JBrowse 1.16.10

Minor improvements

• Added an optimization for BAM that helps for long reads especially
  (@cmdcolin)

• Added generation of the MD tag if none is specified in BAM (issue
  #1022, @cmdcolin)

• Added customRefRename and replaceRefRename global configs for
  extending and replacing ref renaming functionality respectively.
  Ref renaming helps things like chrM and chrMT to be loaded onto the
  same chromosome in jbrowse (@cmdcolin, pull #1506)

• Added support for a -f option for setup.sh. This option causes
  setup to skip installing perl prerequisites and setting up
  sample data. It is primarily intended to support faster builds
  in a Docker context. (@scottcain)

Bug fixes

• Fix the display of mismatches from hard clipped BAM sequences (pull #1513)

• Fix ability to use tracks from Open track dialog in combination tracks.
  Thanks to Sonny Arora for the repo (pull #1536)

• Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq
  (@cmdcolin)