merge blocks in blockmapper when possible.  cut out any mapbackc blocks that overlap existing blocks.  this is to close hole where we cut against flipset but add to mapsegs
revise blockvis stuff to separate out mapped blocks with same query coordinates.  still needs work on edge cases
allow overlapping target paralogies for now.  will want to clip eventually
change halOpenLOD to accept .hal files too
fix c sequence buffer to not be 1 byte too short
add qChrom to dupe list structure
Merge commit 'origin/chains' into development