Eric Coissac
3d2e205722
Refactor rope scanner and add FASTQ rope parser
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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
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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
ac0d3f3fe4
Update obiuniq for very large dataset
2025-12-18 14:11:11 +01:00
Eric Coissac
86e60aedd0
obicsv bug with stat on value map fields
2025-11-21 14:03:31 +01:00
Eric Coissac
4603d7973e
implementation de obilowmask
2025-11-18 15:30:20 +01:00
Eric Coissac
d17a9520b9
work on obiclean chimera detection
2025-10-20 17:29:47 +02:00
Eric Coissac
add9d89ccc
Patch the Min and Max values of the expression language
2025-06-19 16:43:26 +02:00
Eric Coissac
9965370d85
Manage a lock on StatsOnValues
2025-06-17 16:46:11 +02:00
Eric Coissac
8a2bb1fe82
Changes to be committed:
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modified: pkg/obioptions/version.go
modified: pkg/obiseq/merge.go
2025-06-17 12:11:35 +02:00
Eric Coissac
efc3f3af29
Patch a concurrent access problem
2025-06-17 12:05:42 +02:00
Eric Coissac
6cb7a5a352
Changes to be committed:
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modified: cmd/obitools/obitag/main.go
modified: cmd/obitools/obitaxonomy/main.go
modified: pkg/obiformats/csvtaxdump_read.go
modified: pkg/obiformats/ecopcr_read.go
modified: pkg/obiformats/ncbitaxdump_read.go
modified: pkg/obiformats/ncbitaxdump_readtar.go
modified: pkg/obiformats/newick_write.go
modified: pkg/obiformats/options.go
modified: pkg/obiformats/taxonomy_read.go
modified: pkg/obiformats/universal_read.go
modified: pkg/obiiter/extract_taxonomy.go
modified: pkg/obioptions/options.go
modified: pkg/obioptions/version.go
new file: pkg/obiphylo/tree.go
modified: pkg/obiseq/biosequenceslice.go
modified: pkg/obiseq/taxonomy_methods.go
modified: pkg/obitax/taxonomy.go
modified: pkg/obitax/taxonset.go
modified: pkg/obitools/obiconvert/sequence_reader.go
modified: pkg/obitools/obitag/obitag.go
modified: pkg/obitools/obitaxonomy/obitaxonomy.go
modified: pkg/obitools/obitaxonomy/options.go
deleted: sample/.DS_Store
2025-06-04 09:48:10 +02:00
Eric Coissac
f9324dd8f4
add min and max to the obitools expression language
2025-05-13 16:03:03 +02:00
Eric Coissac
f1b9ac4a13
Update the expression language
2025-05-07 20:45:05 +02:00
Eric Coissac
c0ecaf90ab
Add the --number option to obiannotate
2025-04-22 18:35:51 +02:00
Eric Coissac
a57cfda675
Make the replace function of the eval language accepting regex
2025-04-10 15:17:15 +02:00
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
f21f51ae62
Correct the logic of --update-taxid and --fail-on-taxonomy
2025-03-11 16:56:02 +01:00
Eric Coissac
3b5d4ba455
patch a bug in obiannotate
2025-03-11 16:35:38 +01:00
Eric Coissac
286e27d6ba
patch the scienctific_name tag name to "scientific_name"
2025-03-05 14:22:12 +01:00
Eric Coissac
51b3e83d32
some cleaning
2025-02-24 11:31:49 +01:00
Eric Coissac
8671285d02
add the --min-sample-count option to obiclean.
2025-02-24 08:48:31 +01:00
Eric Coissac
4774438644
Changes to be committed:
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modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
2025-02-12 08:40:38 +01:00
Eric Coissac
6a8061cc4f
Add managment of the taxonomy alias politic
2025-02-10 14:05:47 +01:00
Eric Coissac
0df082da06
Adds possibility to extract a taxonomy from taxonomic path included in sequence files
2025-01-30 11:18:21 +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
5d0f996625
Patch a small bug on json write
2024-12-20 19:42:03 +01:00
Eric Coissac
795df34d1a
Changes to be committed:
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modified: cmd/obitools/obitag/main.go
modified: cmd/obitools/obitag2/main.go
modified: go.mod
modified: go.sum
modified: pkg/obiformats/ncbitaxdump/read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/attributes.go
modified: pkg/obiseq/taxonomy_lca.go
modified: pkg/obiseq/taxonomy_methods.go
modified: pkg/obiseq/taxonomy_predicate.go
modified: pkg/obitax/inner.go
modified: pkg/obitax/lca.go
new file: pkg/obitax/taxid.go
modified: pkg/obitax/taxon.go
modified: pkg/obitax/taxonomy.go
modified: pkg/obitax/taxonslice.go
modified: pkg/obitools/obicleandb/obicleandb.go
modified: pkg/obitools/obigrep/options.go
modified: pkg/obitools/obilandmark/obilandmark.go
modified: pkg/obitools/obilandmark/options.go
modified: pkg/obitools/obirefidx/famlilyindexing.go
modified: pkg/obitools/obirefidx/geomindexing.go
modified: pkg/obitools/obirefidx/obirefidx.go
modified: pkg/obitools/obirefidx/options.go
modified: pkg/obitools/obitag/obigeomtag.go
modified: pkg/obitools/obitag/obitag.go
modified: pkg/obitools/obitag/options.go
modified: pkg/obiutils/strings.go
2024-12-19 13:36:59 +01:00
Eric Coissac
00b0edc15a
refactoring of the file chunck writing
2024-11-29 18:15:03 +01:00
Eric Coissac
d29a56dcbf
Changes to be committed:
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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
05bf2bfd6c
Add option related to agrep match on obigrep and obiannotate
2024-09-09 16:52:13 +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
67665a6b40
Xprize update
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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
2024-07-25 18:09:03 -04:00
Eric Coissac
4e4fac491f
Fisrt versin of the two levels indexing
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Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
2024-07-12 15:17:48 +02:00
Eric Coissac
c7ed47e110
first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished
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Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
2024-07-10 15:21:42 +02:00
Eric Coissac
bd855c4965
Adds CSV as an input format
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Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
2024-07-03 21:04:27 +02:00
Eric Coissac
fd663357b5
First version of obicleandb...
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Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
2024-07-01 17:12:42 +02:00
Eric Coissac
93f9dcb95f
Reducing memory allocation events
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Former-commit-id: c94e79ba116464504580fc397270ead154063971
2024-06-22 22:32:31 +02:00
Eric Coissac
e6b87ecd02
Reduce memory allocation events
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Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
2024-06-22 21:01:53 +02:00
Eric Coissac
54a138196c
Patch a bug in fasta and fastq reading
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Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
2024-06-21 14:28:57 +02:00
Eric Coissac
818ce87bab
Patch some bugs in writing files
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Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
2024-06-19 13:15:30 +02:00
Eric Coissac
65f5109957
Plenty of small bugs
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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
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Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
2024-06-04 11:57:16 +02:00
Eric Coissac
dbeb44bc79
Patch a bug in the quality string writing
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Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
2024-05-31 11:07:25 +02:00
Eric Coissac
55ce36f329
Update of obipcr and homogenization of logging
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Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
2024-05-16 15:18:30 +02:00
Eric Coissac
017030bcce
Add obiminion first version
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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
2024-05-14 08:16:12 +02:00
