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

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obialign

work on obiclean chimera detection

2025-10-20 17:29:47 +02:00

obiapat

debug obimultiplex

2025-11-06 15:43:13 +01:00

obichunk

Fix classifier cloning and reset in chunk processing

2026-02-08 15:52:25 +01:00

obicorazick

Add progress bar configuration and conditional display

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

obidefault

refactor: replace single batch size with min/max bounds and memory limits

2026-03-13 15:07:35 +01:00

obidist

Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup

2026-02-05 17:39:23 +01:00

obiformats

fix: validate non-empty sequence IDs in FASTA and FASTQ writers

2026-05-05 18:07:58 +02:00

obifp

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00

obigraph

Add obiminion first version

2024-05-14 08:16:12 +02:00

obiiter

refactor: replace fixed batch size with dynamic flushing based on count and memory

2026-03-16 22:06:44 +01:00

obiitercsv

break the import cyccle

2025-01-27 17:23:07 +01:00

obikmer

Correct Shannon entropy bias for canonical k-mers

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

obilog

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00

obilua

chore: bump version to 4.4.39

2026-04-14 14:48:29 +02:00

obingslibrary

Changes to be committed:

2025-06-17 09:06:42 +02:00

obioptions

[4.4.2] Enhanced taxonomy handling, input robustness & PCR tag validation

2026-04-30 16:57:45 +02:00

obiphylo

Changes to be committed:

2025-06-04 09:48:10 +02:00

obiseq

feat: add min/max filtering and saturating subtraction utilities

2026-05-14 20:58:24 +08:00

obistats

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

2025-03-25 16:44:46 +01:00

obisuffix

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

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

obitable

many changes ;-)

2023-12-05 15:28:29 +01:00

obitax

feat(obiconvert): add --raw-taxid option and refactor taxID formatting

2026-04-30 16:57:38 +02:00

obitools

🔧 Rename mismatch fields to error in pcrtag.go

2026-04-29 15:29:25 +02:00

obiutils

feat: add min/max filtering and saturating subtraction utilities

2026-05-14 20:58:24 +08:00