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

..

attributes.go

obicsv bug with stat on value map fields

2025-11-21 14:03:31 +01:00

biosequence_test.go

correction of several small bugs

2024-09-03 06:08:07 -03:00

biosequence.go

Refactor rope scanner and add FASTQ rope parser

2026-03-10 16:47:03 +01:00

biosequenceslice.go

Changes to be committed:

2025-06-04 09:48:10 +02:00

class.go

Update obiuniq for very large dataset

2025-12-18 14:11:11 +01:00

compare.go

Add the possibility to look for patterns allowing indels.

2023-03-20 15:28:24 +07:00

eval.go

Change the API of workers

2024-03-02 16:03:46 -04:00

iupac_nog.go

work on obiclean chimera detection

2025-10-20 17:29:47 +02:00

join.go

Adds some documentation

2022-08-23 11:11:36 +02:00

kmers.go

implementation de obilowmask

2025-11-18 15:30:20 +01:00

language.go

add min and max to the obitools expression language

2025-05-13 16:03:03 +02:00

merge.go

obicsv bug with stat on value map fields

2025-11-21 14:03:31 +01:00

paired_reads.go

change the model for representing paired reads and extend its usage to other commands

2023-02-23 23:35:58 +01:00

pool.go

Reduce memory allocation events

2024-06-22 21:01:53 +02:00

predicate.go

Manage a lock on StatsOnValues

2025-06-17 16:46:11 +02:00

revcomp_test.go

Patch a bug in Subsequence and adds few unit tests.

2023-11-08 10:16:34 +02:00

revcomp.go

Patch a bug in obitagpcr

2024-11-18 21:10:47 +01:00

subseq_test.go

Patch a bug in the pair-end alignement in case of equality between scores.

2023-11-24 09:59:29 +01:00

subseq.go

Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr

2024-03-11 10:54:37 +01:00

taxonomy_classifier.go

some cleaning

2025-02-24 11:31:49 +01:00

taxonomy_lca.go

Manage a lock on StatsOnValues

2025-06-17 16:46:11 +02:00

taxonomy_methods.go

Changes to be committed:

2025-06-04 09:48:10 +02:00

taxonomy_predicate.go

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

taxonomy_workers.go

Fisrt functional version

2024-11-14 19:10:23 +01:00

worker.go

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