Eric Coissac 623116ab13 Add rope-based FASTA parsing and improve sequence handling ...

Introduce FastaChunkParserRope for direct rope-based FASTA parsing, enhance sequence extraction with whitespace skipping and U->T conversion, and update parser logic to support both rope and raw data sources.

- Added extractFastaSeq function to scan sequence bytes directly from rope
- Implemented FastaChunkParserRope for rope-based parsing
- Modified _ParseFastaFile to use rope when available
- Updated sequence handling to support U->T conversion
- Fixed line ending detection for FASTA parsing

2026-03-10 16:34:33 +01:00

..

kseq

some more cleaning

2024-01-16 21:11:38 +01:00

batch_of_files_reader.go

Update of obipcr and homogenization of logging

2024-05-16 15:18:30 +02:00

batch_reader_type.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

csv_read.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

csv_writer.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

csviterator.go

Make sequence files recognized as a taxonomy

2025-03-14 14:22:22 +01:00

csvtaxdump_read.go

Changes to be committed:

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

dispatcher.go

reduce the memory impact of obiuniq.

2024-11-27 13:30:16 +01:00

ecopcr_read.go

Changes to be committed:

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

embl_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

empty_file.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

fastaseq_read.go

Add rope-based FASTA parsing and improve sequence handling

2026-03-10 16:34:33 +01:00

fastqseq_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

fastqseq_write_generic.go

patch for impot bug

2023-12-01 16:31:35 +01:00

fastseq_header.go

Change the API of workers

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

fastseq_interface.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

fastseq_json_header.go

Manage a lock on StatsOnValues

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

fastseq_obi_header.go

Manage a lock on StatsOnValues

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

fastseq_read.c

Patch reading of annotation from stdin

2022-09-29 14:48:05 +02:00

fastseq_read.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

fastseq_read.h

First commit

2022-01-13 23:27:39 +01:00

fastseq_write_fasta.go

Optimize Fasta batch formatting

2026-03-10 15:43:59 +01:00

fastseq_write_fastq.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

fastseq_write_with_index.go

many changes ;-)

2023-12-05 15:28:29 +01:00

file_chunk_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

file_chunk_write.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

genbank_read.go

Use NewBioSequenceOwning to avoid unnecessary sequence copying

2026-03-10 15:51:35 +01:00

json_writer.go

Patch a small bug on json write

2024-11-29 18:39:18 +01:00

ncbitaxdump_read.go

Changes to be committed:

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

ncbitaxdump_readtar.go

Changes to be committed:

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

newick_write.go

Changes to be committed:

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

ngsfilter_read.go

Patch the fastq detector

2025-08-08 10:23:03 -04:00

options.go

Debug on taxonomy extraction and CSV conversion

2025-07-07 15:29:40 +02:00

taxonomy_read.go

Changes to be committed:

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

universal_read.go

debug url reading

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

universal_write.go

Patch a bug on writing to stdout, and add clearer error on openning data files

2024-08-13 09:45:28 +02:00