Output file size not correct

[gotouerina]

Hi professor,

I used SegAlign on GPU V100 32G with 30 CPU, aligning two pika genome (size > 2G), and I get an 800G MAF format output files.

What's this going on ? Is this result correct?

[richard-burhans]

Did you happen to pass SegAlign the --scoring option? If so, my PR should fix this issue.