[med-svn] [bedtools] 02/03: Add missing input file for tests and fix upstream test script

[Andreas Tille]

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

tille pushed a commit to branch debian/unstable
in repository bedtools.

commit 632c27f2912ed97c17a1803b55ef93397cb75430
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 14 12:07:12 2015 +0200

    Add missing input file for tests and fix upstream test script
---
 debian/bedtools-test.install                     |  6 +++---
 debian/changelog                                 |  1 +
 debian/patches/fix_test_script.patch             | 15 +++++++++++++++
 debian/patches/series                            |  1 +
 debian/test_missing_files/intersect/bug223_d.vcf |  3 +++
 5 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/debian/bedtools-test.install b/debian/bedtools-test.install
index bdf4e75..ff3f4ee 100644
--- a/debian/bedtools-test.install
+++ b/debian/bedtools-test.install
@@ -1,3 +1,3 @@
-test/*	usr/share/bedtools/test
-data/*	usr/share/bedtools/data
-
+test/*				usr/share/bedtools/test
+data/*				usr/share/bedtools/data
+debian/test_missing_files/*	usr/share/bedtools/test
diff --git a/debian/changelog b/debian/changelog
index 5b1590e..eeed671 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
 bedtools (2.24.0-2) UNRELEASED; urgency=medium
 
   * Tests need bgzip from tabix package
+  * Add missing input files for tests
 
  -- Andreas Tille <tille at debian.org>  Tue, 14 Jul 2015 11:01:25 +0200
 
diff --git a/debian/patches/fix_test_script.patch b/debian/patches/fix_test_script.patch
new file mode 100644
index 0000000..6c3e902
--- /dev/null
+++ b/debian/patches/fix_test_script.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 14 Jul 2015 11:01:25 +0200
+Description: Use environment variable to find bedtools in all cases
+
+--- a/test/merge/test-merge.sh
++++ b/test/merge/test-merge.sh
+@@ -444,7 +444,7 @@ chr1	30	100	.,.,.
+ chr2	10	20	.
+ chr2	30	40	.
+ chr2	42	100	.,." >exp
+-../../bin/bedtools merge -i a.full.bam  -c 7 -o collapse > obs
++$BT merge -i a.full.bam  -c 7 -o collapse > obs
+ check exp obs
+ rm obs exp
+ 
diff --git a/debian/patches/series b/debian/patches/series
index d6eb5f4..aeb5e3a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 gzstream.h.patch
+fix_test_script.patch
diff --git a/debian/test_missing_files/intersect/bug223_d.vcf b/debian/test_missing_files/intersect/bug223_d.vcf
new file mode 100644
index 0000000..bfaa751
--- /dev/null
+++ b/debian/test_missing_files/intersect/bug223_d.vcf
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.1
+chr1	1	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-389,-4611;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||
+chr1	4	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||;SVLEN=-45,800,2
\ No newline at end of file

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git