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.
0.5.0 - 2025-06-20¶
Features¶
- store info and format header associate to column in parquet metadata (eca6812 by Pierre Marijon).
- rename option index in child and add documentation (047506b by Pierre Marijon).
- transmission are run in any sample with a parent in ped file (1032d3e by Pierre Marijon).
- add support of any format (7070977 by Pierre Marijon).
- rename option index in child and add documentation (4670526 by Pierre Marijon).
Bug Fixes¶
- if column are missing in format return null (762512a by Pierre Marijon).
- improve documentation (762512a by Pierre Marijon).
0.4.4 - 2025-05-20¶
Bug Fixes¶
- replace int2string by any2string and use uuid instead of python hash function (a63aa8c by Pierre Marijon).
- temporary file name is now a hash of input file name (2af10fc by Pierre Marijon).
- support version 1.29 of polars (810659a by Pierre Marijon).
0.4.3 - 2025-05-14¶
Features¶
- set row group size parameter of sink_polars (9f2285a by Pierre Marijon).
Bug Fixes¶
- correct snpeff annotation script (197297c by Pierre Marijon).
- apply click 8.2 change (4524890 by Pierre Marijon).
0.4.2 - 2025-04-15¶
Features¶
- support compressed vcf with xopen (3310947)
Bug Fixes¶
- remove debug instruction (dd93d54 by Pierre Marijon).
0.4.1 - 2025-04-15¶
Bug Fixes¶
- try to avoid possible random error in int2string (5c7d40e by Pierre Marijon).
0.4.0 - 2025-04-10¶
Bug Fixes¶
- genotype samples_names perform unique sample (64e7274 by Pierre Marijon).
- improve struct variant tmp file naming (3119a40 by Pierre Marijon).
Code Refactoring¶
- rename variantplaner_rs in variantid and rewrite it (3961428 by Pierre Marijon).
0.3.1 - 2024-12-16¶
Features¶
- struct unique variant split variants by chromosome (ae7eb65 by Pierre Marijon).
- struct genotype polars threads parameter have an effect (6419e02 by Pierre Marijon).
- use new functionality of variantplaner_rs in variantplaner cli (f986213 by Pierre Marijon).
- variantplaner_rs partitions could be parameterize (8b2066e by Pierre Marijon).
Bug Fixes¶
- use number of bit ask by user in partitions (4409d8c by Pierre Marijon).
- readd documentation generation (6467ee2 by Pierre Marijon).
- transmission generation not failled if ped file contain only one line (58ee926 by Pierre Marijon).
0.3.0 - 2024-09-30¶
Features¶
- move ped code from io to object (b6638ca by Pierre Marijon).
- parquet2vcf can extract only variant of one chromosome (f29c6ac by Pierre Marijon).
- improve alt '*' management (755a5fa by Pierre Marijon).
- partition support append mode (1b6603f by Pierre Marijon).
- variant merge support append (d12d357 by Pierre Marijon).
- Add python 3.12 in ci test and support (c51c932 by Pierre Marijon).
- Better variant hash we only need store ref length (8a3db5e by Pierre Marijon).
- add documentation on how interogate genotype variants partitions (b843bca by Pierre Marijon).
- New cli (c2cb033 by Pierre Marijon).
Bug Fixes¶
- add output file in struct operation only if it's exist (9a868ad by Pierre Marijon).
- not failled if SVTYPE or SVLEN column isn't present (32a8dad by Pierre Marijon).
- correct benchmark script run (8ebdca0 by Pierre Marijon).
Code Refactoring¶
- Move many variant operation in object. (df36fa0 by Pierre Marijon).
0.2.4 - 2023-12-21¶
Features¶
- add variantplaner logo.
- add method to compute partition value of id.
Bug Fixes¶
- fix: #41 vcf spec indicate Integer must be store in 32bits.
- update to polars 0.20.
0.2.3 - 2023-11-21¶
Features:¶
- Use ruff format in place of black
- Minimal polars version is 0.19.15
- SV cannot have small variant id
- Type of id is include in part of id (all long variant are store in same place)
Fix:¶
- Usage intgerate chromosome2length option
0.2.2 - 2023-10-19¶
Fix:¶
- Correct typo in readme
- Correct change in variantplaner_rs/Cargo.lock
0.2.1 - 2023-10-09¶
Fix:¶
- Hot fix some lazy trouble
0.2.0 - 2023-10-02¶
Features:¶
- Replace hash variant id by a uniq variant id
- Improve variant transmission system to support genome with ploidie lower than 92
- Genotype partitioning now use position part of unique id to get more local request
Fixes:¶
- Documentation fix
- Test coverage improvement