Commit Graph

101 Commits

Author SHA1 Message Date
03f4e88a17 Fisrt functional version 2024-11-14 19:10:23 +01:00
241f2286f2 remove the slice pool management 2024-09-24 16:31:30 +02:00
05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
65ae82622e correction of several small bugs 2024-09-03 06:08:07 -03:00
bdb96dda94 Adds the obimicrosat command 2024-08-05 15:31:20 +02:00
67665a6b40 Xprize update
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
2024-07-25 18:09:03 -04:00
4e4fac491f Fisrt versin of the two levels indexing
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
2024-07-12 15:17:48 +02:00
c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
2024-07-10 15:21:42 +02:00
bd855c4965 Adds CSV as an input format
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
2024-07-03 21:04:27 +02:00
fd663357b5 First version of obicleandb...
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
2024-07-01 17:12:42 +02:00
93f9dcb95f Reducing memory allocation events
Former-commit-id: c94e79ba116464504580fc397270ead154063971
2024-06-22 22:32:31 +02:00
e6b87ecd02 Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
2024-06-22 21:01:53 +02:00
54a138196c Patch a bug in fasta and fastq reading
Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
2024-06-21 14:28:57 +02:00
818ce87bab Patch some bugs in writing files
Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
2024-06-19 13:15:30 +02:00
65f5109957 Plenty of small bugs
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
2024-06-04 16:49:12 +02:00
aa42df326a Correct a bug in the fastq reader affecting the quality of the last record of each chunk
Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
2024-06-04 11:57:16 +02:00
dbeb44bc79 Patch a bug in the quality string writing
Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
2024-05-31 11:07:25 +02:00
55ce36f329 Update of obipcr and homogenization of logging
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
2024-05-16 15:18:30 +02:00
017030bcce Add obiminion first version
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
2024-05-14 08:16:12 +02:00
9e63013bc2 Correction on obiformat of bug leading to partial parsing and add godocs
Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
2024-05-07 10:54:12 +02:00
f4d71d4a66 Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr
Former-commit-id: 7999b917d07545271036af6e66f53aea27fc6e7b
2024-03-11 10:54:37 +01:00
7bd073ccd4 First version of obisplit and patch a bug in the new workers API
Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
2024-03-03 11:16:24 -04:00
0f3871d203 Change the API of workers
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
2024-03-02 16:03:46 -04:00
23758b00f6 Patch a bug in the embl reader and adds some doc
Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
2024-01-31 15:43:02 +01:00
3c48bafab0 patch a low level bug in EnsureCapacity
Former-commit-id: 2d50dc6923e7cfca9b864fb885577c1d1f936fc1
2024-01-16 20:51:45 +01:00
2caaa62485 Implements the kmeans++ algo to select the landmarks in the geometric method
Former-commit-id: 732404a0dc6d7276e4e479dd2481aa4bd42d4ce5
2023-12-11 16:07:03 +01:00
8d77cc4133 Change path of the obitools pkg
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
ce66b0af2f Patch a bug in the pair-end alignement in case of equality between scores.
Former-commit-id: bbdb761a98b76f2421d1f0a72960e72b13b6e626
2023-11-24 09:59:29 +01:00
2e0c1bd801 Correct the number of workers
Former-commit-id: febbccfb853263e0761ecfccb0f09c8c1bf88475
2023-11-22 09:46:30 +01:00
5ea2b8afcf a first version of obisummary
Former-commit-id: cca1019d82a14a322f46a20890b996b5c7491d41
2023-11-09 22:33:06 +02:00
a96ecb4837 Adds some unit test
Former-commit-id: b1a59df1c87187a1538f30c447d42bbe96402419
2023-11-08 11:13:56 +02:00
dedf125f6e Patch a bug in Subsequence and adds few unit tests.
Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383
2023-11-08 10:16:34 +02:00
61c30f9b6a Patch rev complement and first implementation of --auto in obicsv
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
2023-11-07 09:37:07 +02:00
6acce603a1 Patch a bug in the new version of setDefinition()
Former-commit-id: 9a382d9891e158dd3d445bfb4053691739ca9fdb
2023-10-05 07:48:47 +02:00
d23a911080 Change the way sequence definition are managed. They are now when present stored as an attribute
Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
2023-10-05 07:21:12 +02:00
62b57f4ede A go implementation of the fasta reader
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
2023-09-01 09:30:12 +02:00
3f8c0d6a2f Replace MakeBioSequence call by NewBioSequence call,
Implements a new file format guesser
Adds some more API doc


Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
2023-08-30 19:59:46 +02:00
8ebf368a8f Patch an extra mutex unlock in biosequence constructor
Former-commit-id: 87a20acb5def1c6832e114726276c638f0ca9efe
2023-08-29 18:24:02 +02:00
18d3eec24a Change the annotation locker to a pointer to mutex to avoid coying mutex
Former-commit-id: d179d8753b593183312bd11184e5d8ebb301138a
2023-08-27 16:00:35 +02:00
7b7128196a small refactoring including doc
Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
2023-08-27 15:52:28 +02:00
9bf006af93 A first prototype for the space of sequences
Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195
2023-08-27 14:58:55 +02:00
d46f6b06c5 several small changes
Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96
2023-06-07 17:50:10 +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
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
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
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
27d6c60e25 Add the possibility to look for patterns allowing indels.
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
2023-03-20 15:28:24 +07:00