Eric Coissac af7ae3d60c Correct Shannon entropy bias for canonical k-mers ...

Multiple raw k-mers collapsing into identical circular canonical forms introduce bias into complexity estimates. This change pre-computes `log(class_size)` tables and per-word-size maximum entropy bounds. The `KmerEntropy` function and `KmerEntropyFilter` are updated to apply the corrected formula `(log(N) + Σf·log(s) - Σf·log(f))/N / emax`, ensuring accurate sequence complexity estimation.

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

..

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

correction of several small bugs

2024-09-03 06:08:07 -03:00

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

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_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