This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository bedtools.
commit 26760c880e7a5aa3aa5ed935c94e9793fcd3b1f5 Author: Andreas Tille <[email protected]> Date: Sat Feb 10 10:41:05 2018 +0100 Patch g6bf23c4 is included into this release so it cen be droped --- debian/patches/series | 1 - debian/patches/v2.26.0-19-g6bf23c4.patch | 54 -------------------------------- 2 files changed, 55 deletions(-) diff --git a/debian/patches/series b/debian/patches/series index 84290f3..e0b66fe 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -2,4 +2,3 @@ gzstream.h.patch fix_test_script.patch remove_barski_binding_site.png.patch reproducible_build.patch -v2.26.0-19-g6bf23c4.patch diff --git a/debian/patches/v2.26.0-19-g6bf23c4.patch b/debian/patches/v2.26.0-19-g6bf23c4.patch deleted file mode 100644 index 661dc4f..0000000 --- a/debian/patches/v2.26.0-19-g6bf23c4.patch +++ /dev/null @@ -1,54 +0,0 @@ -Author: Upstream -Bug-Debian: https://bugs.debian.org/831833 -Description: Sync with upstream repo at commit 6bf23c - This patch contains bug fixes to upstream issues #429, #418 and #424. - In particular, it repairs the groupby command, which was completely - broken. Cherry-picking a single commit did not result in a buildable - source, and this big patch was the easiest alternative. ---- a/src/utils/Contexts/ContextBase.cpp -+++ b/src/utils/Contexts/ContextBase.cpp -@@ -13,6 +13,7 @@ - ContextBase::ContextBase() - : - _program(UNSPECIFIED_PROGRAM), -+ _files(NULL), - _allFilesOpened(false), - _genomeFile(NULL), - _outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE), ---- a/test/general/test-general.sh -+++ b/test/general/test-general.sh -@@ -333,6 +333,17 @@ $BT intersect -a a.trackheader.bed -b a. - check obs exp - - -+# allow header lines to start with chr or chrom -+echo " general.t43...\c" -+echo "chrom chromStart chromEnd name score strand -+chr14 24800000 24810000 blarg 0 . -+chr11 64610000 64620000 blarg 0 . -+chr14 24710000 24720000 blarg 0 . -+chr11 111230000 111240000 blarg 0 ." > exp -+$BT intersect -a t.bed -b t.bed -header > obs -+check obs exp -+ -+ - rm a.bed.gz b.bed.gz c.bed.gz a.bed b.bed c.bed genome.txt exp obs - - [[ $FAILURES -eq 0 ]] || exit 1; ---- a/test/shift/test-shift.sh -+++ b/test/shift/test-shift.sh -@@ -129,14 +129,4 @@ echo \ - check obs exp - rm obs exp - --########################################################### --# test shift huge genome --########################################################### --echo -e " shift.t10...\c" --echo \ --"chr1 67000638 67217822 NM_032291 0 + --chr1 92146899 92352836 NR_036634 0 -" > exp --$BT shift -i b.bed -s 1000 -g huge.genome > obs --check obs exp --rm obs exp - [[ $FAILURES -eq 0 ]] || exit 1; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
