BioToolBox-v2.00

• MAJOR UPDATE: Change all internal and user-oriented column indexing
  to 1-base instead of 0-base indexing, i.e. column numbers are now
  listed beginning with 1 instead of 0. WARNING!!! THIS WILL BREAK ALL
  PRE-EXISTING SCRIPTS AND CODE THAT USES HARD-CODED COLUMN INDEXES!!!
• MAJOR UPDATE: Use a single unified Bio::ToolBox::Parser module with
  subclasses for bed, gff, gtf, and ucsc table formats. NOTE: This changed
  name capitalization of Bio::ToolBox::Parser subclasses from parser
• Improve parsing of gtf files, especially with duplicate tags
• Replaced old table sorting algorithm to use numeric, mixed digit-string,
  and/or string sorting
• Improved accuracy of detecting standard columns such as name, ID, start, etc
• Add support for column median and trimmed-mean methods when generating a
  summary file
• Fix bug with filtering features by transcript_support_level and gencode
• Remove Bio::Seq::IO requirement for writing fasta files in data2fasta.pl
• Changed behavior to always use 1-base coordinate when generating coordinate
  strings, which is standard behavior e.g. with HTSlib (samtools and tabix) queries
• Improve support for coordinate lookup in merge_datasets.pl, including
  handling either 1-base or 0-base coordinate strings.
• Always report both transcript and gene name IDs and names in text output
  from get_gene_regions.pl
• Add bedpe format support
• Fix bugs with parsing file headers and assigning standard column metadata
• Fix bug with naming empirically derived introns
• Add option to skip chromosomes in get_gene_regions.pl
• Add option to adjust relative coordinates based on narrowPeak peak
  in get_features.pl
• Fix edge-case bugs with low-level bam parsing
• Speed up certain stats functions and improve detection of numbers
  in manipulate_datasets.pl
• Remove defunct supplementary tables in ucsc_table2gff3.pl
• Improve data format verification, and only run it when reading and writing
• Improve error reporting in scripts
• Use a proper prompting module for user-input
• Fix massive numbers of perlcritic and perltidy issues
• Hundreds of other bug fixes