Knockout Lake

Starting in version 2.1.0, insertion quantification has been changed to only include insertions completely contained by the quantification window.
To use the legacy quantification method (i.e. include insertions directly adjacent to the quantification window) please use the parameter --use_legacy_insertion_quantification

This release also includes several updates to:

• prime editing: pegRNA spacer sequences given in the incorrect orientation are no longer tolerated
• HDR: Ambiguous alignments don't contribute to the plot 4g (except when --expand_ambiguous_alignments is provided)
• --fastq_output now also writes alignment scores and alignments for every read