BioToolBox-v1.68

• Script bam2wig.pl script can now record both ends of paired-end
  fragments, rather than faking it as single-end. Paired-end start
  now respectes orientation. Added new option to only record either
  first or second read in a pair. Added new option to ignore
  zero intervals when writing bedGraph format. Changed multi-hit
  scoring to preferentially use NH instead of IH.
• Scripts get_binned_data.pl and get_relative_data.pl now
  can write out column names and associated datasets in separate
  groups file for use in plotting. Also specify score decimal format.
• Script get_features.pl has new option to only keep features with
  explicit tag value.
• High level ToolBox convenience function parse_file now includes
  basic default subfeatures exon, cds, and utr.
• Efficiency improvements in loading large text files by going
  back to chomp. Should still fail appropriately with wrong
  line endings.
• Feature objects now allow certain attribute methods to be both
  get and set, including seq_id, start, end, strand, name, and
  type, so long as the table does not contain parsed or database
  SeqFeature objects.
• Add Data object function to return any single row Feature without
  having to use an iterator.
• Add high level function for iterating over Bam alignments.
• Add support for intron subfeatures in Feature objects and data
  collection scripts.
• Allow bigWigToBedGraph to be explicitly used
• Better handling of verified dataset names
• Bug fixes and improvements in identifying database file
  formats and loading adapters.
• Bug fix in writing bgzip files.