Kevlar version 0.2.0

Kevlar release v0.2 adds new subcommands for read partitioning and variant calling, fixes a major bug with contig assembly, and introduces many minor fixes, improvements, and code refactoring.

Added

• New subcommands
  • partition: group reads by shared interesting k-mers
  • localize: determine an assembled contig's location in the reference genome
  • call: align assembled contigs to reference and call variant
• Documentation suite in docs/, hosted at https://kevlar.readthedocs.io
• New third-party dependency ksw2 for computing alignments. Wrapped with Cython, which is a new development-time dependency (but not install or run time).
• The pandas package is now a dependency, and pysam and networkx are now hard dependencies (rather than conditional).

Fixed

• Bug with assembly when the order of a read pair was swapped and they had the opposite orientation (see #85).