debian/changelog

@@ -5,6 +5,9 @@ hisat2 (2.1.0-4) UNRELEASED; urgency=medium
   [ Saira Hussain ]
   * Add autopkgtest
 
+  [ Andreas Tille ]
+  * Recommends: bcftools, samtools
+
  -- Saira Hussain <saira.h0213@zoho.com>  Fri, 02 Aug 2019 15:18:09 +0100
 
 hisat2 (2.1.0-3) UNRELEASED; urgency=medium

debian/control

@@ -17,7 +17,9 @@ Architecture: amd64 kfreebsd-amd64
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${perl:Depends}
-Recommends: python3-hisat2
+Recommends: python3-hisat2,
+            bcftools,
+            samtools
 Description: graph-based alignment of short nucleotide reads to many genomes
  HISAT2 is a fast and sensitive alignment program for mapping next-generation
  sequencing reads (both DNA and RNA) to a population of human genomes (as well

debian/tests/run-unit-tests

@@ -8,17 +8,14 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   # Double quote below to expand the temporary directory variable now versus
   # later is on purpose.
   # shellcheck disable=SC2064
-#  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
 cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-# Just for debugging
-set -x
-
-cd example
+gunzip -r *
 
 # Run the reproducible suite
 hisat2-build reference/22_20-21M.fa --snp reference/22_20-21M.snp 22_20-21M_snp