add missing comma to header of output csv table for mutations summary
Merge remote-tracking branch 'origin/lod' into development
add some includes and namespaces specifications to make compiler happy in progressive cactus
Add inMemory option to hdf5 alignment interface.  this option will store all arrays entirely in memory and disable the hdf5 cache.
add check for unrecognized option without parameter.  cant believe that was missing until now
add a few heuristics to cut down on lookup times in position cache
fix bug setting updateFlag where it was getting true almost all the time
change to version 1.3 and update doc
Try to fix linewrapping in options help display
add discription to halliftover
fix indent
order on array index instead of start position so as to not thrash the hdf5 cache.
fix test for last insertion of sequence where extension was done before edge test
Merge branch 'development' of github.com:glennhickey/hal into development
Specify path conevntion for LOD files.  Relative paths of HAL files are assumed to be relative to the directory of the LOD file.  Absolute paths are unchanged.
paths with :/ are considered urls and therefore absolute
Update halLodBenchmark to be mroe consistend with halLodInterpolate
Use UDC in halLodManager if defined at compile
Add step to merge compatible adjacent blocks
Fix memory leak where segments in block removed via merge do not get deleted