[med-svn] [Git][med-team/bedtools][master] Fixed build failure.

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bedtools


Commits:
7e36fe2e by Steffen Moeller at 2020-01-23T11:47:03+01:00
Fixed build failure.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix_intersect_test.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,10 @@
-bedtools (2.29.2+dfsg-1) UNRELEASED; urgency=medium
+bedtools (2.29.2+dfsg-1) unstable; urgency=medium
 
   * Team upload.
   * New upstream version
-
-  * BLOCKER: Tests for 'intersect' fail
-             https://github.com/arq5x/bedtools2/issues/814
+  * Fixed failing intersect.new #78 test as instructed on
+    https://github.com/arq5x/bedtools2/issues/814
+  * Standard-Version: 4.5.0
 
  -- Steffen Moeller <moeller at debian.org>  Sat, 18 Jan 2020 01:44:47 +0100
 


=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
                libbz2-dev,
                liblzma-dev,
                samtools
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/bedtools
 Vcs-Git: https://salsa.debian.org/med-team/bedtools.git
 Homepage: https://github.com/arq5x/bedtools2


=====================================
debian/patches/fix_intersect_test.patch
=====================================
@@ -0,0 +1,15 @@
+Index: bedtools/test/intersect/new_test-intersect.sh
+===================================================================
+--- bedtools.orig/test/intersect/new_test-intersect.sh
++++ bedtools/test/intersect/new_test-intersect.sh
+@@ -975,8 +975,8 @@ rm exp obs
+ #  Test intersect preserve the text header in bam
+ ############################################################
+ echo -e "    intersect.new.t78...\c"
+-echo -e "@HD     VN:1.5  SO:coordinate" > exp
+-echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
++echo -e "@HD	VN:1.5	SO:coordinate" > exp
++echo "@HD	VN:1.5	SO:coordinate" | samtools view --no-PG -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ remove_barski_binding_site.png.patch
 # not Debian-specific, upstream has worked on that, too
 #flag_no_overwrite
 2to3.patch
+fix_intersect_test.patch



View it on GitLab: https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a

-- 
View it on GitLab: https://salsa.debian.org/med-team/bedtools/commit/7e36fe2ecf316b673af22f8aea5754f706249c7a
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