[med-svn] [seqtk] 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 seqtk.

commit f09254245a4c86aa0e16c332ddeeaed8640053e6
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Tue Jul 11 23:52:41 2017 -0400

    add autopkgtest test-suite
---
 debian/README.test              |  8 ++++++++
 debian/changelog                |  9 +++++++++
 debian/docs                     |  3 +++
 debian/tests/control            |  3 +++
 debian/tests/run-unit-test      | 33 +++++++++++++++++++++++++++++++++
 debian/tests/test_data/in.fa    | 18 ++++++++++++++++++
 debian/tests/test_data/in.fq    | 36 ++++++++++++++++++++++++++++++++++++
 debian/tests/test_data/name.lst |  3 +++
 8 files changed, 113 insertions(+)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..39fbde9
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+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 f1d09b0..5ce287e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+seqtk (1.2-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+
+  [ Nadiya Sitdykova ]
+  * Add autopkgtest test-suite
+
+ -- Nadiya Sitdykova <rovenskasa at gmail.com>  Tue, 11 Jul 2017 23:50:21 -0400
+
 seqtk (1.2-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..d5a881e
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/test_data
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..6164bfb
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,33 @@
+#!/bin/sh -e
+
+pkg=seqtk
+
+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}/test_data/* .
+gunzip -r *
+
+seqtk seq -a in.fq > out.fa
+
+seqtk seq -aQ64 -q20 in.fq > out.fa
+seqtk seq -aQ64 -q20 -n N in.fq > out.fa
+
+seqtk seq -Cl60 in.fa > out.fa
+
+seqtk seq -l0 in.fq > out.fq
+
+seqtk seq -r in.fq > out.fq
+
+seqtk subseq in.fq name.lst > out.fq
+
+seqtk sample -s100 in.fq 2 > sub.fq
+
+seqtk trimfq in.fq > out.fq
+
+seqtk trimfq -b 5 -e 10 in.fa > out.fa
+
diff --git a/debian/tests/test_data/in.fa b/debian/tests/test_data/in.fa
new file mode 100644
index 0000000..e24b6e0
--- /dev/null
+++ b/debian/tests/test_data/in.fa
@@ -0,0 +1,18 @@
+>CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+>CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+>CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
+>CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+>CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
+>CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+>CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
diff --git a/debian/tests/test_data/in.fq b/debian/tests/test_data/in.fq
new file mode 100644
index 0000000..d3386dd
--- /dev/null
+++ b/debian/tests/test_data/in.fq
@@ -0,0 +1,36 @@
+ at CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+ at CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+ at CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+ at CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+ at CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+ at CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+ at CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+ at CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+ at CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/debian/tests/test_data/name.lst b/debian/tests/test_data/name.lst
new file mode 100644
index 0000000..1c47397
--- /dev/null
+++ b/debian/tests/test_data/name.lst
@@ -0,0 +1,3 @@
+CSHL_3_FC042AGLLWW:1:2:7:169
+CSHL_3_FC042AGLLWW:1:2:7:1436
+

-- 
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