mrmckain/Fast-Plast: Fast-Plast v.1.2.6

Multiple fixes and additions since v.1.2.2.

--skip parameter added. Allows users to skip the trimming step when "trim" option is include. Syntax: --skip trim

--only_coverage option added. Allows users to provide a chloroplast genome and reads to run the coverage analysis portion of Fast-Plast.

--Coverage used by Fast-Plast is printed to log and summary files.

--N's allowed in coverage and IR/SC identification from scaffolding.

--Faster runs of afin after initial coverage analysis.

--Minimum coverage for coverage analysis no longer defaulted as 0. Now estimated as 0.25 of average coverage across plastome.

--General bug fixes accuracy.

--Subsampling option added to allow for faster completion.