Adding a test script for abismal that uses two threads

Author: andrewdavidsmith

test_scripts/test_abismal_threads.test

@@ -0,0 +1,47 @@
+#!/usr/bin/env bash
+
+f () {
+    error_code=$? # save exit code first
+    echo "error $error_code"
+    echo "command with error:"
+    echo "${BASH_COMMAND}"
+    echo "on line ${BASH_LINENO[0]}"
+    exit $error_code
+}
+trap f ERR
+
+infile=tests/reads_1.fq
+infileidx=tests/tRex1.idx
+if [[ -e "${infile}" && -e "${infileidx}" ]]; then
+    ./abismal -v -B -t 2 -i ${infileidx} ${infile} > /dev/null;
+else
+    echo "missing input file(s); skipping test";
+    exit 77;
+fi
+
+infile1=tests/reads_pe_1.fq
+infile2=tests/reads_pe_2.fq
+if [[ -e "${infile1}" && -e "${infile2}" ]]; then
+    ./abismal -v -B -t 2 -i ${infileidx} ${infile1} ${infile2} > /dev/null;
+else
+    echo "missing input file(s); skipping test";
+    exit 77;
+fi
+
+infile1=tests/reads_pbat_pe_1.fq
+infile2=tests/reads_pbat_pe_2.fq
+if [[ -e "${infile1}" && -e "${infile2}" ]]; then
+    ./abismal -v -B -t 2 -P -i ${infileidx} ${infile1} ${infile2} > /dev/null;
+else
+    echo "missing input file(s); skipping tests";
+    exit 77;
+fi
+
+infile1=tests/reads_rpbat_pe_1.fq
+infile2=tests/reads_rpbat_pe_2.fq
+if [[ -e "${infile1}" && -e "${infile2}" ]]; then
+    ./abismal -v -B -t 2 -P -i ${infileidx} ${infile1} ${infile2} > /dev/null;
+else
+    echo "missing input file(s); skipping test";
+    exit 77;
+fi