diff options
| author | Christian Krause | 2016-06-02 11:33:06 +0200 |
|---|---|---|
| committer | Christian Krause | 2016-06-02 11:33:06 +0200 |
| commit | 4bb5f7f538b0640f41d78651cbef939ac46b91c7 (patch) | |
| tree | 4778c4ab1bd6e673f412822fdd5480898e00a556 | |
| parent | 1058cf08d5e6449bf7bf9d4b44b3e0883169d069 (diff) | |
| download | aur-4bb5f7f538b0640f41d78651cbef939ac46b91c7.tar.gz | |
fix make_pair issue
| -rw-r--r-- | .SRCINFO | 6 | ||||
| -rw-r--r-- | PKGBUILD | 10 | ||||
| -rw-r--r-- | make_pair.patch | 24 |
3 files changed, 35 insertions, 5 deletions
@@ -1,9 +1,9 @@ # Generated by mksrcinfo v8 -# Wed Mar 23 13:58:02 UTC 2016 +# Thu Jun 2 09:32:08 UTC 2016 pkgbase = tophat pkgdesc = fast splice junction mapper for RNA-Seq reads pkgver = 2.1.1 - pkgrel = 1 + pkgrel = 2 url = http://ccb.jhu.edu/software/tophat/index.shtml arch = x86_64 arch = i686 @@ -13,7 +13,9 @@ pkgbase = tophat depends = bowtie2 depends = python2 source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz + source = make_pair.patch md5sums = 4b2391de46457ba6b2b7268a9da593e4 + md5sums = 53378885f3620a1d02fb345077609d05 pkgname = tophat @@ -2,15 +2,17 @@ pkgname=tophat pkgver=2.1.1 -pkgrel=1 +pkgrel=2 pkgdesc="fast splice junction mapper for RNA-Seq reads" arch=('x86_64' 'i686') url="http://ccb.jhu.edu/software/tophat/index.shtml" license=('custom') depends=('boost-libs' 'bowtie2' 'python2') makedepends=('boost') -source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz") -md5sums=('4b2391de46457ba6b2b7268a9da593e4') +source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz" + 'make_pair.patch') +md5sums=('4b2391de46457ba6b2b7268a9da593e4' + '53378885f3620a1d02fb345077609d05') prepare() { cd $srcdir/$pkgname-$pkgver @@ -24,6 +26,8 @@ prepare() { src/sra_to_solid \ src/tophat-fusion-post \ src/tophat.py + + patch -Np1 -i $srcdir/make_pair.patch } build() { diff --git a/make_pair.patch b/make_pair.patch new file mode 100644 index 000000000000..44b71d1059ab --- /dev/null +++ b/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()); |