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