Low complexity read removal; assorted fixes

Changes:

• Komplexity now removes low-complexity reads by default instead of masking them.
• Better single-end rule behavior
• Documentation updates
• Various other bug fixes

Bugfixes and report format changes

• report outputs number of removed reads for each host after decontam
• use static binary for komplexity filtering to fix reliance on glibc
• remove max length for contigs (was 50k)

Version 1.0.0 (Stable)

First stable release.

Major changes from the pre-release version:

• Support for single-end sequencing reads
• Low-complexity masking using Komplexity
• Support for extensions
• Ergonomic command-line interface (via sunbeam command)
• Documentation on ReadTheDocs
• Better assembler
• Better ORF finder
• Arbitrary host/contaminant genome filtering
• Semantic versioning and updating
• Robust install and test scripts

Bugfixes

This update fixes numerous bugs.

Initial version

NOTE: This release is in alpha stage and any pipeline endpoints, config file parameters, and other major features may change at any time.

Initial release.