Literature and Los Angeles

What's Changed

• Improve performance by removing regex from indel location analysis by @Colelyman #182
• Fastq output produced by --fastq_output now includes the inserted bases. Previously, a string like "DEL= INS=78(1) SUB= " would indicate a 1bp insertion at site 78. This update outputs strings like "DEL= INS=78(1+G) SUB= " with the insertion described as a plus character followed by the inserted bases. (2f84dd0)
• Adds features for providing aligned bams as input to CRISPRessoPooled and for a faster demultiplexing when amplicons and genome are provided. The added parameters are:
  • --aligned_pooled_bam: Path to aligned input for CRISPRessoPooled processing. If this parameter is specified, the alignments in the given bam will be used to demultiplex reads. If this parameter is not set (default), input reads provided by --fastq_r1 (and optionally --fastq_r2) will be aligned to the reference genome using bowtie2. If the input bam is given, the corresponding reference fasta must also be given to extract reference genomic sequences via the parameter --bowtie2_index. Note that the aligned reads are paired-end seqenced, they should already be merged into 1 read (e.g. via Flash) before alignment.
  • --demultiplex_only_at_amplicons: If set, and an amplicon file (--amplicons_file) and reference sequence (--bowtie2_index) are provided, reads overlapping alignment positions of amplicons will be demultiplexed and assigned to that amplicon. If this flag is not set, the entire genome will be demultiplexed and reads with the same start and stop coordinates as an amplicon will be assigned to that amplicon.

Minor bug fixes:

• Fix deprecated pandas indexers (eea442a, f4b6cfc)
• Update ylabel_values -> y_label_values by @swrosati in #174
• Allow mixed-case prime-editing input (e999079)
• Fix int bug for CRISPRessoPooled n_reads (ef15cae)

Full Changelog: v2.2.6...v2.2.7