HiCUP-Plus v1.0.2

RELEASE NOTES FOR HICUP-Plus v1.0.2 (2 NOVEMBER 2022)

HiCUP+ v1.0.2 is a mnior update incorporating the changes described below:

• updated checks in the HiCUP modules to check for SSH connections

• updated Dragen call to run via SSH if hostname does not include "dragen"

Full Changelog: v1.0.1...v1.0.2

HiCUP-Plus v1.0.1

HiCUP+ v1.0.1 is a mnior update incorporating the changes described below:

• implements built-in timing reported to stdout

• bug fixes to post-processing in pairing step of hicup_mapper:
  ensures that reads are not sorted in intermeidiate SAM files
  and that reads are correctly paired in order. Index numbers
  are used for Bowtie, Bowtie2, and HiSAT2 in stream inputs.
  Matching strings in Dragen output is implemented without
  assuming FASTQ header format.

Full Changelog: v1.0.0...v1.0.1

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
  simonthomas.kelly@hugp.com (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