Eric Coissac 60b3753673 feat(obiconvert): add --raw-taxid option and refactor taxID formatting ...

- Add new `--tax-id` mode (`obiconvert --raw-taxid`) to output bare numeric taxIDs instead of full-format strings.
- Introduce `TaxNode.FullString()` to always return the complete "code:id [name]@rank" format, regardless of global `UseRawTaxids()` setting.
- Update `.String(taxonomyCode)` to respect the global flag, returning bare ID when `--raw-taxid` is active.
- Extract raw taxID from full-format strings in taxonomy methods when needed (e.g., fallback without loaded DB).
- Add comprehensive test suite covering:
a) `--raw-taxid` execution and idempotency
b) full-format taxID output with `--taxonomy`
c interaction of both flags
d format validation
- Add test data: new reference files `out_ecotag.fasta`, taxonomy.csv, and updated shell script.

2026-04-30 16:57:38 +02:00

..

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

[obiseq] Add length validation for qualities in SetQualities, Take Qualites and Subsequence

2026-04-15 18:20:53 +02:00

biosequenceslice.go

Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting

2026-03-12 18:41:28 +01:00

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

Add memory-based batching support

2026-03-13 14:54:21 +01:00

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

Refactor: Extract utility function for string reversal

2026-04-16 13:42:51 +02:00

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

[obiseq] Add length validation for qualities in SetQualities, Take Qualites and Subsequence

2026-04-15 18:20:53 +02:00

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

feat(obiconvert): add --raw-taxid option and refactor taxID formatting

2026-04-30 16:57:38 +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

refactor: replace fixed batch size with dynamic flushing based on count and memory

2026-03-16 22:06:44 +01:00