reduce memomry inprint of obipcr
Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
|
2023-03-31 10:53:53 +02:00 |
|
|
|
e7b9ba3f30
|
Limit allocation during genbank parsing
Former-commit-id: eee3c1fa7ffb79943109ee32dbf21e78bf11b14f
|
2023-03-28 22:42:58 +07:00 |
|
|
|
4bf041be62
|
Add some option to the obiconsensus command
Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028
|
2023-03-28 21:23:27 +07:00 |
|
|
|
e863dc456a
|
Add an option --pprof
Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
|
2023-03-28 20:07:26 +07:00 |
|
|
|
988ae79989
|
Optimize memory allocation of the apat algorithms
Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
|
2023-03-28 19:37:05 +07:00 |
|
|
|
21819cd41e
|
Add some geometry data to the GML edges
Former-commit-id: 81022c8b6916819e5351026ebabe9641856cc06d
|
2023-03-28 11:43:46 +07:00 |
|
|
|
bc82422bc5
|
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
|
2023-03-28 11:43:04 +07:00 |
|
|
|
e8a8f746d3
|
few bug in the graph algorithm
Former-commit-id: b61bdd9f671e2f5e90d32c1beac1ed84efa5e05c
|
2023-03-27 22:43:45 +07:00 |
|
|
|
a33e471b39
|
First attempt for obiconsensus... The graph traversing algorithm is too simple
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
|
2023-03-27 19:51:10 +07:00 |
|
|
|
d5e84ec676
|
rename goutils to obiutils
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
|
2023-03-24 10:25:12 +07:00 |
|
|
|
42aae88520
|
complete the correction related to the tag detection
Former-commit-id: 98326fb0f27788de672cdbd686b32b4dc2615038
|
2023-03-23 11:52:08 +07:00 |
|
|
|
57474214e7
|
Patch excessive log in obimultiplex and an error in detecting the tag.
Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
|
2023-03-23 11:40:24 +07:00 |
|
|
|
7ed567fbad
|
Make the --help or -h options working when mandatory options are declared
Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
|
2023-03-21 22:01:20 +07:00 |
|
|
|
d09011fac2
|
Finalyse the obimultiplex with indels
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
|
2023-03-21 22:01:02 +07:00 |
|
|
|
27d6c60e25
|
Add the possibility to look for patterns allowing indels.
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
|
2023-03-20 15:28:24 +07:00 |
|
|
|
5fbe52368c
|
Patch the empty batch bug
Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e
|
2023-03-07 20:16:06 +07:00 |
|
|
|
b3922c3896
|
Produce less weird crash on non existing files
Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
|
2023-03-07 17:34:25 +07:00 |
|
|
|
d88de15cdc
|
Refactoring codes for removing buffer size options. An some other changes...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
|
2023-03-07 11:12:13 +07:00 |
|
|
|
b9bf88d4df
|
Adds some new columns to the ratio file.
Former-commit-id: 1b2d6116622b754670e86b683077aceac2db4ce7
|
2023-02-25 15:56:23 +01:00 |
|
|
|
6f28d2ab68
|
Patch a bug introduced by the new model for paired sequences
Former-commit-id: 7947e28ac8252b7ed46bdb9175077d412bad0aca
|
2023-02-24 10:23:26 +01:00 |
|
|
|
072b85e155
|
change the model for representing paired reads and extend its usage to other commands
|
2023-02-23 23:35:58 +01:00 |
|
|
|
56722895e4
|
Adds to every obitools the ability to save in gzip compressed files
|
2023-02-18 12:06:52 +01:00 |
|
|
|
1a08ad4254
|
Flush the buffered io
|
2023-02-18 07:23:14 +01:00 |
|
|
|
3e1f88b37b
|
adds the subspc function to the gval language
|
2023-02-17 23:10:43 +01:00 |
|
|
|
d04eb915b3
|
adds a directory option to obidistribute
|
2023-02-17 22:52:53 +01:00 |
|
|
|
9554a32490
|
Add capacity to obidistribute to save gzipped files
|
2023-02-17 12:52:19 +01:00 |
|
|
|
6fd426d8be
|
Update obiapat.c
|
2023-02-17 11:29:27 +01:00 |
|
|
|
9cf9d4d504
|
Update obiapat.c by removing dependancy to asprintf by using snprintf
|
2023-02-17 11:28:14 +01:00 |
|
|
|
8458c0cd8b
|
Patch a bug in the genbank reader for the sequence longer than 10kb.
|
2023-02-17 10:54:03 +01:00 |
|
|
|
ed87f821eb
|
adds the _taxid suffix to the rank taxid attributes.
|
2023-02-16 16:13:55 +01:00 |
|
|
|
2975042982
|
Adds the possiblility to append to files to obidistribute
|
2023-02-16 16:13:13 +01:00 |
|
