Squirrel v1.0.12

Release notes

• APOBEC3-reconstruction tree figure customisation. Occasionally, you may want to adjust the final APOBEC3-reconstruction tree figure output. There are now a number of options to help you achieve this. Firstly, rather than having to rerun the entire analysis, there is now an option that allows the user to re-render the tree figure only (-tfig/--tree-figure-only). The user must supply a tree file and matching branch reconstruction file that has been output by a previous squirrel run. This can be done with the -brf/--branch-reconstruction-file and -tf/--tree-file arguments.

• Alongside these files, the user can then specify a custom height (--fig-height) or width (--fig-width) for the final tree vizualisation.

• The user may now also specify whether the reconstructed mutations vizualised on the branch are either represented by a circle hovering over the branch or a square spanning the branch with the --point-style argument, and whether they want the points to begin stacking from the left or right with --point-justify.

• Adding in reference column in absence of bed file formats accepting a notes column.

• Updating gene boundary files to have record of accession number in.

• Squirrel now offers a sequence-specific mask option for making particular sites in a problematic sequence, rather than masking out the entire column across the alignment. This can be achieved with --sequence-mask and requires the user to supply a csv file with a sequence column that contains the sequence name (must match an id in the supplied FASTA file) and a site column, with a 1-based position to mask. If a sequence needs multiple sites masked, specify them on separate lines in the file with the same sequence name.

• fix for issue #53 when a file is forgotten to be supplied, exits with handling

• adding additional flag to either write binary mask file for beast or now an optoin to sep out dimers with a 0,1,2 mask string.