Add file demultiplex_multiple_index_runs
demultiplex_multiple_index_runs.py script to run demultiplexing with
indexes of different length
more changes to demultiplex_multiple_index_runs
	- added option to keep original index (needed for molecular tagging)
	- added function for fastq_utils to return number of bases with quality
>Q30
	- output almost all the information needed to mimic
Demultiplex_stats.htm
fastq_utils.py now uses streams in place of files in order to read and
wirte in a more efficent way

Fix problems in reported statistics

This is a working version
Added funcitonality to demultiplex only specified indexes:
 -it overwrites existing Unmultiplexed and Ambiguous folders
version.py... something.
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