Junction Salt

Major changes

• Improvement of processing speed by
  • parallelization of alignments in #480
  • memory usage reduction in #478 and #509
• 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>.
• Progress percentages are displayed in the CLI output.

What's Changed

• Prefix the release Docker tag with a v by @Colelyman in #434
• Fix typo and move flexiguide to debug (#77) by @Colelyman in #438
• 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
• Asymmetrical cut point by @kclem in #457
• d3 plot enhancements by @trevormartinj7 in #459
• Matplotlib Compatibility Fix by @mbowcut2 and @Snicker7 in #464
• 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
• Fix CRISPRessoAggregate bug and other improvements (#95) by @Colelyman in #470
• 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
• Add flexiguide alignment parameters by @Colelyman in #491
• Mckay/halt on plot fail by @mbowcut2 in #494
• Add pyproject.toml and support numpy v2 by @Snicker7 in #496
• Fix missing substitution in name of WGS, Compare and Meta reports by @Colelyman in #498
• Update jinja_partials and bring Reports into sync by @Colelyman in #500
• Update CRISPRessoPooledCORE.py by @kclem in #502
• Add customizable samtools exclude flag by @Colelyman in #503
• Pooled multi region map fix by @kclem in #505
• Add support for octal and comma separated samtools exclude flags (#113) by @kclem in #507
• Fix get_n_fastq function by @trevormartinj7 in #508
• Slots implementation by @mbowcut2 in #509
• Suppress printing by @kclem in #511
• Update detailed alleles table help option by @Colelyman in #513

Full Changelog: v2.3.1...v2.3.2