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

v1.13.7

Changed

• bit-get-cov-stats now also reports mean percent ID of mapped reads for each input reference when the input includes a bam file (leveraging bit-get-mapped-reads-pid)

v1.13.6

Added

• bit-get-mapped-reads-pid to pull out percent-identity information of mapped reads from an input bam
  • for each mapped read:
    • calculated percent ID = (full_aligned_length - NM) / full_aligned_length * 100
      • where full_aligned_length = Matches + Mismatches + Insertions + Deletions
• added a 'genome' option to bit-get-test-data that pulls an E. coli genome

Changed

• modularized and added tests for bit-get-workflow, bit-get-test-data, bit-dedupe-fasta-headers, bit-fasta-to-genbank, and bit-fasta-to-bed
• added more tests to bit-gen-reads
• improved coverage on some other modules with more unit tests
• moved more setup info into pyproject.toml, but retained minimal setup.py to be able to glob because bit has a lot of separate scripts

v1.13.5

Changed

• bit-count-bases-per-seq has been removed with its function combined into bit-count-bases
  • if input fasta has one sequence, it prints the length to the terminal; if it has 2 or more, it will print out summary stats; in either of the two prior cases, if an output file is specified, the program will additionally write lengths of all sequences to that specified file
  • modularized, test added
• modularized and added unit tests for bit-lineage-to-tsv
• bit-mutate-seqs
  • --seed-for-randomization long-parameter shortened to just --seed
  • modularized and test added

Fixed

• bit-assemble now properly filters spades-assembled contigs based on user-specific min-contig length

v1.13.4

Changed

• updates to bit-get-cov-stats
  • can start from bam file now in addition to mosdepth per-base.bed.gz (will generate the mosdepth output if starting from bam)
  • modularized, integration test added
• updates to bit-check-for-fastq-dup-headers
  • autodetect gzipped or not
  • modularized, test added

v1.13.3

Added

• more test coverage of bit-ez-screen
• added tests for bit-gen-kraken2-tax-plots, bit-kraken2-to-taxon-summaries, and bit-calc-variation-in-msa
• integration test for bit-cov-analyzer

Changed

• modularized bit-calc-variation-in-msa
• updates to bit-gen-kraken2-tax-plots
  • modularized
  • appropriately adds domain letter to plots from GTDB tax kraken2 reports now

v1.13.2

• updates to bit-kraken2-to-taxon-summaries
  • modularized
  • no longer takes the larger kraken.out file, it now works off of the kraken.report
  • no longer works based on taxid lookup, it now works based on the taxonomy in the kraken report
    • this means it will exactly match the taxonomy used in the kraken2 db, and not swap anything if taxids or rank names changed
    • also means it works with GTDB-kraken2-db produced reports (which previously would not work with the standard taxid lookup method)

v1.13.1

• modularized bit-filter-seqs-by-length and added a test for it
  • also changed the name to bit-filter-fasta-by-length, though i'm retaining a stub for the old name so it still works when called that way too
• modularized bit-summarize-column and added tests
• added a temp fix for the latest megahit osx-64 build not working (see smk/envs/assemble-osx-64.yaml; if that's gone it was no longer needed and removed in the future)
• fix to bit-summarize-column when standard input is only one column (was erroring out before)

v1.13.0

• added bit-assemble
  • command-line wrapper for an assembly workflow with optional qc and digital normalization
• modularized bit-gen-reads
• added more integration tests

v1.12.3

• modifications to bit-cov-analyzer
  • default --min-region-length set to 500 to help reduce overwhelming output and focus on larger regions
  • added a column for "zero_cov_bases" to output low- and high-coverage region tsvs