Use --enable-libgsl --enable-perl-filters when testing

Add packages needed for these options and enable them
on configure builds.  The perl IO::Pty package is also added
for Debian and Ubuntu so the usage tests work.

Also adjust how flags are set in the CI builds to ensure they
are applied consistently.

.cirrus.yml

@@ -42,16 +42,34 @@ compile_template: &COMPILE
     if test "$USE_CONFIG" = "yes"; then
       (cd $HTSDIR && autoreconf -i)
       autoreconf -i
-      ./configure --enable-werror || (cat config.log; /bin/false)
+      ./configure --enable-werror $CONFIG_OPTS \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"} \
+         || (cat config.log; /bin/false)
       make -j3
     else
-      make -j3 plugindir=$CIRRUS_WORKING_DIR/plugins -e
+      make -j3 plugindir="$CIRRUS_WORKING_DIR/plugins" \
+           ${HTSDIR:+HTSDIR="$HTSDIR"} \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
     fi
 
 test_template: &TEST
   test_script: |
-    make -e test
-
+    if test "$USE_CONFIG" = "yes"; then
+        make test
+    else
+        make test  \
+           ${HTSDIR:+HTSDIR="$HTSDIR"} \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
+    fi
 
 #--------------------------------------------------
 # Task: linux builds.
@@ -68,15 +86,23 @@ gcc_task:
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
-    CFLAGS:  -fsanitize=address
-    LDFLAGS: -fsanitize=address
 
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS:  -g -Og -Wall -Werror -fsanitize=address
+       LDFLAGS: -fsanitize=address
     - environment:
        USE_CONFIG: yes
-       CFLAGS: -std=gnu99 -O0
+       CONFIG_OPTS: --enable-libgsl --enable-perl-filters 
+       CFLAGS: -std=gnu99 -g -Og -Wall -fsanitize=address
+       LDFLAGS: -fsanitize=address
+
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends \
+        libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl
+
 
   << : *COMPILE
   << : *TEST
@@ -92,18 +118,19 @@ ubuntu_task:
 
   environment:
     CC: clang
-    CFLAGS: -g -O2 -Werror -Wall -Wformat -Wformat=2
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
 
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS: -g -O2 -Werror -Wall -Wformat -Wformat=2
     - container:
        memory: 2G
       environment:
        USE_CONFIG: yes
+       CONFIG_OPTS: --enable-libgsl --enable-perl-filters
        CFLAGS: -g -Wall -O3
        LDFLAGS: -Wl,-rpath,`pwd`/inst/lib
 
@@ -114,7 +141,7 @@ ubuntu_task:
     apt-get install -y --no-install-suggests --no-install-recommends \
         ca-certificates clang git autoconf automake  \
         make zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev   \
-        libssl-dev libdeflate-dev
+        libssl-dev libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl
 
   << : *COMPILE
   << : *TEST
@@ -133,13 +160,14 @@ rockylinux_task:
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
     USE_CONFIG: yes
+    CONFIG_OPTS: --enable-libgsl --enable-perl-filters
 
   # NB: we could consider building a docker image with these
   # preinstalled and specifying that instead, to speed up testing.
   install_script: |
     yum install -y autoconf automake make gcc perl-Data-Dumper perl-FindBin \
         zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel \
-        git diffutils
+        git diffutils gsl-devel perl-ExtUtils-Embed
 
   << : *COMPILE
   << : *TEST