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refactoring of obikmer

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This commit is contained in:
Eric Coissac
2026-02-05 15:56:22 +01:00
parent 6c6c369ee2
commit 16f72e6305
7 changed files with 200 additions and 11612 deletions
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pkg/obitools/obilowmask/obilowmask.go
+5 -4
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@@ -48,12 +48,12 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
// - We calculate the entropy of a distribution where all words appear
// cov or cov+1 times (most uniform distribution possible)
//
// IMPORTANT: Uses CanonicalKmerCount to get the actual number of canonical words
// IMPORTANT: Uses CanonicalCircularKmerCount to get the actual number of canonical words
// after circular normalization (e.g., "atg", "tga", "gat" → all "atg").
// This is much smaller than 4^word_size (e.g., 10 instead of 16 for word_size=2).
emax := func(lseq, word_size int) float64 {
nw := lseq - word_size + 1 // Number of words in a k-mer of length lseq
na := obikmer.CanonicalKmerCount(word_size) // Number of canonical words after normalization
nw := lseq - word_size + 1 // Number of words in a k-mer of length lseq
na := obikmer.CanonicalCircularKmerCount(word_size) // Number of canonical words after normalization
// Case 1: Fewer positions than possible words
// Maximum entropy is simply log(nw) since we can have at most nw different words
@@ -215,7 +215,8 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
// *** CIRCULAR NORMALIZATION ***
// Convert word to its canonical form (smallest by circular rotation)
// This is where "atg", "tga", "gat" all become "atg"
words[i] = obikmer.NormalizeInt(word_index, wordSize)
// Now using uint64-based NormalizeCircular for better performance
words[i] = int(obikmer.NormalizeCircular(uint64(word_index), wordSize))
}
// ========================================================================