[med-svn] [Git][med-team/bioawk][master] 2 commits: Change test dependency from swarm to seqkit-examples so as to test on all architectures

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / bioawk


Commits:
e3ca5c8e by Nilesh Patra at 2021-02-28T20:37:48+05:30
Change test dependency from swarm to seqkit-examples so as to test on all architectures

- - - - -
7afac90b by Nilesh Patra at 2021-02-28T20:41:00+05:30
Update changelog

- - - - -


3 changed files:

- debian/changelog
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+bioawk (1.0-3) unstable; urgency=medium
+
+  * Change test dependency from swarm to
+    seqkit-examples so as to test on all architectures
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 28 Feb 2021 20:37:56 +0530
+
 bioawk (1.0-2) unstable; urgency=medium
 
   * Source-only-upload


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @, swarm, samtools-test
+Depends: @, seqkit-examples, samtools-test
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -6,40 +6,41 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp /usr/share/doc/swarm/test-data/input.fasta.gz $AUTOPKGTEST_TMP
+cp /usr/share/doc/seqkit-examples/tests/SIRV_150601a.fasta.gz $AUTOPKGTEST_TMP
 cp /usr/share/samtools/test/ampliconclip/ac_test.bed $AUTOPKGTEST_TMP
 cp /usr/share/samtools/test/dat/view.001.sam $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
 gunzip -r *
+mv SIRV_150601a.fasta input.fasta
 
 echo "Test 1 - Get length for sequences"
-bioawk -c fastx '{ print $name, length($seq) }' input.fasta 1> test1 2> test1
+bioawk -c fastx '{ print $name, length($seq) }' input.fasta 1>test1 2>>test1
 [ -s test1 ] || exit 1
 echo "================================="
 echo "PASS"
 
 echo "Test 2 - Get reverse compliment"
-bioawk -c fastx '{ print ">"$name;print revcomp($seq) }' input.fasta 1>test2 2>test2
+bioawk -c fastx '{ print ">"$name;print revcomp($seq) }' input.fasta 1>test2 2>>test2
 [ -s test2 ] || exit 1
 echo "=================================="
 echo "PASS"
 
 echo "Test 3 - Convert FASTA to tabular form"
-bioawk -t -c fastx '{ print $name, $seq }' input.fasta 1>test3 2>test3
+bioawk -t -c fastx '{ print $name, $seq }' input.fasta 1>test3 2>>test3
 [ -s test3 ] || exit 1
 echo "=================================="
 echo "PASS"
 
 echo "Test 4 - Print feature length"
-bioawk -c bed '{ print $end - $start }' ac_test.bed 1>test4 2>test4
+bioawk -c bed '{ print $end - $start }' ac_test.bed 1>test4 2>>test4
 [ "$(cat test4 | wc -l)" -gt 1 ] || exit 1
 [ -s test4 ] || exit 1
 echo "=================================="
 echo "PASS"
 
 echo "Test 5 - Extract mapped reads"
-bioawk -c sam -H '!and($flag,4)' view.001.sam 1>test5 2>test5
+bioawk -c sam -H '!and($flag,4)' view.001.sam 1>test5 2>>test5
 [ -s test5 ] || exit 1
 echo "=================================="
 echo "PASS"



View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/compare/9309cf58153be8c547ea95eaffaeef2ba974cc94...7afac90bb68ed64888aa06ba6f436246003f74c9

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioawk/-/compare/9309cf58153be8c547ea95eaffaeef2ba974cc94...7afac90bb68ed64888aa06ba6f436246003f74c9
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