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Kevlar version 0.3.0
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@standage standage released this 03 Nov 18:31
· 480 commits to master since this release
0.3.0
ef73d5b

This release includes many new features, some refactoring of the core codebase, and the first end-to-end analysis workflow implemented in a single command.
Details are included below.

Fixed

  • Abundances reported by kevlar filter now correctly show re-computed proband k-mer abundances, not pre-filtering abundances (see #111).
  • The kevlar localize and kevlar call procedures now handle multiple assembled contigs, calling variants from the best reference match for each contig (see #124, #126, and #147).

Added

  • New abundance screen now a part of kevlar novel. If any k-mer in a read is below some abundance threshold, the entire read is discarded (see #106).
  • Better error reporting and handling of various issues with assembly, localization, and alignment (see #113, #114).
  • Support for VCF output (see #130 and #144), including "windows" with all k-mers containing the reference allele (RW) and alternate allele (VW) to facilitate distinguishing inherited mutations from novel mutations (see #144 and #152).
  • New subcommands
    • alac: assembles, localizes, aligns, and calls variants on a single partition basis
    • simplex: invokes the entire simplex analysis workflow

Changed

  • The kevlar filter procedure now handles both contamination and reference matches under a single "mask" interface (see #103).
  • Explicitly dropped support for Python 2.7. Now supports only Python >=3.5 (see #125).
  • Main methods for each core subcommand are now implemented as minimal wrappers around generator functions, to facilitate composing different steps of the workflow or invoking them from third-party Python code (see #95, #126, #133, #148, #149, #150, #159, #161).
  • The home-grown greedy assembly implementation has been replaced by calls to the fermi-lite library, which is now bundled with kevlar (see #156).
  • The default behavior of kevlar partition is now to output a single stream of reads.
    Writing each partition to a distinct file is still supported with the --split option.

Removed

  • The kevlar collect command and associated tests. Its functionality has now been fully distributed to other subcommands.
    • Read filtering to kevlar filter
    • Junction count contig assembly to kevlar filter as an optional mode
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