[med-svn] [Git][med-team/blasr][master] 3 commits: Add test data

[Shruti Sridhar (@shruti_sridhar)]

Shruti Sridhar pushed to branch master at Debian Med / blasr


Commits:
ba610e32 by Shruti Sridhar at 2021-07-31T23:19:28+05:30
Add test data

- - - - -
0d6a57ef by Shruti Sridhar at 2021-07-31T23:19:48+05:30
Add autopkgtest

- - - - -
65276bd0 by Shruti Sridhar at 2021-07-31T23:20:04+05:30
Install docs

- - - - -


8 changed files:

- + debian/README.test
- debian/copyright
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/query.fasta
- + debian/tests/data/ref.fa
- + 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 
+────────────────────────────────────────
+Files: debian/tests/data/*
+
+The test files query.fasta and ref.fa were written for testing this package. 
\ No newline at end of file


=====================================
debian/copyright
=====================================
@@ -14,6 +14,9 @@ Files: debian/*
 Copyright: 2015-2016 Afif Elghraoui <afif at debian.org>
 License: PacBio-BSD-3-Clause
 
+Files: debian/tests/data
+Copyright: Shruti Sridhar <shruti.sridhar99 at gmail.com>
+
 License: PacBio-BSD-3-Clause
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions


=====================================
debian/docs
=====================================
@@ -1 +1,3 @@
-README*
+README.md
+debian/README*
+debian/tests/run-unit-test


=====================================
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: @
+Restrictions: allow-stderr


=====================================
debian/tests/data/query.fasta
=====================================
@@ -0,0 +1,2 @@
+>movie/0/0_64
+ATGTCAGTGACGATGACAGTAGACAGATAGAGAGGAGAGATAGACAGATAG
\ No newline at end of file


=====================================
debian/tests/data/ref.fa
=====================================
@@ -0,0 +1,2 @@
+>test/0/0_68
+ATGTCAGTGACGATGACAGTAGACAGATAGAGAGGAGAGATAGACAGATAGATGCTAGC
\ No newline at end of file


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -e
+
+pkg=blasr
+
+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}"
+
+blasr query.fasta ref.fa --sam --out alignment.sam
+blasr query.fasta ref.fa --minMatch 1 --maxMatch 10 > output
+if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
+then
+	echo "8db2f4d5737a90d087da90a6779c8d7b  output" >> checksums
+	echo "0a61b96282acbc63df897dd1510ea0ad  alignment.sam" >> checksums
+	
+  md5sum --check checksums
+	echo "Expected output and generated output are same: PASS Test"
+else
+	[ -s "output" ] && [ -s "alignment.sam" ] || exit 1
+	echo "PASS Test"
+fi
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f

-- 
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f
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