debian/changelog

+hisat2 (2.1.0-3) UNRELEASED; urgency=medium
+
+  * Install hisat2_extract_splice_sites.py
+
+ -- Andreas Tille <tille@debian.org>  Mon, 25 Mar 2019 11:35:33 +0100
+
 hisat2 (2.1.0-2) unstable; urgency=medium
 
   * Team upload.

debian/install

 hisat2 /usr/bin/
+hisat2_extract_splice_sites	/usr/bin
 hisat2-build /usr/bin/
 hisat2-build-s /usr/bin/
 hisat2-build-l /usr/bin/

debian/lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+hisat2: script-with-language-extension usr/bin/*.*