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
added warning that p-values are not adjusted for multiple comparisons
expanded help text
updated to use os.path.join for joining file path components
removing old output as formatting of output files has been updated