update doxygen settings to include all c++ source and provide internal developer details
improved debug output
fix fragment size selection in proper pair function
rename read local to avoid clib function name collision
refresh source formatting
add additional self-edge tests
fix self edge merging and include new test cases reproducing original issue
close iterator invalidation bug due to self-edges in the sv-locus graph
push size down to 2kb
fix another self-edge handling issue
extra debug info
more debug info
Merge remote-tracking branch 'upstream/master'