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

Screen King

What’s Changed

• Cole/refactor jinja undefined (#66) by @Colelyman and @Skicker7 in #421
• Remove extra imports from CRISPRessoCore by @Colelyman in #422
• Fix CRISPRessoPooled error reporting by @kclem in #423
• Update README by @Colelyman in #424
• Extract jinja_partials and fix CRISPRessoPooled fastp errors by @Colelyman and @trevormartinj7 in #425
• Bump version to 2.3.1 and change default CRISPRessoPooled behavior to change in 2.3.2 by @Colelyman in #428
• Fix batch mode pandas warning. (#70) by @mbowcut2 and @Colelyman in #429
• Fix issues with file_prefix by @Colelyman and @Snicker7 in #430
• Fix plots and improve plot error handling by @Snicker7 and @mbowcut2 in #431
• Showing sgRNA sequences on hover in CRISPRessoPro by @Colelyman in #432
  Full Changelog: v2.3.0...v2.3.1

Targeting Minato

Targeting Minato v2.3.0

Major changes:

• Flash and Trimmomatic are replaced with Fastp by @trevormartinj7, @Snicker7, and @Colelyman
• Guardrails (checking experimental conditions and raising warnings) by @Snicker7
• Failed runs are displayed with the error by @trevormartinj7

Minor changes:

• Replace link to CRISPResso schematic with raw URL in README by @Colelyman in #329
• Fix samtools piping by @Colelyman in #325
• Prime editing alignment params by @kclem in #336
• Fix for recent Matplotlib v3.8 by @mbowcut2 in #346
• Enable quantification by sgRNA by @kclem in #348
• Fix Matplotlib breaking change issue by @mbowcut2 in #352
• Fix assigning multiple qwc by @Snicker7 in #375
• Run unit tests via Github Actions and fix matplotlib character issue by @Snicker7 and @mbowcut2 in #386
• Remove future Pandas warnings and sort CRISPRessoCompare tables by @mbowcut2 and @Snicker7 in #389
• Fix interleaved fastq input in CRISPRessoPooled and suppress CRISPRessoWGS params by @Colelyman in #392
• Fix #367, reads only align to prime edited amplicon, not to reference by @mbowcut2 in #393
• Run integration tests on every push by @Snicker7 in #394
• Move read filtering to after merging in CRISPResso by @Colelyman in #397
• Fix the assignment of multiple quantification window coordinates by @Snicker7 in #403
• Decrease Docker image size and fix PE naming and parameter behavior by @Colelyman, @Snicker7 and @mbowcut2 in #404
• fix space character in README by @DennyDai in #400
• Fix Jinja2 undefined variables by @Colelyman in #417
  Full Changelog: v2.2.14...v2.3.0

Specific São Paulo

What's Changed

• CRISPRessoPooled
  • Fix missing ' in CRISPRessoPooled --demultiplex_only_at_amplicons
  • CRISPRessoPooled --compile_postrun_references bug fixes
• Prime editing quantification
  • Fix bug in prime-editing scaffold-incorporation plotting

Full Changelog: v2.2.13...v2.2.14

With Montgomery

What's Changed

This release improves parallel processing performance and increases flexibility in input file headers and output file naming conventions.

Major updates

• Parallelization updates
  • Don't start pool when only using single thread by @Colelyman in #302
  • Parallel plotting fix by @Colelyman and @kclem in 546446e and #286
  • Raise exceptions from within futures in plot_pool in a439f09
  • Enable CRISPRessoPooled multiprocessing when os allows multi-thread file append in ebb016d
• Allow multiple overlapping sgRNA matches in reference (previous behavior was to only search for non-overlapping sgRNA sites in the reference sequence in 32e1e97
• Assert correct input fastq file format in 7248ba8

Minor updates:

• Sort pandas dataframes by # of reads and sequences so that the order is consistent for testing by @Snicker7 and @Colelyman in #316
• Update base_editor parameters in README and add Plot Harness by @Colelyman in #301
• Add verbosity argument to CRISPRessoAggregate (#18) fixes #306 by @Colelyman in #307
• Clarify CRISPRessoWGS intended use by @Colelyman in #303
• Update plotCustomAllelePlot.py script for #292 by @kclem in #293
• Case-insensitive headers accepted in CRISPRessoPooled e577318
• Fix multiprocessing lambda pickling by @Colelyman in #311
• Allow dashes in filenames in 712eb2a

Full Changelog: v2.2.12...v2.2.13

Protospace Utah

What's Changed

• Add deprecation notice in #260
• Fix CRISPRessoPooled bam input in #265
• Add snippet about installing CRISPResso2 via bioconda on Apple silicon in #274
• Fix deprecated numpy type names (fixes #269) in #270
• CRISPRessoPooled custom header fix in #278
• Status Updates + Pooled Mixed Mode Update in #279

Full Changelog: v2.2.11...v2.2.12

Of Weber

What's Changed

• Fix batch quilt plot name by @Colelyman in #249
• Batch amplicon plots by @kclem in #251
• Fix typo of CRISPResssoPlot when plotting nucleotide quilt by @Colelyman in #250

Full Changelog: v2.2.10...v2.2.11

Overhangs Alameda

New Features

• Add --zip_output parameter to produce a zipped file report by @Colelyman and @Snicker7 in c80f828
• Allow N's in bam output by @kclem in b0b7d41
• Autodetect reference amplicons from interleaved fastq input

What's Changed

• Parallel plot refactor in #247
• Add plotly to dockerfile in b68a432

Minor Fixes

• Fix bug when comparing two samples with the same name in #228
• Fix bug when name is provided instead of amplicon_name in pooled input file in #229
• Fix for aggregate plots in Batch mode in #237
• Fix loading of crispressoInfo from WGS and pooled in 49740ba

Full Changelog: v2.2.9...v2.2.10

Long Surrey

New Features

• fastq_to_bam implementation in #219
  If the parameter --bam_output is provided, CRISPResso alignments will be written to a file called 'CRISPResso_output.bam' with the alignments in bam format. If the bowtie2_index is provided, alignments will be reported in reference to that genome. If the bowtie2_index is not provided, alignments will be reported in reference to a custom reference created by the amplicon sequence(s) and written to the file 'CRISPResso_output.fa'.
  This enables the viewing of CRISPResso alignments in other browsers (e.g., IGV). If no bowtie2_index is provided, the reference genome should be set to the produced 'CRISPResso_output.fa' file, and then the alignment bam can be loaded into IGV.

Minor Fixes

• CRISPRessobatch: put directory in quotes by @sshen8 in #222
• Don't run global frameshift plot when there are no modified reads by @Colelyman in #226

Full Changelog: v2.2.8...v2.2.9

High Waikato

Welcome to High Waikato

New Features:

• Interactive plotly summary plots in CRISPRessoAggregate and CRISPRessoBatch for visualizing and comparisons
• CRISPRessoPooled enhancement that allows the amplicons file to have a header and additional columns to be provided
• CRISPRessoCompare generates a report of the number of significant reads at each base

What's Changed

• minor bug fixes for plotCustomAllelePlot.py to work with Python3 by @dharjanto in #212
• Coerce ints in batch file checking by @Snicker7 in #200
• Large aggregation by @Colelyman in #192
• flexible pooled input by @Snicker7 and @kclem in #217

Full Changelog: v2.2.7...v2.2.8