Commit 7e36fe2e authored by Steffen Möller's avatar Steffen Möller
Browse files

Fixed build failure.

parent d6f90339

debian/changelog

+4 −4
Original line number Diff line number Diff line 
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

  * Fixed failing intersect.new #78 test as instructed on

    https://github.com/arq5x/bedtools2/issues/814

  * Standard-Version: 4.5.0



 -- Steffen Moeller <moeller@debian.org>  Sat, 18 Jan 2020 01:44:47 +0100

debian/control

+1 −1
Original line number Diff line number Diff line
@@ -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 → 100644
+15 −0
Original line number Diff line number Diff line 
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

+1 −0
Original line number Diff line number Diff line
@@ -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