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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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