search

ruiguo-bio / replong

source code of the paper "RepLong - de novo repeat discovery from long reads"
16 stars 2 forks source link

Is all.out supposed to be all.ovl? #6

Closed rsharris closed 6 years ago

rsharris commented 6 years ago

In processRead.sh, at lines 420..429, the file all.OUT is deleted, and then the results of overlapConvert are appended to the file all.OVL.

I can't find all.OUT used anywhere else. If that was intended to be all.OVL, then if the user runs replong more than once all.OVL will contain leftovers from early runs.

OR at least I guess that's what happens. After running replong I can't find all.ovl, yet I don't see anything in the scripts that would delete it. And I do see one file listed by the echo $i at line 427, so all.ovl should have been created at that point.

bzvew commented 6 years ago

Yes, your first guess is correct. I change that to all.ovl now.