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3d2e2057228d111aadfbd0d4cd6a73c71480947d
obitools4/pkg
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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
..
obialign
work on obiclean chimera detection
2025-10-20 17:29:47 +02:00
obiapat
debug obimultiplex
2025-11-06 15:43:13 +01:00
obichunk
Fix classifier cloning and reset in chunk processing
2026-02-08 15:52:25 +01:00
obicorazick
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obidefault
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obidist
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
2026-02-05 17:39:23 +01:00
obiformats
Refactor rope scanner and add FASTQ rope parser
2026-03-10 16:47:03 +01:00
obifp
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
obigraph
Add obiminion first version
2024-05-14 08:16:12 +02:00
obiiter
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obiitercsv
break the import cyccle
2025-01-27 17:23:07 +01:00
obikmer
Refactor k-mer matching pipeline with improved concurrency and memory management
2026-02-10 22:10:36 +01:00
obilog
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
obilua
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
obingslibrary
Changes to be committed:
2025-06-17 09:06:42 +02:00
obioptions
Bump version to 4.4.19
2026-03-10 15:51:36 +01:00
obiphylo
Changes to be committed:
2025-06-04 09:48:10 +02:00
obiseq
Refactor rope scanner and add FASTQ rope parser
2026-03-10 16:47:03 +01:00
obistats
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
obisuffix
Swich to the system min and max functions and remove the version from obiutils
2024-05-30 08:27:24 +02:00
obitable
many changes ;-)
2023-12-05 15:28:29 +01:00
obitax
debug url reading
2025-11-18 15:30:20 +01:00
obitools
Support new sequence file formats and improve error handling
2026-02-11 06:31:10 +01:00
obiutils
implementation de obilowmask
2025-11-18 15:30:20 +01:00