update logScale readme
update logScale readme
undo interval stats hack from compareBedStates.. to be replaced with one-sided test
add intersect method
add new interval comparison function and tests
fix up interval graphing and summary. also tweak markers for plots
little cleanup of compare display and filter
redo some accuracy graphs.  add steps on filtering to results
fix window offset bug for right window which was shifted 1 right because of open bed interval
Add length comparison
add maxScore option
add maxScore option
code a bunch of tsd options into clean script..  will need better place eventually but at least we can keep track for now
fix typo
add option to compare to i-1 or segment start for segmenting.  and change default logic to start
Merge branch 'development' of github.com:glennhickey/teHmm into development
fix l1 r1 etc coordinates remembering they are all inclusive
jack up overlap for nonltr tsd since we have no idea where chaux borders are
try to speedup fasta read by skipping to line of target sequence before calling fasta read api
boost scores