Eric Coissac d735ac6188 feat: add JSON input support for biological sequences ...

Introduce a streaming JSON parser that decodes biological sequences using `goccy/go-json` with configurable batching to minimize memory overhead. Extend the CLI, file suffix filters, and MIME type detection to automatically recognize and route JSON inputs. Refactor header parsing into a centralized switch-case handler for improved maintainability.

2026-07-03 10:16:55 +02:00

..

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

Add EMBL rope parsing support and improve sequence extraction

2026-03-10 17:02:14 +01:00

empty_file.go

Change path of the obitools pkg

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

fastaseq_read.go

Refactor rope scanner and add FASTQ rope parser

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

fastqseq_read.go

Refactor rope scanner and add FASTQ rope parser

2026-03-10 16:47:03 +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

feat: add JSON input support for biological sequences

2026-07-03 10:16:55 +02:00

fastseq_obi_header.go

Update ignore patterns, configure Serena, and refactor FASTSEQ parser

2026-07-02 08:49:26 +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

fix: validate non-empty sequence IDs in FASTA and FASTQ writers

2026-05-05 18:07:58 +02:00

fastseq_write_fastq.go

fix: validate non-empty sequence IDs in FASTA and FASTQ writers

2026-05-05 18:07:58 +02:00

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

Refactor rope scanner and add FASTQ rope parser

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

json_read.go

feat: add JSON input support for biological sequences

2026-07-03 10:16:55 +02:00

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

[ngsfilter] Trim whitespace from primer and sample fields

2026-04-30 08:14:39 +02:00

options.go

Debug on taxonomy extraction and CSV conversion

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

rope_scanner.go

replace fixed-size carry buffer with dynamic slice

2026-03-11 20:44:45 +01:00

taxonomy_read.go

Changes to be committed:

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

universal_read.go

feat: add JSON input support for biological sequences

2026-07-03 10:16:55 +02:00

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