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|
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
|
