pretext_to_tpf feature updates

[DomAbsolon]

• Use fasta input instead of TPF. script is rapid_split.pl

• Creation of fasta output rather than TPF, so that curators don't have to run another script, might be nice to save an AGP alongside the fast script is rapid_join.pl/multi_join.py

• Separate summary stats for each haplotype - also format stats into more readable format for curators.

• Add a new Target tag which acts in the same way that Contaminant already does

• Fix bug with 1 pixel gap between fragments during cuts Or should they be reported in an error message that makes them easy to find in PretextView?

• Print sensible error message where -a and -p command line arguments are the wrong way round, which results in pretext-to-tpf failing to parse the Pretext bp per pixel value

• Make matching of haplotype names to scaffold names case insensitive

• Enable switching scaffolds to another haplotype when they are not in a painted chromosome in that haplotype

• Print error/ warning message when a scaffold has the metadata tag 'unloc' but is not painted into a super scaffold

• Add interpretation of roman numeral metadata tags

[DomAbsolon]

Note that the "Target" tag should also create a csv in the way the "HAP" tags do