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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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negative genome size #24

Closed bwlang closed 7 years ago

bwlang commented 7 years ago

I see this when I start up pilon

Genome: ../quiver_polished_0307.fasta
Fixing bases, gaps, local
Input genome size: -1800804444

Looks like genomeSize is a long... and my genome is only 2.5Gbase I thought about maybe some individual contig lengths are overflowing, but my longest is 32961348, which should not overflow an int.

Any ideas?

w1bw commented 7 years ago

Oops. It's probably using a signed 32 bit int for the total size. I'll see if I can put in a quick fix, as I'm about to do a new release.