Merge branch 'dev'
Working on fixing tests.
wq
Added stashed changes.
Fixed individual subcommands.
Updated pysam version

New versions seem to work fine now.
Updated pysam instructions.
Fixed default value for location of 'R1 starts' file location
Updated tests to correctly assign R1 start filename (= None)
Updated default value for stacks file(s)
Removed min_depth argument and fixed default check for stacks files
fixed missing R2s bug
Worked on INSTRUCTIONS
Fixed locus identification code

Passes tests, but may not entirely work.