Author: Shayan Doust
Last-Update: 2020-06-04 13:39:11 +0100
Description: Use system libraries in test

--- a/test/test.sh
+++ b/test/test.sh
@@ -8,38 +8,18 @@
 
 export COVTOBED_QUIET=1
 REMOVE=0
-if [ ! -e "test/demo.bam" ]; then
-	echo "WARNING: running this test from a bad location"
-	DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
-	cd "$DIR"/..
-fi
-
-if [ ! -e "./covtobed" ]; then
-	REMOVE=1
-	echo "WARNING:"
-	echo "Binary not found: tring to use pre-compiled...";
-	if [ `uname` == 'Darwin' ]; then
-		echo " - Copying macOS binary"  || echo " ERROR: pre-compiled binary not working"
-		cp ./binaries/covtobed_mac ./covtobed
-		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
-	else
-		echo " - Trying Ubuntu binary"
-		cp ./binaries/covtobed ./covtobed
-		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
-	fi
-fi
 
-./covtobed --version
+covtobed --version
 
 echo " ================================================ "
 set -eou pipefail
 # Compilation success, checking that --version emits the expected "progname" string
 echo -n " - Compiled binary prints version: "
-if [ $(./covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
+if [ $(covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
 then
-        echo PASS $(./covtobed --version | grep covtobed |head -n 1)
+        echo PASS $(covtobed --version | grep covtobed |head -n 1)
 else
-        echo FAIL $(./covtobed --version  | grep covtobed | wc -l )
+        echo FAIL $(covtobed --version  | grep covtobed | wc -l )
 		exit
 fi
 
@@ -63,7 +43,7 @@ else
 fi
 # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)
 echo -n " - Minimum coverage, expected BED lines check: "
-if [ $(./covtobed -m 15 test/demo.bam  | wc -l) -eq "12" ];
+if [ $(covtobed -m 15 demo.bam  | wc -l) -eq "12" ];
 then
 	echo PASS 2
 else
@@ -73,7 +53,7 @@ fi
 
 # Checking thath --physical-coverage will work, and it fits the expected number of lines
 echo -n " - Physical coverage, expected BED lines check: "
-if [ $(./covtobed --physical-coverage test/mp.bam  | wc -l) -eq "136" ];
+if [ $(covtobed --physical-coverage mp.bam  | wc -l) -eq "136" ];
 then
 	echo PASS 3
 else
@@ -83,7 +63,7 @@ fi
 
 # Checking stranded output: it should produce content in the fifth column of the bed file
 echo -n " - Stranded output, testing column #5: "
-if [ $(./covtobed --out test/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
+if [ $(covtobed --out demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
 then
 	echo PASS 4
 else
@@ -93,7 +73,7 @@ fi
 
 # Checking the "counts" output (counting the lines containing a ">")
 echo -n " - Testing 'counts' format (printed headers): "
-if [ $(./covtobed --format counts test/demo.bam | grep '>' | wc -l) -eq "2" ];
+if [ $(covtobed --format counts demo.bam | grep '>' | wc -l) -eq "2" ];
 then
 	echo PASS 5
 else
@@ -101,29 +81,29 @@ else
 	exit 1
 fi
 echo -n " - Testing 'counts' format (printed lines): "
-if [ $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) -eq "202" ];
+if [ $(covtobed --format counts demo.bam | grep -v \> | wc -l) -eq "202" ];
 then
         echo PASS 6
 else
-	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
+	echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected
 	exit 1
 fi
 
 echo -n " - Testing strand with adjacent intervals: "
-if [[ $(./covtobed  test/stranded.bam | wc -l) -eq "1"  && $(./covtobed --output-strands test/stranded.bam | wc -l) -eq "2" ]];
+if [[ $(covtobed  stranded.bam | wc -l) -eq "1"  && $(covtobed --output-strands stranded.bam | wc -l) -eq "2" ]];
 then
         echo PASS 7
 else
-	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
+	echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected
 	exit 1
 fi
 # Checking BED output with reference output file
 echo -n " - Checking identity of BED output with pre-calculated: "
-./covtobed test/demo.bam > test/output.test
-if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];
+covtobed demo.bam > output.test
+if [ $(diff output.test output.bed | wc -l) -eq "0" ];
 then
         echo PASS 8
-	rm test/output.test
+	rm output.test
 else
 	echo FAIL
 	exit 1
@@ -131,11 +111,11 @@ fi
 
 ## Synthetic BAM test
 echo -n " - Checking computed coverage for a synthetic BAM file: "
-./covtobed -m 1 test/mock.bam > test/output.test
-if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];
+covtobed -m 1 mock.bam > output.test
+if [ $(diff output.test mock.bed | wc -l) -eq "0" ];
 then
         echo PASS 9
-	rm test/output.test
+	rm output.test
 else
 	echo FAIL
 	exit 1
@@ -143,23 +123,23 @@ fi
 
 ## Filter non valid alignments
 echo -n " - Checking filtering of invalid alignments: "
-if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then
+if [ $(covtobed -m 1 -d filtered.bam | wc -l) -eq "2" ] ; then
 	echo -n "PASS 10,"
 else
 	echo FAIL
 	exit 1
 fi
-if [ $(./covtobed -m 1 test/filtered.bam | wc -l) -eq "6" ] ; then
+if [ $(covtobed -m 1 filtered.bam | wc -l) -eq "6" ] ; then
 	echo 10
 else
-	echo "FAIL: $(./covtobed -m 1 -d test/filtered.bam | wc -l)"
+	echo "FAIL: $(covtobed -m 1 -d filtered.bam | wc -l)"
 	exit 1
 fi
 
 # A synthetic BAM containing reference name {n}X that should only print one reagion 
 # covered exactly {n}X times
 echo  " - Checking artificial coverage values:"
-./covtobed test/test_cov.bam -m 1 |cut -f 1,4| while read LINE;
+covtobed test_cov.bam -m 1 |cut -f 1,4| while read LINE;
 do
 	echo "$LINE" | perl -ne '($exp, $cov)=split /\s+/, $_; if ("$exp" ne "${cov}X") {
 		die "$exp != $cov\n";
@@ -170,5 +150,5 @@ done
 echo "ALL TESTS: PASSED"
 
 if [[ $REMOVE -eq 1 ]]; then
- rm ./covtobed
+ rm covtobed
 fi