This is an automated email from the git hooks/post-receive script. cbk-guest pushed a commit to branch master in repository bwa.
commit 81356eb05a4ccfaac9f5eb866da3d8f8abe428de Author: cbk-guest <[email protected]> Date: Sat Jun 25 23:37:25 2016 +0300 Autopkgtests and example directory added --- debian/bwa.examples | 1 + debian/changelog | 10 ++++++++-- debian/examples/read1.fq | 4 ++++ debian/examples/read2.fq | 4 ++++ debian/examples/reads.fq | 16 ++++++++++++++++ debian/examples/ref.fa | 8 ++++++++ debian/tests/control | 3 +++ debian/tests/run-unit-test | 23 +++++++++++++++++++++++ 8 files changed, 67 insertions(+), 2 deletions(-) diff --git a/debian/bwa.examples b/debian/bwa.examples new file mode 100644 index 0000000..55b78ae --- /dev/null +++ b/debian/bwa.examples @@ -0,0 +1 @@ +debian/examples/* diff --git a/debian/changelog b/debian/changelog index 769b6d8..9d67e71 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,10 +1,16 @@ bwa (0.7.15-1) unstable; urgency=medium - + * team upload + + [ Andreas Tille ] * New upstream version * cme fix dpkg-control * better hardening + + [ Canberk Koç ] + * Added testsuite + * debian/examples directory added - -- Andreas Tille <[email protected]> Fri, 03 Jun 2016 17:53:03 +0200 + -- Canberk Koç <[email protected]> Sat, 25 Jun 2016 23:36:31 +0300 bwa (0.7.13-1) unstable; urgency=medium diff --git a/debian/examples/read1.fq b/debian/examples/read1.fq new file mode 100644 index 0000000..2292db9 --- /dev/null +++ b/debian/examples/read1.fq @@ -0,0 +1,4 @@ +@HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh diff --git a/debian/examples/read2.fq b/debian/examples/read2.fq new file mode 100644 index 0000000..0d0aa2f --- /dev/null +++ b/debian/examples/read2.fq @@ -0,0 +1,4 @@ +@HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG ++HWUSI +acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff diff --git a/debian/examples/reads.fq b/debian/examples/reads.fq new file mode 100644 index 0000000..ef4abd4 --- /dev/null +++ b/debian/examples/reads.fq @@ -0,0 +1,16 @@ +@HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG ++HWUSI +acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff +@HWUSI +CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC ++HWUSI +hhhcfhhhhhhhhhhhhghhhhhhffhhhhhhhhhhhhhg +@HWUSI +AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhh +@HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh diff --git a/debian/examples/ref.fa b/debian/examples/ref.fa new file mode 100644 index 0000000..0eb11c7 --- /dev/null +++ b/debian/examples/ref.fa @@ -0,0 +1,8 @@ +>HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG +>HWUSI +CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC +>HWUSI +AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG +>HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC 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..94fa4b5 --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,23 @@ +#!/bin/bash +set -e + +pkg="bwa" + +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi + +cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP + +bwa index ref.fa +bwa mem ref.fa reads.fq > aln-se.sam +bwa mem ref.fa read1.fq read2.fq > aln-pe.sam +bwa aln ref.fa read1.fq > aln_sa.sai +bwa samse ref.fa aln_sa.sai read1.fq > aln-se.sam +bwa aln ref.fa read2.fq > aln_sa2.sai +bwa sampe ref.fa aln_sa.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam +bwa bwasw ref.fa reads.fq > aln.sam + +echo "PASS" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bwa.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
