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@ManuelTgn ManuelTgn released this 13 Nov 10:06
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v0.1.1
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CRISPR-HAWK v0.1.1 – Release Notes

Date: November 2025

What's New

  • Added support for off-target annotation via CLI and core logic – users can now supply BED files and custom column names for enriched off-target reporting. (PR #3)

  • Refactored the workflow into discrete modules (annotation.py, scoring.py, search_offtargets.py) with the main driver (crisprhawk.py) updated accordingly for better readability, testability and maintainability. (PR #3)

  • Enhanced CLI argument parsing/validation in crisprhawk_argparse.py, including a new flag --candidate-guides for detailed guide analysis and graphical reporting. (PR #3)

  • Introduced a CandidateGuide class and associated logic in candidate_guides.py; provided new report generation features (dot plot & scatter plot) for variant effect analysis of candidate guides. (PR #3)

  • Adopted a unified CrisprHawkSearchInputArgs object for major modules to streamline parameter passing and reduce redundancy. (PR #3)

  • Removed the need for the user to supply a FASTA index file (FAI) – index handling is now automatic within the Fasta class. (PR #3)

  • Improved handling of IUPAC nucleotide codes in micro-homology scoring and guide search routines (supporting ambiguous bases better). (PR #3)

  • Documentation improvements: updated docstrings and formatting in modules such as microhomology.py, crisprhawk_scores.py, search_guides.py. (PR #3)

Bug Fixes & Enhancements

  • Added parallel computation for DeepCpf1 scoring (chunking guide sequences + ProcessPoolExecutor) to improve performance on large guide sets. (PR #4)

  • Refactored candidate-guide handling and graphical reports: updated coordinate parsing to require strand information, improved helper functions for guide ID assignment, delta calculations and color palette generation. (PR #4)

  • Fixed IUPAC encoding logic in haplotypes.py (use of IUPACTABLE for reference base conversion) and cleaned up variant addition logic. (PR #4)

  • Fixed bugs in variant annotation and guide mapping logic: guide retrieval and annotation functions now use position‐maps and variant normalization; multiallelic variant handling improved. (PR #4)

  • Improved formatting for allele frequencies (scientific notation) and pie‐chart representation in graphical reports; corrected parsing of AF field when no additional info present. (PR #4)

  • Refactored CLI argument groups: made --outdir optional in search & converter subcommands; updated README logo file. (PR #4)

  • Adjusted test assertions to reflect changes in allele frequency formatting and scoring logic. (PR #4)

Backwards Compatibility / Migration Notes

  • If you were previously passing a FASTA index file via the CLI (FAI), you no longer need to; the index is handled automatically.

  • Some function signatures changed (because of the move to CrisprHawkSearchInputArgs), so if you have custom downstream code extending CRISPR-HAWK modules, you may need to update accordingly.

  • Existing workflows remain supported and will continue to run as before; the new CLI flags and reporting modules are additive.

Changelog

Full Changelog: v0.1.0...v0.1.1

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