Bigmaf conversion is very sensitive to "." characters in genome names. cactus-maf2bigmaf hacks around this using genome names in the halfile. But this logic doesn't work when running withpout the halfile. Simplest fix seems to just make the hal file mandatory, which is what this PR does.
Bigmaf conversion is very sensitive to "." characters in genome names.
cactus-maf2bigmafhacks around this using genome names in the halfile. But this logic doesn't work when running withpout the halfile. Simplest fix seems to just make the hal file mandatory, which is what this PR does.Resolves #1332