Eric Coissac
3d2e205722
Refactor rope scanner and add FASTQ rope parser
...
This commit refactors the rope scanner implementation by renaming gbRopeScanner to ropeScanner and extracting the common functionality into a new file. It also introduces a new FastqChunkParserRope function that parses FASTQ chunks directly from a rope without Pack(), enabling more efficient memory usage. The existing parsers are updated to use the new rope-based parser when available. The BioSequence type is enhanced with a TakeQualities method for more efficient quality data handling.
2026-03-10 16:47:03 +01:00
Eric Coissac
1342c83db6
Use NewBioSequenceOwning to avoid unnecessary sequence copying
...
Replace NewBioSequence with NewBioSequenceOwning in genbank_read.go to take ownership of sequence slices without copying, improving performance. Update biosequence.go to add the new TakeSequence method and NewBioSequenceOwning constructor.
2026-03-10 15:51:35 +01:00
Eric Coissac
5a3705b6bb
Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
2025-03-25 16:44:46 +01:00
Eric Coissac
9acb4a85a8
Refactoring of the default values
2025-01-24 18:09:59 +01:00
Eric Coissac
ccd3b06532
Merge branch 'master' into taxonomy
2024-12-20 20:06:57 +01:00
Eric Coissac
d29a56dcbf
Changes to be committed:
...
modified: Release-notes.md
modified: pkg/obialign/pairedendalign.go
modified: pkg/obilua/obiseq.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/biosequence.go
modified: pkg/obitools/obipairing/pairing.go
2024-11-27 09:56:22 +01:00
Eric Coissac
7884a74f9c
Patch a bug in obitagpcr
2024-11-18 21:10:47 +01:00
Eric Coissac
03f4e88a17
Fisrt functional version
2024-11-14 19:10:23 +01:00
Eric Coissac
241f2286f2
remove the slice pool management
2024-09-24 16:31:30 +02:00
Eric Coissac
65ae82622e
correction of several small bugs
2024-09-03 06:08:07 -03:00
Eric Coissac
bdb96dda94
Adds the obimicrosat command
2024-08-05 15:31:20 +02:00
Eric Coissac
93f9dcb95f
Reducing memory allocation events
...
Former-commit-id: c94e79ba116464504580fc397270ead154063971
2024-06-22 22:32:31 +02:00
Eric Coissac
e6b87ecd02
Reduce memory allocation events
...
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
2024-06-22 21:01:53 +02:00
Eric Coissac
65f5109957
Plenty of small bugs
...
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
2024-06-04 16:49:12 +02:00
Eric Coissac
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
Eric Coissac
dbeb44bc79
Patch a bug in the quality string writing
...
Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
2024-05-31 11:07:25 +02:00
8d77cc4133
Change path of the obitools pkg
...
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
2e0c1bd801
Correct the number of workers
...
Former-commit-id: febbccfb853263e0761ecfccb0f09c8c1bf88475
2023-11-22 09:46:30 +01:00
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
9bf006af93
A first prototype for the space of sequences
...
Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195
2023-08-27 14:58:55 +02:00
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
d88de15cdc
Refactoring codes for removing buffer size options. An some other changes...
...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
2023-03-07 11:12:13 +07:00
072b85e155
change the model for representing paired reads and extend its usage to other commands
2023-02-23 23:35:58 +01:00
f97f92df72
rename the iterator class
2023-01-22 22:04:17 +01:00
20b16c0ba1
Force sequence reading to produce lowercase sequences.
...
Adds two columns to the obiclean ratio csv file
2022-11-22 15:06:09 +01:00
29563aa94e
Rename the Length methods Len to follow GO standart
2022-11-17 11:09:58 +01:00
f3ddac0f50
Small adjustment
2022-10-27 11:18:44 +02:00
8aa323dad5
Add a first version of obitag the successor of ecotag
2022-10-26 13:16:56 +02:00
f8df48338d
Several bug in annotation management
2022-10-12 23:01:47 +02:00
ebefa28cc0
Patch memory error related to []byte pool
2022-09-28 14:28:37 +02:00
6b8f4490cf
Change obiclean algorithm for a better evaluation of ratio
2022-08-31 20:38:03 +02:00
62968aaa26
patch the Taxid method
2022-08-23 11:06:51 +02:00
31c45bf46f
Adds documentation and few methods to the BioSequences
2022-08-21 17:53:19 +02:00
f14860a486
Patch header parting and formatiing
2022-05-27 11:53:29 +03:00
abcf02e488
Start to use leveled log
2022-02-24 12:14:52 +01:00
2e7c1834b0
Big change iin the data model, and a first version of obiuniq
2022-02-21 19:00:23 +01:00
9737f97084
before big changes
2022-02-18 22:53:09 +01:00
aef546dae3
Patch a bug in the recycle method
2022-02-18 10:00:15 +01:00
8dbda68746
Adds the command obimultiplex
2022-02-01 17:31:28 +01:00
64676db3f4
Connect the command line options to the algorithm of obipairing
2022-01-16 17:30:30 +01:00
576a9f4d2d
A global version of a Slice pool
2022-01-16 00:21:42 +01:00
