Junction Salt

[kclem]

Major changes

• Improvement of processing speed by
  • parallelization of alignments in Read Alignment Parallelization (#98) #480
  • memory usage reduction in Reduce memory usage for allele plots #478 and Slots implementation #509
• New parameters, --flexiguide_gap_open_penalty and --flexiguide_gap_extend_penalty, to customize flexiguide alignment in Add flexiguide alignment parameters #491
• New parameter --halt_on_plot_fail so that errors and exceptions in plots don't fail silently in Mckay/halt on plot fail #494
• New parameter --samtools_exclude_flag to customize the filtering of reads in Add customizable samtools exclude flag #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 Prefix the release Docker tag with a v #434
• Fix typo and move flexiguide to debug (reversed output with two sequences in -amplicon_seq and one sequence in –expected_hdr_amplicon_seq #77) by @Colelyman in Fix typo and move flexiguide to debug (#77) #438
• Pin versions of numpy and matplotlib in CI environment by @Snicker7 in Pin versions of numpy and matplotlib in CI environment #452
• Implement new pooled mixed-mode default behavior by @mbowcut2 in Implement new pooled mixed-mode default behavior #454
• Update README by @Snicker7, @mbowcut2, @trevormartinj7, @Colelyman and @kclem in Update README #456
• Asymmetrical cut point by @kclem in Asymmetrical cut point #457
• d3 plot enhancements by @trevormartinj7 in d3 plot enhancements #459
• Matplotlib Compatibility Fix by @mbowcut2 and @Snicker7 in Matplotlib Compatibility Fix #464
• Cache conda packages in GIthub Actions by @Colelyman in Cache conda packages in GIthub Actions #466
• Replace zcat by @Colelyman in Replace zcat #468
• Cache read merging step in CRISPRessoPooled on no_rerun by @kclem in Cache read merging step in CRISPRessoPooled on no_rerun #467
• Fix CRISPRessoAggregate bug and other improvements (CRISPResso2 not working after conda installation #95) by @Colelyman in Fix CRISPRessoAggregate bug and other improvements (#95) #470
• Display percentages in the CLI output by @Colelyman in Display percentages in the CLI output #473
• No processor pool when running in single thread by @Snicker7 in No processor pool when running in single thread  #474
• Round percentage complete in CLI and add initial 0% complete by @Colelyman in Round percentage complete in CLI and add initial 0% complete #477
• Reduce memory usage for allele plots by @Colelyman in Reduce memory usage for allele plots #478
• Sync reports by @Colelyman in Sync reports #479
• Read Alignment Parallelization (#98) by @trevormartinj7 in Read Alignment Parallelization (#98) #480
• Add all_deletion_coordinates to be returned by find_indels_substitutions_legacy function by @Colelyman in Add all_deletion_coordinates to be returned by find_indels_substitutions_legacy function #486
• Add flexiguide alignment parameters by @Colelyman in Add flexiguide alignment parameters #491
• Mckay/halt on plot fail by @mbowcut2 in Mckay/halt on plot fail #494
• Add pyproject.toml and support numpy v2 by @Snicker7 in Add pyproject.toml and support numpy v2 #496
• Fix missing substitution in name of WGS, Compare and Meta reports by @Colelyman in Fix missing substitution in name of WGS, Compare and Meta reports #498
• Update jinja_partials and bring Reports into sync by @Colelyman in Update jinja_partials and bring Reports into sync #500
• Update CRISPRessoPooledCORE.py by @kclem in Update CRISPRessoPooledCORE.py #502
• Add customizable samtools exclude flag by @Colelyman in Add customizable samtools exclude flag #503
• Pooled multi region map fix by @kclem in Pooled multi region map fix #505
• Add support for octal and comma separated samtools exclude flags (add ci.yml, config.yml #113) by @kclem in Add support for octal and comma separated samtools exclude flags (#113) #507
• Fix get_n_fastq function by @trevormartinj7 in Fix get_n_fastq function #508
• Slots implementation by @mbowcut2 in Slots implementation #509
• Suppress printing by @kclem in Suppress printing #511
• Update detailed alleles table help option by @Colelyman in Update detailed alleles table help option #513

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

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This discussion was created from the release Junction Salt.