19.08.1

New features:

• Addition of mode flags:

  • FastQ output modes:
    • "F" (default): Outputs full validation set of combined acceptor and donor reads
    • "A": Combines pre-existing FastQ donor files with filtered acceptor reads (requires pre-existing variant context file)
    • "D": Outputs combined donor reads only
    • "P": Outputs individual FastQ files per variant
    • "X": No FastQ output
  • Variant context modes:
    • No option specified (default): Builds a variant context file from inputs
    • "C": Accepts a pre-existing variant context file to build FastQ files from

• Restructured variant context building and FastQ writing

• Added support for input of configuration files with preset argument parameters

• "A" mode donor FastQ files are distributed across acceptor FastQ files

Future plans:

• May implement distribution of individual donor FastQ reads across validation set FastQ output files, instead of distributing whole FastQ files
• Parellelization of FastQ writing
• Variant context file checks, to ensure that user-created variant context files do not contain overlapping contexts