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

v1.13.15

Changed

• bit-assemble
  • the threads parameter is now passed to bbnorm and fastp (if run) in addition to the assemblers
• bit-gen-reads
  • --type long will no longer preferentially start reads at position 0 if the requested read size is larger than the contig; now it will start randomly and just produce a read that ends where the contig ends (unless --circularize is added)
• bit-cov-analyzer
  • no longer writes out individual window stats by default (to save spacetime), it needs to be turned on with the --write-window-stats now if wanted

Full Changelog: v1.13.14...v1.13.15

v1.13.14

Fixed

• bit-gen-reads previously may have by chance created reads with identical headers (since only coordinates were being added), now there is also a counter to prevent this

Full Changelog: v1.13.13...v1.13.14

SRA download workflow v1.1.1

• fix duplication of "fastq" in output filenames

v1.13.13

Added

• to bit-gen-reads
  • added single-end and long-read capabilities (through --type argument now, see Changed below)
  • single can be used up to any size, but if specifying --long, it will also generate reads with lengths spanning a range around the specified read size (50% by default)
• to bit-calc-variation-in-msa
  • 3Di as an option for --type

Changed

• bit-gen-reads
  • now has --type flag for paired-end, single-end, or long (paired-end still by default)
  • did more work than it's worth to ensure the exact number of requested reads are always returned
• bit-calc-variation-in-msa
  • --gaps-treatment changed to "include" by default

Full Changelog: v1.13.12...v1.13.13

v1.13.12

Added

• bit-add-insertion

Full Changelog: v1.13.11...v1.13.12

v1.13.11

Changed

• bit-update-ncbi-taxonomy replaced with get-ncbi-tax-data (prior still retained for now)
• dropped bit-calc
  • if you are the one other person that ever used this and you want it back, you can add this to your ~/.bashrc: bit-calc () { awk "BEGIN { print $1 }"; } :)
• modified bit-colnames to try to autodetect delimeter

Fixed

• added back in setup.py glob portion needed for scripts not fully integrated into python-packaging yet

v1.13.10

Changed

• bit-get-cov-stats
  • the --include-non-primary flag now in addition to calculating percent ID including supplemental and secondary alignments also runs mosdepth with --flag 1540
• bit-dl-ncbi-assemblies
  • in python now instead of bash (i hope this doesn't hinder performance too much...)
  • default concurrent downloads is 10 now instead of 1
  • default format is fasta now instead of gbk
  • downloads only happen in http now, no more ftp, so the -P flag to specify http has been removed
  • added optional output dir
• no longer keeping stubs in scripts/, instead keeping a ton of entry points in pyproject.toml
• bit-filter-seqs-by-length renamed to bit-filter-fasta-by-length to be more specific (prior still retained for now)

Full Changelog: v1.13.9...v1.13.10

v1.13.9

Added

• bit-get-cov-stats by default now produces per-contig level info also (can be shut off with --skip-per-contig)

Changed

• bit-get-cov-stats
  • the original ref-based output file is now called <output-prefix>-per-ref.tsv (changed from <output-prefix>.tsv)
  • outputs include median coverage in addition to mean
  • for speed (and consistency with expectations of known most-frequent users), when bit-get-cov-stats runs mosdepth, it uses the -x | --fast-mode flag now
  • added progress bar when parsing coverage info
• bit-assemble
  • re-arranging of help menu
  • memory setting now passable to spades too
• report_message function from modules.general slightly altered
  • this is more a note to myself for if/when i see weird things in terminal-printing format show up later
• general help-menu formatting

Full Changelog: v1.13.8...v1.13.9

v1.13.8

Added

• --circularize option added to bit-gen-reads so that generated fragments can span the end-to-start of contigs if wanted