remove length limitation in fixing AHRD
add apps.gsnap to wrap GMAP/GSNAP
allow gapsize=0 in formats.agp.OO.write_AGP()
+ Added ACTION annotation.pasa.assemble() to run PASA alignAssembly
+ If 2 transcript files are provided (DN & GG), run the PASA compreh trans pipeline
+ This ACTION be invoked with `--prepare` to generate a run.sh script
- The old ACTION annotation.pasa.prepare() is no longer needed
+ Updated formats.base.write_file() append handling
+ Updated apps.base.set_align() with some PASA specific alignment params