History

The changelog for MPRAsnakeflow is included below. It provides a detailed history of changes, updates, and improvements made to the project.

Changelog

0.10.5 (2026-05-07)

Bug Fixes

  • cli: :bug: Implemented an overflow-safe fix for the sigmoid calculation on postProbEffect (#108) (0c694c6)

0.10.4 (2026-05-04)

Bug Fixes

  • Set reporter (genomic) varints empty ref/alt allele to 0 (3c39029)

0.10.3 (2026-03-05)

Bug Fixes

  • replace None with pd.NA in MPRAData allele processing for improv… (1c724b2)

  • replace None with pd.NA in MPRAData allele processing for improved compatibility (8ec5372)

0.10.2 (2026-03-04)

Bug Fixes

  • replace None with pd.NA in variant map processing for better compatibility (#98) (c58769a)

0.10.1 (2026-03-03)

Bug Fixes

  • remove pysam library for better compatibility (#96) (8e92c38)

0.10.0 (2026-03-02)

⚠ BREAKING CHANGES

  • modification of normalization (over total counts not average per barcode per oligo) (#87)

Bug Fixes

  • modification of normalization (over total counts not average per barcode per oligo) (#87) (9c00463)

0.9.1 (2026-01-08)

Documentation

  • overview update (83bb09e)

  • quickstart and other improvements (66a2771)

  • update quictstart and minor other updates (36622f7)

  • Zenodo link and documentation update (5e4c62d)

0.9.0 (2025-09-16)

⚠ BREAKING CHANGES

  • Renames cli sequence_design to combine (#79)

  • Some othere CLI commands changed (#75)

  • Normalization only done on raw or sampled counts. Var filter (barcode filter) not used (#78)

Bug Fixes

  • validate empty files as invalid (1fddaeb)

Features

  • Normalization only done on raw or sampled counts. Var filter (barcode filter) not used (#78)

  • Outlier detection is now in line with the manuscript (#75)

0.8.2 (2025-07-01)

Features

  • improved cli get reporter genomic elements/variants (044b2a5)

Bug Fixes

  • chromosome maps with X and Y (0becc21)

  • chromosome_map can distiguish between hg19 and hg38 (dd8afe5)

0.8.1 (2025-06-27)

Bug Fixes

  • correctly defining extra data in pyproject.toml (#69) (9e0a09d)

0.8.0 (2025-06-27)

⚠ BREAKING CHANGES

  • loading chro map files in source. requires python 3.9+ (#67)

Bug Fixes

  • loading chro map files in source. requires python 3.9+ (#67) (5852748)

0.7.4 (2025-06-26)

Bug Fixes

  • correct header of count file (reporter experiment file format) (#65) (d8fe22d)

0.7.3 (2025-06-17)

Bug Fixes

  • BC counts per oligo where not dropped and therefor enot recomputed after (down) sampling (#63) (d615251)

0.7.2 (2025-06-12)

Documentation

  • better API documentation on readthedocs (d289a4c)

0.7.1 (2025-06-11)

Documentation

  • readthedocs documentation inkluding API (22023bd)

0.7.0 (2025-06-04)

⚠ BREAKING CHANGES

  • MPRAlib is now always in lowercase (also on pypi)

Bug Fixes

  • minimum required anndata 0.11.3 (7d56652)

  • Python compatibility 3.8+ compatibility using Optional for typing. (7649bc9)

Documentation

  • update docs for lowercase (0631f7c)

Miscellaneous Chores

  • MPRAlib is now always in lowercase (also on pypi) (0b6108a)

0.6.5 (2025-06-03)

Features

  • complexity estimates on barcode level (06a2173)

0.6.4 (2025-05-28)

Bug Fixes

  • validate files. empty ref/alt allele for variant files must be 0 (391703a)

0.6.3 (2025-05-23)

Bug Fixes

0.6.2 (2025-05-22)

Features

  • cli to validate standardized file formats for MPRA using json schema (a078ad9)

  • coverage report and automatic tests using github actions (d8139b6)

0.6.1 (2025-04-09)

Bug Fixes

  • SyntaxError: EOL while scanning string literal (11ce617)

Documentation

0.6.0 (2025-04-03)

⚠ BREAKING CHANGES

  • barcode_counts is now part available in MPRAdata as layer

Code Refactoring

  • barcode_counts is now part available in MPRAdata as layer (c9b04ec)

0.5.0 (2025-04-01)

⚠ BREAKING CHANGES

  • gobal variant map. Now metadata is called “sequence design”

  • dna_vs_rna and barcodes per oligo plots.

  • correlation plot. breaks corrrelation due to new count type enum

  • new utils sub library

Features

  • correlation plot. breaks corrrelation due to new count type enum (f0e46a1)

  • dna_vs_rna and barcodes per oligo plots. (3430538)

  • gobal variant map. Now metadata is called “sequence design” (2743e20)

  • normalized counts in output files (8526f9f)

  • outlier plot (17cf8d1)

  • pairwise correlation plots (bd1d118)

  • plot functionality (b789c41)

Bug Fixes

  • bcalm and mpralm element scripts with empty rows (Not observed) (174657b)

  • reporter genomic variant or element (b250470)

Code Refactoring

0.4.0 (2025-03-21)

⚠ BREAKING CHANGES

  • the whole code

refactoring

Features

  • add filtering options for elements and variants in get_counts function (971986b)

  • full cli functionality (6f2f2b7)

Bug Fixes

0.3.0 (2025-03-04)

⚠ BREAKING CHANGES

  • splitting oligo and barcode counts resulting in different interface

Features

  • adding qc metric notebook (ab17436)

Documentation

Code Refactoring

  • splitting oligo and barcode counts resulting in different interface (ef09d7a)

0.2.2 (2025-02-27)

Bug Fixes

  • initialize barcode_threshold when it is not there (4f09174)

0.2.1 (2025-02-27)

Features

  • adding rna and dna counts correlations (b2b4d60)

0.2.0 (2025-02-21)

⚠ BREAKING CHANGES

  • implemented count sampling

Features

  • Control pseudo counts (0534bb6), closes #14

  • implement RNA and DNA count methods with sampling and filtering (95e3be9)

  • implemented count sampling (bfa4da5)

  • utils method for barcode output format (#20) (81273de), closes #15

Bug Fixes

  • issues and prepare to split up counts (484d936)

0.1.0 (2025-02-17)

Features

  • add chromosome mapping utility and data files for hg19 and hg38 (f037b92)

  • add MPRA analysis script and enhance MPRAdata class with variant mapping and counts (00de9c0)

  • add MPRA element analysis script and enhance MPRAdata class with element DNA and RNA counts (df5e5fe)

  • add output option for MPRA data object and enhance element and variant reporting functions (4a81736)

  • random sampling of barcodes (62330d0)

Bug Fixes

  • adjust YAML linter configuration for comments spacing (ab6c18f)