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7a979ba77f03ae48da7fafd2258861debe1d9069
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16 Commits

Author SHA1 Message Date
Eric Coissac
7a979ba77f Add obisuperkmer command implementation and tests 
This commit adds the implementation of the obisuperkmer command, including:

- The main command in cmd/obitools/obisuperkmer/
- The package implementation in pkg/obitools/obisuperkmer/
- Automated tests in obitests/obitools/obisuperkmer/
- Documentation for the implementation and tests

The obisuperkmer command extracts super k-mers from DNA sequences, following the standard OBITools architecture. It includes proper CLI option handling, validation of parameters, and integration with the OBITools pipeline system.

Tests cover basic functionality, parameter validation, output format, metadata preservation, and file I/O operations.
 2026-02-07 13:54:02 +01:00
Eric Coissac
ac0d3f3fe4 Update obiuniq for very large dataset 2025-12-18 14:11:11 +01:00
Eric Coissac
8c26fc9884 Add a new test on obisummary 2025-07-07 15:28:29 +02:00
Eric Coissac
0aec5ba4df change the tests according to the corrections in obipairing 2025-04-04 17:10:17 +02:00
Eric Coissac
3a1cf4fe97 Accelerate the speed of very long fasta sequences, and more generaly of every format 2025-03-12 13:29:41 +01:00
Eric Coissac
78caabd2fd Add basic test on -h for all the commands 2025-03-08 16:28:06 +01:00
Eric Coissac
d4209b4549 Add a basic test for obiparing 2025-02-22 09:57:44 +01:00
Eric Coissac
090633850d Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 15:28:42 +01:00
Eric Coissac
15a058cf63 with all the sample files for tests 2025-02-19 15:27:38 +01:00
Eric Coissac
2f5f7634d6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:50:10 +01:00
Eric Coissac
48138b605c Changes to be committed: 
modified:   .github/workflows/obitest.yml
	modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:37:05 +01:00
Eric Coissac
aed22c12a6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:34:22 +01:00
Eric Coissac
443a9b3ce3 Changes to be committed: 
modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:28:49 +01:00
Eric Coissac
7e90537379 For run of test using bash in makefile 2025-02-19 13:58:52 +01:00
Eric Coissac
d3d15acc6c Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
	modified:   pkg/obioptions/version.go
 2025-02-19 13:54:01 +01:00
Eric Coissac
952f85f312 A first trial of a test for obicount 2025-02-19 13:17:36 +01:00