Changelog

v2.3.2 - Junction Salt - 01/16/2025

ADDED

• New parameters, --flexiguide_gap_open_penalty and --flexiguide_gap_extend_penalty, to customize flexiguide alignment in #491

• New parameter --halt_on_plot_fail so that errors and exceptions in plots don't fail silently in #494

• New parameter --samtools_exclude_flag to customize the filtering of reads in #503

• New documentation website at <docs.crispresso.com>.

• Asymmetrical cut point by @kclem in #457

• d3 plot enhancements by @trevormartinj7 in #459

• Add flexiguide alignment parameters by @Colelyman in #491

• Add pyproject.toml and support numpy v2 by @Snicker7 in #496

• Add customizable samtools exclude flag by @Colelyman in #503

• Add support for octal and comma separated samtools exclude flags (#113) by @kclem in #507

FIXED

• Fix typo and move flexiguide to debug (#77) by @Colelyman in #438

• Matplotlib Compatibility Fix by @mbowcut2 and @Snicker7 in #464

• Fix CRISPRessoAggregate bug and other improvements (#95) by @Colelyman in #470

• Fix missing substitution in name of WGS, Compare and Meta reports by @Colelyman in #498

• Fix get_n_fastq function by @trevormartinj7 in #508

CHANGED

• Improvement of processing speed by

  • parallelization of alignments in #480

  • memory usage reduction in #478 and #509

• Progress percentages are displayed in the CLI output.

• Prefix the release Docker tag with a v by @Colelyman in #434

• Pin versions of numpy and matplotlib in CI environment by @Snicker7 in #452

• Implement new pooled mixed-mode default behavior by @mbowcut2 in #454

• Update README by @Snicker7, @mbowcut2, @trevormartinj7, @Colelyman and @kclem in #456

• Cache conda packages in GIthub Actions by @Colelyman in #466

• Replace zcat by @Colelyman in #468

• Cache read merging step in CRISPRessoPooled on no_rerun by @kclem in #467

• Display percentages in the CLI output by @Colelyman in #473

• No processor pool when running in single thread by @Snicker7 in #474

• Round percentage complete in CLI and add initial 0% complete by @Colelyman in #477

• Reduce memory usage for allele plots by @Colelyman in #478

• Sync reports by @Colelyman in #479

• Read Alignment Parallelization (#98) by @trevormartinj7 in #480

• Add all_deletion_coordinates to be returned by find_indels_substitutions_legacy function by @Colelyman in #486

• Mckay/halt on plot fail by @mbowcut2 in #494

• Update jinja_partials and bring Reports into sync by @Colelyman in #500

• Update CRISPRessoPooledCORE.py by @kclem in #502

• Pooled multi region map fix by @kclem in #505

• Slots implementation by @mbowcut2 in #509

• Suppress printing by @kclem in #511

• Update detailed alleles table help option by @Colelyman in #513