[med-svn] [bedtools] 02/07: Patch g6bf23c4 is included into this release so it cen be droped

[Andreas Tille]

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tille pushed a commit to branch master
in repository bedtools.

commit 26760c880e7a5aa3aa5ed935c94e9793fcd3b1f5
Author: Andreas Tille <tille at debian.org>
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;

-- 
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