v1.14.0

Added

• to bit-cov-analyzer
  • progress updates while running
  • zero-coverage region outputs now also generated
  • output region tsvs now have a "low_complexity" column that holds True or False
    • this is based on:
      • low_complexity = True if: unique 3-mers / all-possible-3mers <= 0.4
• bit-extract-seqs
  • enables pulling out target seqs from a fasta by bed file or specified primers via subcommands
• to bit-gen-reads
  • --fragment-size-range option added, defaults to 10% of fragment size

Changed

• bit-cov-analyzer
  • -s | --sliding-window-size changed to -w | --window-size, and -S | --step-size changed to -s | --step-size (lower-case)
  • default window size change from 50 to 100, and default step size changed from 10 to 20
  • drastic improvements to efficiency when working with large genomes (e.g., 3GB)
  • histogram of coverages no longer plotted by default, only done now when adding the --write-window-stats flag
  • no longer produces window-coverage-overview.txt as all of that info is captured within window-coverage-overview.tsv
• bit-get-mapped-reads-pid
  • minor improvements to efficiency
• bit-get-cov-stats
  • improvements to efficiency
  • now also reports median percent id of mapped reads per ref and per contig (when provided an input bam file)
• bit-summarize-assembly
  • adds commas when printing stats to terminal for readability
• bit-extract-seqs-by-coords is now combined into bit-extract-seqs
• bit-gen-reads
  • now has a --fragment-size-range that defaults to 10% of fragment size
  • by default will not include regions with Ns in generated reads, add --include-Ns to allow that