Eric Coissac f3250984a5 Implement robust clique search configuration and testing ...

The changes introduce new configuration options for clique searching, state tracking for search outcomes, and logic for handling unreachable targets. Tests are added to verify search modes, failure conditions, and the correctness of coloring bounds.

2026-11-03 09:27:21 +11:00

..

counting.go

Swich to the system min and max functions and remove the version from obiutils

2024-05-30 08:27:24 +02:00

debruijn.go

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +11:00

encodefourmer.go

Bugfix: result of 0 4mers not caught if sequence length == 3

2026-04-10 14:05:30 +02:00

encodekmer_test.go

Refactor k-mer normalization functions and add quorum operations

2026-02-05 17:11:34 +01:00

encodekmer.go

Refactor SuperKmer extraction to use iterator pattern

2026-02-07 12:23:12 +01:00

entropy.go

Correct Shannon entropy bias for canonical k-mers

2026-05-17 14:54:57 +08:00

enumkmer_test.go

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +11:00

enumkmer.go

Feature: Implement constrained k-mer generation and clique search

2026-11-03 09:25:34 +11:00

kdi_merge_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kdi_merge.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kdi_reader.go

Add sparse index support for KDI files with fast seeking

2026-02-10 13:24:24 +01:00

kdi_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kdi_writer.go

Add sparse index support for KDI files with fast seeking

2026-02-10 13:24:24 +01:00

kdx.go

Add sparse index support for KDI files with fast seeking

2026-02-10 13:24:24 +01:00

kmer_constraints_test.go

Feature: Implement constrained k-mer generation and clique search

2026-11-03 09:25:34 +11:00

kmer_constraints.go

Feature: Implement constrained k-mer generation and clique search

2026-11-03 09:25:34 +11:00

kmer_dissimilarity_test.go

Implement robust clique search configuration and testing

2026-11-03 09:27:21 +11:00

kmer_dissimilarity.go

Feature: Implement constrained k-mer generation and clique search

2026-11-03 09:25:34 +11:00

kmer_distance_test.go

Feature: Introduce k-mer distance and SIMD LCS logic

2026-11-03 09:24:00 +11:00

kmer_distance.go

Feature: Introduce k-mer distance and SIMD LCS logic

2026-11-03 09:24:00 +11:00

kmer_lcs_obialign_test.go

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +11:00

kmer_lcs_scalar.go

Feature: Introduce k-mer distance and SIMD LCS logic

2026-11-03 09:24:00 +11:00

kmer_lcs_simd.go

Feature: Introduce k-mer distance and SIMD LCS logic

2026-11-03 09:24:00 +11:00

kmer_match.go

Refactor k-mer matching pipeline with improved concurrency and memory management

2026-02-10 22:10:36 +01:00

kmer_set_builder_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kmer_set_builder.go

Add entropy-based filtering for k-mers

2026-02-10 18:20:35 +01:00

kmer_set_disk_ops_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kmer_set_disk_ops.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

kmer_set_disk.go

Add entropy-based filtering for k-mers

2026-02-10 18:20:35 +01:00

kmermap.go

Add progress bar configuration and conditional display

2026-02-08 16:14:02 +01:00

minimizer_utils.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

skm_reader.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

skm_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

skm_writer.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

spectrum.go

Add max frequency filtering and top-kmer saving capabilities

2026-02-10 09:27:04 +01:00

superkmer_iter_test.go

Fix super k-mer minimizer bijection and add validation test

2026-02-08 13:47:33 +01:00

superkmer_iter.go

Fix super k-mer minimizer bijection and add validation test

2026-02-08 13:47:33 +01:00

superkmer.go

Refactor SuperKmer extraction to use iterator pattern

2026-02-07 12:23:12 +01:00

varint_test.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00

varint.go

Refactor k-mer index building to use disk-based KmerSetGroupBuilder

2026-02-10 06:49:31 +01:00