Thank you for your quick and gracious response! While looking through the Ubuntu diff, I noticed that the autopkgtest needs to be updated too. I'm attaching a simple patch for that.
Thanks, Jeremy
=== modified file 'debian/tests/run-unit-test' --- debian/tests/run-unit-test 2016-12-23 15:34:24 +0000 +++ debian/tests/run-unit-test 2016-12-23 15:36:28 +0000 @@ -5,6 +5,6 @@ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` fi cd $ADTTMP -snap /usr/share/snap/HMM/thale /usr/share/doc/${pkg}/examples/DNA/thale.dna.gz -snap /usr/share/snap/HMM/worm /usr/share/doc/${pkg}/examples/DNA/worm.dna.gz +snap-hmm /usr/share/snap/HMM/thale /usr/share/doc/${pkg}/examples/DNA/thale.dna.gz +snap-hmm /usr/share/snap/HMM/worm /usr/share/doc/${pkg}/examples/DNA/worm.dna.gz