changed package number
added checks for boost's program_options library
cleanup configure.ac
most function objects to lambda expressions
rest of functors converted to lambda expressions
deleted unused functions/function objects
deleted code that was commented out of previous version
starting to add CLI parsing
commented out old main
big hack
reorganizing a bit
-1 replaces NA
some cleanup
removed legacy function
no more converting chrom names internally
removed another header
removed function object
function object to lambda
typedefs, warning cleanup, getting rid of unneeded variables
removed code for functions we're no longer using