an attempt to layout tool
code backup
code backup
code backup
Merge branch 'dev' into layout
layout-477: output unit score, not the raw score
Merge branch 'dev' into layout

Conflicts:
	main.c
Merge branch 'dev' into layout

Conflicts:
	main.c
Merge branch 'dev' into layout

Conflicts:
	main.c
r707: change params for pacbio-to-pacbio
fixed a bug in overlap type inferrence
better readability for the neighbor struct
code backup
code backup
code backup
r716: changed -x pbread
Merge branch 'master' into layout

Conflicts:
	main.c
r718: merge alnregs overlapping on both query/ref
r719: more stringent overlap merge

Will consider to make it the default
r720: improved overlap hit merging