add option to write deletion breakpoints in reference
fix bugs with how deletions are called
fix header
start new code to do simple bed histograms
start debuggin histogram code
start debuggin histogram code
script to print sorted branch mutations for tree
update treemutations
fix clean
temp checkin.. still need work
fix sequence coordinates for delbreaks
Merge branch 'development' into turnover
update histogram code
prototype conservation detection with neutral indel
add framewoark for mask tools
fix glaring bug in getting end iterators from sequences
add mask extractor to turn repeat annotations into bed files
option for halstats to make a bed file
add background rate code
update long indel conservation code.  background rate can now be estimated from arbitrary bed file