Version 1.0.0 Alpha

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Date Created:

• 20 May 2020

Changes affecting BISCUIT, in general, or multiple subcommands/scripts:

• This version is not backwards compatible with BISCUIT Version 0.3.16 and earlier.
• Contact person for BISCUIT updated.
• biscuit markdup removed from API
• Unnecessary files removed from code base
• All subcommands now have a help option (-h)
• General consistency applied for help output
• Small changes to wording of option descriptions (default values included if not obvious)
• Error messages added for missing command line arguments
• Flag/option characters changes for consistency across subcommands (see next section for specific changes)

Changes affecting specific subcommands/scripts:

• bsconv:
  • Flag change: -b → -p for printing output in TSV format
• mergecg:
  • Flag change: -n → -N for NOMe-seq mode
• tview:
  • Flag change: -f was not originally being read, now is included
• epiread:
  • Flag change: -q → -@ for number of threads to use
• pileup:
  • Flag change: -q → -@ for number of threads
  • Flag change: added in -s flag for step of window dispatching
• align:
  • Flag change: -t → -@ for number of threads to use
  • Flag change: -h → -g for max number of hits output in XA tag
  • Flag change: -h now used for help
• QC.sh:
  • Updated script to reflect changes made to flag/option characters