NINJA-OPS v1.3.1

• Explicit paired-end support (in wrapper; optional distance parameter)
• Filtered file shows reasons for filtering
• Alternative ambiguous base handling schemes (discard or convert A)
• New commandline options and documentation
• Fix Mac crash in parser in certain situations
• Streamlined BIOM 1.0 format
• Re-added relative path support if binaries aren't in PATH
• Python script tweaks for handling drop-in bowtie2
• Renamed Linux binaries to be compatible with script calls