Regression tests

.github/workflows/c-cpp.yml

@@ -0,0 +1,30 @@
+name: C/C++ CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Install autotools
+      run: sudo apt-get install -y autoconf automake libtool
+    - name: Generate configure script
+      run: ./autogen.sh
+    - name: configure
+      run: ./configure
+    - name: make
+      run: make
+    - name: make check
+      run: make check
+    - name: make distcheck
+      run: make distcheck

Makefile.am

@@ -14,7 +14,22 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 # General Public License for more details.
 
-EXTRA_DIST = README.md LICENSE docs
+EXTRA_DIST = \
+	README.md \
+	LICENSE \
+	docs \
+	data/tRex1.fa \
+        data/md5sum.txt \
+	test_scripts/test_abismalidx.test \
+	test_scripts/test_simreads.test \
+	test_scripts/test_abismal.test \
+	test_scripts/test_simreads_pe.test \
+	test_scripts/test_abismal_pe.test \
+	test_scripts/test_simreads_pbat.test \
+	test_scripts/test_abismal_pbat.test \
+	test_scripts/test_simreads_rpbat.test \
+	test_scripts/test_abismal_rpbat.test
+
 ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp
@@ -46,3 +61,46 @@ bin_PROGRAMS = abismal abismalidx simreads
 abismal_SOURCES = src/abismal_main.cpp
 abismalidx_SOURCES = src/abismalidx_main.cpp
 simreads_SOURCES = src/simreads_main.cpp
+
+TESTS = test_scripts/test_abismalidx.test \
+	test_scripts/test_simreads.test \
+	test_scripts/test_abismal.test \
+	test_scripts/test_simreads_pe.test \
+	test_scripts/test_abismal_pe.test \
+	test_scripts/test_simreads_pbat.test \
+	test_scripts/test_abismal_pbat.test \
+	test_scripts/test_simreads_rpbat.test \
+	test_scripts/test_abismal_rpbat.test
+
+TEST_EXTENSIONS = .test
+
+test_scripts/test_abismal.log: \
+	test_scripts/test_abismalidx.log \
+	test_scripts/test_simreads.log
+test_scripts/test_abismal_pe.log: \
+	test_scripts/test_abismalidx.log \
+	test_scripts/test_simreads_pe.log
+test_scripts/test_abismal_pbat.log: \
+	test_scripts/test_abismalidx.log \
+	test_scripts/test_simreads_pbat.log
+test_scripts/test_abismal_rpbat.log: \
+	test_scripts/test_abismalidx.log \
+	test_scripts/test_simreads_rpbat.log
+
+CLEANFILES = \
+    tests/tRex1.idx \
+    tests/reads_1.fq
+    tests/reads.mstats \
+    tests/reads.sam \
+    tests/reads_pe_1.fq \
+    tests/reads_pe_2.fq \
+    tests/reads_pe.mstats \
+    tests/reads_pe.sam \
+    tests/reads_pbat_pe_1.fq \
+    tests/reads_pbat_pe_2.fq \
+    tests/reads_pbat_pe.mstats \
+    tests/reads_pbat_pe.sam \
+    tests/reads_rpbat_pe_1.fq \
+    tests/reads_rpbat_pe_2.fq \
+    tests/reads_rpbat_pe.mstats \
+    tests/reads_rpbat_pe.sam

configure.ac

@@ -47,5 +47,12 @@ dnl check for the Zlib library
 AC_CHECK_LIB([z], [zlibVersion], [],
   [AC_MSG_FAILURE([Zlib must be installed to build abismal])], [])
 
-AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([
+Makefile
+])
+dnl make the test data files available in the build tree
+AC_CONFIG_LINKS([
+tests/md5sum.txt:data/md5sum.txt
+tests/tRex1.fa:data/tRex1.fa
+])
 AC_OUTPUT

data/md5sum.txt

@@ -0,0 +1,18 @@
+8e5ad0faefe241de9c2c5748e005e2e8  tests/reads_1.fq
+15de230061bbf34a46af8c1d5d7fd5cf  tests/reads.mstats
+3edbf931e6f0da55a50b24e01a975565  tests/reads_pbat.mstats
+b9699416969133224b620f05af97ac90  tests/reads_pbat_pe_1.fq
+12c9d36ab3bf2b9ecb5683d7a093a10d  tests/reads_pbat_pe_2.fq
+3edbf931e6f0da55a50b24e01a975565  tests/reads_pbat_pe.mstats
+51b695cd3aeb3cead392821628acf0f1  tests/reads_pbat_pe.sam
+58d6c1157b187a66d43087fe3e70a38c  tests/reads_pbat.sam
+8e5ad0faefe241de9c2c5748e005e2e8  tests/reads_pe_1.fq
+4ebacfec717182fafce46b037591b228  tests/reads_pe_2.fq
+072a7df62d45dc3d3d4350d79efc9ca1  tests/reads_pe.mstats
+56318794f9e55549c9050a636161e883  tests/reads_pe.sam
+e66339e591563032af436ca2af9b75b1  tests/reads_rpbat_pe_1.fq
+aed5705c4a99601d5799fc8ee42af5b2  tests/reads_rpbat_pe_2.fq
+da00a63969113e09406b61cbe280daa5  tests/reads_rpbat_pe.mstats
+7f3f547ff06296ef2fcc7d1cb8169766  tests/reads_rpbat_pe.sam
+50ec2af709639fa242654f9b3a46981b  tests/reads.sam
+3ba5a1c4c420ca7a2dbd88290033c3bc  tests/tRex1.idx