Kevlar version 0.6

Added

• The kevlar count operation now supports masks and 8-, 4-, or 1-bit counters (see #277 and #291).
• A Jupyter notebook and supporting code and data for evaluating kevlar's performance on a simulated data set (see #271).
• New flags for filtering gDNA cutouts or calls from specified sequences (see #285).
• New filter that discards any contig/gDNA alignment with more than 4 mismatches (see #288).
• A new feature that generates a Nodetable containing only variant-spanning k-mers to support re-counting k-mers and computing likelihood scores in low memory (see #289, #292, #302).
• A new ProgressIndicator class that provides gradually less frequent updates over time (see #299).

Changed

• Ported augfastx handling from kevlar.seqio module to a new Cython module (see #279).
• Dynamic error model for likelihood calculations is now an configurable option (see #286).
• Cleaned up overlap-related code with a new ReadPair class (see #283).
• Updated kevlar assemble, kevlar localize, and kevlar call to accept streams of partitioned reads; previously, only reads for a single partition were permitted (see #294).
• Overhauled the kevlar localize command to compute seed locations for all seeds in all partitions with a single BWA call, massively improving efficiency (see #294 and #301).
• Updated the variant calling procedure to discard alignment blocks less than ksize in length (see #303).

Fixed

• Minor bug with .gml output due to a change in the networkx package (see #278).

Removed

• Buggy home-grown greedy assembler dropped (see #279). Some parts of the overlap code retained and refactored (see #283).