Replaced various scripts for fasta renaming with seqkit replace.
Resolves #54
Fixed some truncated centromeres by removing dna-brnn filtering parameter percentile filtering.
Fixed centromere mapping script using incorrect arm column resulting in false mappings.
Fixed centromere mapping script falsely mapping when using sequence identity metrics by switching to the greatest number of matches when building reference to contig mapping.
Resolves #49
Added various tests for custom scripts.
Added omission of rules by commenting out specific sections of the config file.
Resolves #53
Improved dna-brnn filtering so the contig cutoff is closer to the main HOR array(s).
Improved centromere mapping script to handle cases where contig maps to CHM13 at only a single p or q-arm.
Improved trimming of centromeres by removing script to calculate bp to add to edges and using a static 500kbp.
Removed unused code/files.
Removed remapping by CenStats as too unreliable and can be achieved more accurately by centromere mapping script.
Updated default CHM13 RepeatMasker annotations so they are closer to trimmed output.
seqkit replace.dna-brnnfiltering parameter percentile filtering.dna-brnnfiltering so the contig cutoff is closer to the main HOR array(s).CenStatsas too unreliable and can be achieved more accurately by centromere mapping script.RepeatMaskerannotations so they are closer to trimmed output.NucFlagdefaults to detect misjoins.