HiCUP-Plus v1.0.0

HiCUP+ v1.0.0 is a major update incorporating the changes described below:

• refactors error handling and warnings without changes to results from
  Bowtie or Bowtie2 aligners

• initialises reverse read for pairing and migrates filtering to use
  matches in header strings rather than index numbers

• adds calls to the HiSAT2 aligner (Kim et al., 2019) using stream
  inputs and parameters equivalent to the Bowtie2 parameters

• adds a call to the proprietary Dragen (Illumina Inc., 2021) aligner
  via a system call with the error handling and log outputs adjusted
  for compatibility

• updates to pairing and reporting scripts for compatibility with
  the Dragen aligner run only if this aligner is chosen

• updates the documentation to describe configuration of changing
  aligners to HiSAT2 or Dragen

• updates R graphical devices to PDF (removing need for Cairo graphics in SVG format)

• updates Maintainer of this fork to S. Thomas Kelly
  [email protected] (Bioinformatics Team,
  H.U. Group Research Institute G.K., Tokyo, Japan; SRL Inc., Tokyo, Japan)

This release is a fork of the original HiCUP pipline. See the release notes
for previous versions below and the GitHub repository for more details:
https://github.com/StevenWingett/HiCUP

This fork has been renamed to HiCUP-Plus (HiCUP+) to avoid it being
mistaken to the original implementation.

Full details of changes can be viewed on GitHub

Full Changelog: v0.8.2...v1.0.0