Changelog¶

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.3.0 - 2025-06-13¶

better chromosome detection for add_annotations and allow user to choose the chromosome name (25c389 by Pierre Marijon).
interval method now allow user to add comment to each interval (9ae9f8d by Pierre Marijon).

add_recurence perform unique before compute (c865c85 by Pierre Marijon).
show utils submodule in documentation (b661e37 by Pierre Marijon).
if preindication is empty produce preindication path correctly (6f8ca8 by Pierre Marijon).

add method to get cnv (68afdbc by Pierre Marijon).
create duckdb object in each threads (c9132a1 by Pierre Marijon).
add ability of add genotype to scan file (585dbd4 by Pierre Marijon).
support unique variants in one file or split by chromosome (f9a801e by Pierre Marijon).

issue #3 (4432ba8 by Pierre Marijon).
genotype query not use left join (9259900 by Pierre Marijon).
simplify snpeff and variant2gene add_annotation (53b0b3c by Pierre Marijon).
2 (4c4fc82 by Pierre Marijon).¶
change in duckdb (d94a2a9 by Pierre Marijon).
add test for all_variants (28ddd29 by Pierre Marijon).

transmissions use same code as genotyping and could be paralellize (c14aa96 by Pierre Marijon).
move string query in specific module (df7ac12 by Pierre Marijon).
preindication target is set at object level not at method (4c6fb43 by Pierre Marijon).
move tqdm wrapper stuff in specific function (0fc601f by Pierre Marijon).

add_genotypes support variables number of bits (ef01687 by Pierre Marijon).
switch to github (a6e96d5 by Pierre Marijon).
duckdb connection object is public (cd5f822 by Pierre Marijon).
disable progress bar (bd210c7 by Pierre Marijon).
add support of tqdm (f3ede2d by Pierre Marijon).
add code to support python3.9 (f21c322 by Pierre Marijon).
add methode to get multiple interval (b3c11e8 by Pierre Marijon).
reach high test coverage (178a73c by Pierre Marijon).
Sake threads value also control polars threads (9e9ac60 by Pierre Marijon).
Sake object could be create and unique variants are extractable (0ee518e by Pierre Marijon).

if chromosome file isn't present durring annotations skip it (f824c13 by Pierre Marijon).
better formating of code in usage (47e3656 by Pierre Marijon).
correct typo in utils function. (faa8273 by Pierre Marijon).
test evaluate all path and number of thread (dc462ba by Pierre Marijon).