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author | Matteo Bernardini | 2019-02-17 19:00:23 +0100 |
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committer | Matteo Bernardini | 2019-02-17 19:00:23 +0100 |
commit | 728d1f98285ca36c6f63c48b4a9f3125ef7396ff (patch) | |
tree | b9f9d2618fd06436d8eb61488edebac987197d5e /academic/tophat | |
parent | 77c0f4770537aea300fccd3189b723bfada95f22 (diff) | |
download | slackbuilds-728d1f98285ca36c6f63c48b4a9f3125ef7396ff.tar.gz |
20190217.1 global branch merge.current-20190217.1
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
Diffstat (limited to 'academic/tophat')
-rw-r--r-- | academic/tophat/make_pair.patch | 24 | ||||
-rw-r--r-- | academic/tophat/tophat.SlackBuild | 3 |
2 files changed, 27 insertions, 0 deletions
diff --git a/academic/tophat/make_pair.patch b/academic/tophat/make_pair.patch new file mode 100644 index 0000000000..44b71d1059 --- /dev/null +++ b/academic/tophat/make_pair.patch @@ -0,0 +1,24 @@ +diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.cpp +--- tophat-2.1.1/src/juncs_db.cpp 2016-02-14 19:21:17.354079000 +0100 ++++ tophat-2.1.1-patched/src/juncs_db.cpp 2016-06-02 11:26:34.097425159 +0200 +@@ -338,7 +338,7 @@ + uint32_t left_coord = atoi(scan_left_coord); + uint32_t right_coord = atoi(scan_right_coord); + bool antisense = *orientation == '-'; +- junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats())); ++ junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats())); + } + } + +diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp +--- tophat-2.1.1/src/tophat_reports.cpp 2016-02-23 22:20:44.320710000 +0100 ++++ tophat-2.1.1-patched/src/tophat_reports.cpp 2016-06-02 11:26:22.057239478 +0200 +@@ -2705,7 +2705,7 @@ + junction_stat.gtf_match = true; + junction_stat.accepted = true; + +- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + } + } + fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild index e579ff1e9a..bdddfa4182 100644 --- a/academic/tophat/tophat.SlackBuild +++ b/academic/tophat/tophat.SlackBuild @@ -69,6 +69,9 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +# Thanks archlinux +patch -p1 < $CWD/make_pair.patch + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ |