Removed file extension check for .fan and .qual files with split_libraries.py as this caused issues with galaxy
Fixed order bug for unit test issue #988
Merge pull request #1016 from walterst/test_pick_otus_order_bug

Fixed order bug for unit test issue #988
Merge pull request #1015 from walterst/split_libraries_file_check

Removed file extension check for .fan and .qual files with split_librari...
fixes #1017

more extensive testing to follow - this is a commit of the first working version
modifications to documentation and output filenames
renamed variables
updated usage examples
removed old output
added new example output
added note to change log regarding these changes
updated to handle multiple per-sample fastq file
deleted old example output
added new example output
fixed bug that i introduced in my last commit (thank you script usage tests)
added note describing these changes
changed spacing between values in output to tabs
fixed bug where result summary wouldn't be written if monte carlo tests weren't being performed
updated example output
fixed bug in placement of variable definition