[med-svn] [picard-tools] 01/01: Add simple autopkgtest test-suite

[Nadiya Sitdykova]

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

commit 244c81e12aca5435ab1431c2135bcad1369239b1
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Fri Mar 31 01:17:01 2017 -0400

    Add simple autopkgtest test-suite
---
 debian/changelog           |  7 ++++++
 debian/picard-tools.docs   |  4 ++++
 debian/tests/control       |  3 +++
 debian/tests/run-unit-test | 55 ++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 69 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index d56584e..c1f3495 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+picard-tools (2.8.1+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add simple autopkgtest test-suite
+
+ -- Nadiya Sitdykova <rovenskasa at gmailc.om>  Fri, 31 Mar 2017 01:15:20 -0400
+
 picard-tools (2.8.1+dfsg-1) unstable; urgency=medium
 
   [ Vincent Danjean ]
diff --git a/debian/picard-tools.docs b/debian/picard-tools.docs
new file mode 100644
index 0000000..aef3914
--- /dev/null
+++ b/debian/picard-tools.docs
@@ -0,0 +1,4 @@
+testdata/picard/sam/unmapped.sam
+testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam
+testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta
+testdata/picard/vcf/mini.vcf*
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/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..c23ede2
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,55 @@
+#!/bin/sh -e
+
+pkg=picard-tools
+
+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}/unmapped.sam .
+cp -a /usr/share/doc/${pkg}/test.* .
+cp -a /usr/share/doc/${pkg}/mini.vcf* .
+gunzip -r *
+
+PicardCommandLine ViewSam INPUT=unmapped.sam
+
+PicardCommandLine CollectSequencingArtifactMetrics I=test.sam O=test R=test.fasta
+
+o1="test.bait_bias_detail_metrics"
+o2="test.bait_bias_summary_metrics"
+o3="test.error_summary_metrics"
+o4="test.pre_adapter_detail_metrics"
+o5="test.pre_adapter_summary_metrics"
+
+if [ -e "$o1" ] && [ -e "$o2" ] && [ -e "$o3" ] && [ -e "$o4" ] && [ -e "$o5" ]; then
+  echo "All output files generated" >&2
+else
+  echo "Some files are not generated" >&2
+  exit 1
+fi
+
+PicardCommandLine SortVcf I=mini.vcf O=mini_sorted.vcf
+
+out_vcf="mini_sorted.vcf"
+
+if [ -e "$out_vcf" ]; then
+  echo "sorted vcf generated" >&2
+else
+  echo "sorted vcf haven't been generated" >&2
+  exit 1
+fi
+
+PicardCommandLine SplitVcfs I=mini.vcf SNP_OUTPUT=snp.vcf INDEL_OUTPUT=indel.vcf
+
+out_snp="snp.vcf"
+out_indel="indel.vcf"
+
+if [ -e "$out_snp" ] && [ -e "$out_indel" ]; then
+  echo "snp and indel vcfs generated" >&2
+else
+  echo "not all output files have been generated" >&2
+  exit 1
+fi

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