[med-svn] [bamtools] 01/01: add autopkgtest test-suite

[Nadiya Sitdykova]

This is an automated email from the git hooks/post-receive script.

rovenskasa-guest pushed a commit to branch master
in repository bamtools.

commit 93993686502bad3bf2056549c1479c156bc42fe0
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Mon Aug 7 17:03:30 2017 -0400

    add autopkgtest test-suite
---
 debian/README.test         |  9 +++++++++
 debian/changelog           |  9 +++++++++
 debian/docs                |  4 ++++
 debian/tests/control       |  3 +++
 debian/tests/filter_script | 17 +++++++++++++++++
 debian/tests/run-unit-test | 38 ++++++++++++++++++++++++++++++++++++++
 6 files changed, 80 insertions(+)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..74ce729
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by executing
+
+    sh run-unit-test
+
+in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
index e896029..62488c8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+bamtools (2.4.1+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  
+  [ Nadiya Sitdykova ]
+  * add autopkgtest test-suite 
+
+ -- Nadiya Sitdykova <rovenskasa at gmail.com>  Mon, 07 Aug 2017 17:01:19 -0400
+
 bamtools (2.4.1+dfsg-2) UNRELEASED; urgency=medium
 
   * debian/upstream/metadata: Added refs to bio.tools and OMICtools
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..6b01fc1
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,4 @@
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/filter_script
+debian/sam_spec_example.bam
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/filter_script b/debian/tests/filter_script
new file mode 100644
index 0000000..e30f78c
--- /dev/null
+++ b/debian/tests/filter_script
@@ -0,0 +1,17 @@
+{
+  "filters" : 
+    [
+      { "id" : "inAnyErrorReadGroup",
+        "tag" : "RG:ERR*"
+      },
+      { "id" : "highMapQuality",
+        "mapQuality" : ">=75"
+      },
+      { "id" : "bothMatesMapped",
+        "isMapped" : "true",
+        "isMateMapped" : "true"
+      }
+    ],
+  "rule" : "!inAnyErrorReadGroup & (highMapQuality | bothMatesMapped)"
+}
+
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..e2fd2b4
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,38 @@
+#!/bin/sh -e
+
+pkg=bamtools
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $ADTTMP
+
+cp -a /usr/share/doc/${pkg}/sam_spec_example.bam .
+cp -a /usr/share/doc/${pkg}/filter_script .
+gunzip -r *
+
+bamtools convert -format fastq -in sam_spec_example.bam -out test.fastq
+
+bamtools convert -format json -in sam_spec_example.bam -out test.json
+
+bamtools count -in sam_spec_example.bam
+
+bamtools coverage -in sam_spec_example.bam -out out
+
+bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
+
+bamtools header -in sam_spec_example.bam
+
+bamtools index -in sam_spec_example.bam
+
+bamtools random -n 100 -in sam_spec_example.bam -out out.bam
+
+bamtools revert -in sam_spec_example.bam -out out.bam
+
+bamtools sort -in sam_spec_example.bam -out out.bam
+
+bamtools split -mapped -in sam_spec_example.bam
+
+bamtools stats -in sam_spec_example.bam

-- 
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