[med-svn] [Git][med-team/nanosv][master] 4 commits: Add test data
Shruti Sridhar (@shruti_sridhar)
gitlab at salsa.debian.org
Wed May 26 12:45:40 BST 2021
Shruti Sridhar pushed to branch master at Debian Med / nanosv
Commits:
2362cc5b by Shruti Sridhar at 2021-05-26T16:55:48+05:30
Add test data
- - - - -
c18ddd01 by Shruti Sridhar at 2021-05-26T16:56:25+05:30
Add autopkgtests
- - - - -
5d43959f by Shruti Sridhar at 2021-05-26T17:04:15+05:30
Add examples and docs
- - - - -
db6441a0 by Shruti Sridhar at 2021-05-26T17:11:22+05:30
Update changelog
- - - - -
9 changed files:
- + debian/README.test
- debian/changelog
- + debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/read.sorted.bam
- + debian/tests/data/read.sorted.bam.bai
- + debian/tests/data/target.bed
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,14 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
+
+Notes on the files used for testing
+────────────────────────────────────────
+
+
+
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+nanosv (1.2.4+git20190409.c1ae30c-4) UNRELEASED; urgency=medium
+
+ * Add test data
+ * Add autopkgtests
+ * Add examples and docs
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com> Wed, 26 May 2021 17:09:51 +0530
+
nanosv (1.2.4+git20190409.c1ae30c-3) unstable; urgency=medium
* Team upload.
=====================================
debian/docs
=====================================
@@ -0,0 +1,3 @@
+README.md
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, sambamba
+Restrictions: allow-stderr
=====================================
debian/tests/data/read.sorted.bam
=====================================
Binary files /dev/null and b/debian/tests/data/read.sorted.bam differ
=====================================
debian/tests/data/read.sorted.bam.bai
=====================================
Binary files /dev/null and b/debian/tests/data/read.sorted.bam.bai differ
=====================================
debian/tests/data/target.bed
=====================================
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=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,21 @@
+#!/bin/bash
+set -e
+
+pkg=nanosv
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+ NanoSV read.sorted.bam -b target.bed -s sambamba -o output.vcf
+[ -s "output.vcf" ] || exit 1 && echo "PASS Test"
+
+#Output generated is not consistent and cannot be compared with a reference.
+
+
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/fcf9c9468c7d6bf5cddfb8dce2c2f0022ede69bc...db6441a042f73803c9081cc57f9af31078de0601
--
View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/fcf9c9468c7d6bf5cddfb8dce2c2f0022ede69bc...db6441a042f73803c9081cc57f9af31078de0601
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