v2.0.38: Bam processing + Prime Editing updates

• Input can now be read from bam using the parameter --bam_input and (optionally) --bam_chr_loc to use the reads in the bam at this location as input.
  An output bam is produced with an additional soace-separated field prefixed by c2 (e.g. c2:Z:ALN=Inferred CLASS=Inferred_MODIFIED MODS=D47;I0;S0 DEL=56(47) INS= SUB= ALN_REF=TTGGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGCATGGCCCCATTCGCACGGCTCT----------------------------------------------- ALN_SEQ=ACACCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGA-----------------------------------------------TCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGCATGGCCCCATTCGCACGGCTCTGGAGCGGCGGCTGCACAACCAGTGGAGGCAAGAGGGCGGCTTTGGGC). Note that the alignment details (location, cigar string, etc) are not modified.. this may be done in the future). Bam file input cannot be trimmed or pre-processed with quality filtering.

• Prime editing scaffold incorporation is now more accurate (looks for the scaffold sequence at the expected position directly after the extension sequence). A plot showing the number of bases matching the scaffold, as well as insertions after the extension sequence, and a data file with these numbers is produced. Added parameter --prime_editing_pegRNA_scaffold_min_match_length to define the minimum length required to classify a read as 'Scaffold-incorporated'

• Renamed split_paired_end parameter to --split_interleaved_input for interleaved input

• Auto mode now considers 5000 reads to detect amplicon sequences

• Add new paramter --annotate_wildtype_allele to annotate wildtype alleles on the allele plots

• Update output when reporting missing files -- only lists first 15 files in the current directory and directory of input parameter

--reference https instead of http

v2.0.37

• max processors can be used in WGS and Pooled modes by setting -p max
• CRISPRessoPooled demultiplexing is performed in parallel and with reduced filesystem demand
• Prime editing analysis can be performed by specifying the parameters:
  --prime_editing_pegRNA_spacer_seq
--prime_editing_pegRNA_extension_seq
  and optionally
  --prime_editing_pegRNA_extension_quantification_window_size
--prime_editing_pegRNA_scaffold_sequence
--prime_editing_nicking_guide_seq
  with a summary shown in the report
• Nucleotide plots are shaded when the nucleotide matches the reference sequence
• sgRNA improvements:
  • sgRNA annotations are plotted on multiple lines if they overlap
  • sgRNAs can have their own cut site and quantification window size
• N's don't count as substitutions
• extended read analysis data available with --write_detailed_allele_table flag

Pooled Parallelization

v2.0.34

Pooled Set flag to skip reporting problematic regions

v2.0.33 plot updates

Parallelization and checkpointing of CRISPRessoWGS and Pooled
Increase of alignment efficiency of CRISPRessoPooled amplicons in genome +amplicons mode
Plotting computation window is shaded

v2.0.32

Plotting updates, dsODN detection, and general improvements and bug fixes.

v2.0.31 CRISPRessoPooled chr names fix, allele plot colors

Update dependency requirements
Add custom post-processing plot functions for allele tables
Fix CRISPRessoPooled handling of chromosomes with underscores

v2.0.30

add nucleotide summary for batch mode
fix bug for reporting amplicons with no reads
case-insensitive checking for guides

v2.0.29

By default, the html report is created on the outside of the output folder, so if the output is:
CRISPResso_on_SAMPLE/
the html report will be at
CRISPResso_on_SAMPLE.html
This functionality can be reverted to place the report inside of the output folder using the parameter --place_report_in_output_folder
which will place the html report at:
CRISPResso_on_SAMPLE/CRISPResso2_report.html

v2.0.28

Standardize window definitions (plot window and quantification window specify the distance from the cut site to the edge of the window, so the entire window is 2*plot window)
Standardize file names
Add CRISPREssoCompare output html
CRISPRessoBatch guide-specific output are plotted as separate plots

v2.0.27

Add reports for pooled and WGS
Add Batch pickle info
More precise plotting of cleavage cut site and quantification window
Bioconda updates