Update ovl-cov-stats

• Stop writing nan (into JSON) for ovl-cov-stats

New subtools (e.g. paf-splitter)

• Added a PAF splitter and indexer to be used with the new mapping via read tracking
• PAF splitter for the read-to-contig tracking-based-mapping for polishing.
• Subtool to rename IPA contig headers to the Falcon-compatible format, so that the contigs can be used with Falcon-Phase.
• Exposed the min average coverage cutoff which was previously hardcoded to 5. (For m4filt* subtools; new parameter --min-avg-cov.)
• New subtool gfftools-gffsubtract.
• Updated the hts-nim vendor library.

Minor fixes

• Remove -e by default from purge_dups get_seqs.
• Accept unknown config options, for now. (So we do not crash when they are added.)
• Close files when not needed in polish_prepare. (Note: There may still be too many open file-handles in nighthawk.)
  • PacificBiosciences/pbbioconda#327

Support for purge_dups

Sharding for parallel mapping before purge_dups.