[med-svn] [Git][med-team/covtobed][master] 2 commits: Add more example data to covtobed-examples
Shayan Doust
gitlab at salsa.debian.org
Thu Jun 4 13:39:46 BST 2020
Shayan Doust pushed to branch master at Debian Med / covtobed
Commits:
1a7224f5 by Shayan Doust at 2020-06-04T13:27:51+01:00
Add more example data to covtobed-examples
- - - - -
f173df56 by Shayan Doust at 2020-06-04T13:39:11+01:00
Patch test script so it uses covtobed binary installed on system and works with autopkgtest
- - - - -
3 changed files:
- debian/covtobed-examples.install
- + debian/patches/series
- + debian/patches/test_use_system_installed_binary.patch
Changes:
=====================================
debian/covtobed-examples.install
=====================================
@@ -1 +1,2 @@
-test/ usr/share/doc/covtobed-examples/
+test/* usr/share/doc/covtobed-examples/examples
+example_data/* usr/share/doc/covtobed-examples/examples
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+test_use_system_installed_binary.patch
=====================================
debian/patches/test_use_system_installed_binary.patch
=====================================
@@ -0,0 +1,144 @@
+Description: modify test script so it works with autopkgtest
+Author: Shayan Doust <hello at shayandoust.me>
+Last-Update: 2020-06-04
+---
+--- covtobed.orig/test/test.sh
++++ covtobed/test/test.sh
+@@ -7,40 +7,20 @@
+ # ./test/mock.bam
+
+ 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
+- else
+- echo " - Trying Ubuntu binary"
+- cp ./binaries/covtobed ./covtobed
+- covtobed --version || echo " ERROR: pre-compiled binary not working"
+- fi
+-fi
+
+-./covtobed --version
++covtobed --version
+
+ 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 ) -eq "1" ];
++if [ $(covtobed --version | grep covtobed | wc -l ) -eq "1" ];
+ then
+ echo PASS 1
+ 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 /usr/share/doc/covtobed-examples/examples/demo.bam | wc -l) -eq "12" ];
+ then
+ echo PASS 2
+ else
+@@ -50,7 +30,7 @@
+
+ # 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 /usr/share/doc/covtobed-examples/examples/mp.bam | wc -l) -eq "136" ];
+ then
+ echo PASS 3
+ else
+@@ -60,7 +40,7 @@
+
+ # 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 /usr/share/doc/covtobed-examples/examples/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
+ then
+ echo PASS 4
+ else
+@@ -70,7 +50,7 @@
+
+ # 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 /usr/share/doc/covtobed-examples/examples/demo.bam | grep '>' | wc -l) -eq "2" ];
+ then
+ echo PASS 5
+ else
+@@ -78,7 +58,7 @@
+ 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 /usr/share/doc/covtobed-examples/examples/demo.bam | grep -v '>' | wc -l) -eq "202" ];
+ then
+ echo PASS 6
+ else
+@@ -88,8 +68,8 @@
+
+ # 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 /usr/share/doc/covtobed-examples/examples/demo.bam > output.test
++if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/output.bed | wc -l) -eq "0" ];
+ then
+ echo PASS 7
+ rm test/output.test
+@@ -100,8 +80,8 @@
+
+ ## 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 /usr/share/doc/covtobed-examples/examples/mock.bam > output.test
++if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/mock.bed | wc -l) -eq "0" ];
+ then
+ echo PASS 8
+ rm test/output.test
+@@ -112,23 +92,23 @@
+
+ ## 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 /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "2" ] ; then
+ echo -n "PASS 9,"
+ else
+ echo FAIL
+ exit 1
+ fi
+-if [ $(./covtobed -m 1 test/filtered.bam | wc -l) -eq "6" ] ; then
++if [ $(covtobed -m 1 /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "6" ] ; then
+ echo 10
+ else
+- echo "FAIL: $(./covtobed -m 1 -d test/filtered.bam | wc -l)"
++ echo "FAIL: $(covtobed -m 1 -d /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l)"
+ exit 1
+ fi
+
+ # A synthetic BAM containing reference name {n}X that should only print one reagion
+ # covered exactly {n}X times
+ echo " - Checking artificial coverage values:"
+-./covtobed test/test_cov.bam -m 1 |cut -f 1,4| while read LINE;
++covtobed /usr/share/doc/covtobed-examples/examples/test_cov.bam -m 1 |cut -f 1,4| while read LINE;
+ do
+ echo "$LINE" | perl -ne '($exp, $cov)=split /\s+/, $_; if ("$exp" ne "${cov}X") {
+ die "$exp != $cov\n";
+@@ -137,7 +117,3 @@
+ }'
+ done
+ echo "ALL TESTS: PASSED"
+-
+-if [[ $REMOVE -eq 1 ]]; then
+- rm ./covtobed
+-fi
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/b3e2773294ecb4ac8daacc4b597e3c025b64e73d...f173df5696a49a31b75bebb2dbab036e405daf29
--
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/b3e2773294ecb4ac8daacc4b597e3c025b64e73d...f173df5696a49a31b75bebb2dbab036e405daf29
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