Pull index from read 2 (of 3)
Start rewrite of haloplex demultiplexer
Add initial index parsing, comparison against supplied indexes.
Initial parsing / writing to files
Fix some things / add complicated argument parsing that doesn't really work right
Parsing by index length and manually specified files complete.
Added FastQParser code to the module for local testing (don't need to load scilifelab modules)
Added some TODOs
Various refactoring/improvements, added index file parsing / matching
Added a progress bar. Neat!
More output to keep the user apprised of what's happenin'
Improved status output for large files
Added index frequency counter
Remove unused functions, add subsampling for index frequency tally
More verbose info
Improve line counting speed
Fix progress bug
Fix output bug, direct to stdout
Fix printing bug, clarify variables
Improved progress bar output