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Update chromosome sorting to properly handle chromosomal arms, for
example with Drosophila
Change .groups.txt group file name to .col_groups.txt when writing
column metadata file for scripts get_binned_data.pl and get_relative_data.pl
Change back to _summary.txt file name when writing a summary file
Change --blacklist option to --exclude in bam2wig.pl
Improve error handling scenarios in data2wig.pl, including invalid indexes
Fix bugs in manipulate_datasets.pl, including missing lines in the view function
and restricting the addname function to only update a proper "Name" column
Update any remaining POD text references about 0-base indexing to 1-base