Eric Coissac a0d8187fd6 Implement k-mer distance metrics and constrained generation ...

Adds support for Hamming distance, constrained k-mer generation, and optimized Longest Common Subsequence (LCS) calculations using scalar, batch, and SIMD methods.

This includes new methods for k-mer distance calculation, structures for k-mer constraints, and SIMD-based batch processing for LCS to improve performance and correctness.

2026-11-03 09:23:37 +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

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +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_distance_test.go

Implement k-mer distance metrics and constrained generation

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

kmer_distance.go

Implement k-mer distance metrics and constrained generation

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

kmer_lcs_archsimd_arm64_test.go

Implement k-mer distance metrics and constrained generation

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

kmer_lcs_archsimd_arm64.go

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +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

Implement k-mer distance metrics and constrained generation

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

kmer_lcs_simd.go

Implement k-mer distance metrics and constrained generation

2026-11-03 09:23:37 +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