<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/7dd634c4cf752145633edae38baca97af2f93b91">https://github.com/macports/macports-ports/commit/7dd634c4cf752145633edae38baca97af2f93b91</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 7dd634c4cf752145633edae38baca97af2f93b91
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Sun Jan 27 16:53:29 2019 -0700
<span style='display:block; white-space:pre;color:#404040;'> tophat: update version 1.2.0->2.1.2
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Fixes https://trac.macports.org/ticket/35068
</span>---
science/tophat/Portfile | 78 ++++++++++++++-----
science/tophat/files/patch-cflags.diff | 12 +++
science/tophat/files/patch-cxx14.diff | 12 +++
science/tophat/files/patch-macports_libs.diff | 108 ++++++++++++++++++++++++++
science/tophat/files/src_GList.hh.patch | 29 -------
5 files changed, 191 insertions(+), 48 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/tophat/Portfile b/science/tophat/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 5f670be..2d53aaf 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/tophat/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/tophat/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +1,12 @@
</span> # -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
PortSystem 1.0
<span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup github 1.0
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-name tophat
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version 1.2.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup infphilo tophat 2.1.2 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span> categories science biology
<span style='display:block; white-space:pre;background:#ffe0e0;'>-license LGPL-3+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license Boost-1
</span> platforms darwin
maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -17,26 +18,65 @@ long_description TopHat is ${description}. It aligns RNA-Seq reads to \
</span> results to identify splice junctions between exons.
homepage https://ccb.jhu.edu/software/tophat/
<span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites ${homepage}downloads/
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums sha1 0e697b16c64fa12180b93ecf87fdf25f722973a5 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- rmd160 da62ddc6b2bf8deeda19a95965b1ff2cfd4b95b2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 5a5525f810a38efd5d95303224477d62eb2bd110 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 ec4c522a1caa6cc7c52e2ed7d60f8cdfb21d010523de93d60c64cd5c1b0f352a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 4538707
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-use_parallel_build no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+use_autoconf yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+autoconf.cmd ./bootstrap
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+autoconf.args
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib port:zlib \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:samtools \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:bowtie
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-cflags.diff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-macports_libs.diff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-cxx14.diff
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# samtools and bowtie are not universal
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-universal_variant no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-patch {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace -W ${worksrcpath}/src \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bed_to_juncs \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ contig_to_chr_coords \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ generate_chromosome.py \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sra_to_solid \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ tophat-fusion-post \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ tophat.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles src_GList.hh.patch
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# replicate default optimization level
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.optflags -O3
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# defines _POSIX_SOURCE which by itself means 1003.1-1988, but uses fseeko
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# which is from 1003.1-2001, and strsep which is a BSD extension
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.cppflags-append -D_DARWIN_C_SOURCE
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.cppflags-prepend -I${prefix}/include/seqan-1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -I${prefix}/include/bam-0.1
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.type regex
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.url [lindex ${master_sites} 0]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.regex ${name}-(\[0-9.\]+)${extract.suffix}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# find correct Boost library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# allow MacPort to set optimization level
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append --with-boost-thread=-mt \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ --enable-optim=no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# need for autoconf
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build-append port:autoconf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:automake \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:libtool
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:python27 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:zlib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:samtools-0.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:seqan-1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:boost
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# TopHat attempts to install its own versions
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_run-append port:py27-intervaltree \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:py27-sortedcontainers
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-destroot {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ delete \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ${destroot}${prefix}/bin/intervaltree \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ${destroot}${prefix}/bin/sortedcontainers
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# TopHat uses BowTie 2 by default, so make it a runtime dependency
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_run-append port:bowtie2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+notes {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ By default, TopHat uses BowTie version 2, so the port bowtie2 was installed as a dependency.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ To use BowTie version 1 as well, please install the port bowtie manually.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/tophat/files/patch-cflags.diff b/science/tophat/files/patch-cflags.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..e3be1f2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/tophat/files/patch-cflags.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+remove default debug and warning flags
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- configure.ac.orig 2018-05-24 08:24:31.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ configure.ac 2019-01-26 23:50:37.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -80,7 +80,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # set CFLAGS and CXXFLAGS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #user_CFLAGS="${CXXFLAGS}"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ user_CFLAGS=${CFLAGS}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++generic_CFLAGS=""
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ext_CFLAGS=""
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ debug_CFLAGS=""
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ user_LDFLAGS="$LDFLAGS"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/tophat/files/patch-cxx14.diff b/science/tophat/files/patch-cxx14.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..392ad12
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/tophat/files/patch-cxx14.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+see https://bugs.gentoo.org/594544
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/tophat_reports.cpp.orig 2018-05-24 08:24:31.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/tophat_reports.cpp 2019-01-26 23:15:57.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2705,7 +2705,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ junction_stat.gtf_match = true;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ junction_stat.accepted = true;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/tophat/files/patch-macports_libs.diff b/science/tophat/files/patch-macports_libs.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..541fd3e
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/tophat/files/patch-macports_libs.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,108 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+use MacPorts versions of external libraries
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- configure.ac.orig 2018-05-24 08:24:31.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ configure.ac 2019-01-26 23:12:22.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -38,16 +38,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fi
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# BAM related:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ac_bam_path=samtools-0.1.18
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BAM_LIB="-lbam"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BAM_LDFLAGS="-L./$ac_bam_path"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BAM_CPPFLAGS="-I./$ac_bam_path"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- AC_SUBST(BAM_CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- AC_SUBST(BAM_LDFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- AC_SUBST(BAM_LIB)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # Checks for header files.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -104,8 +94,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ [debug_CFLAGS="-DNDEBUG"])
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CXXFLAGS="$CFLAGS"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/Makefile.am.orig 2018-05-24 08:24:31.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/Makefile.am 2019-01-26 23:13:48.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -681,17 +681,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SeqAn-1.4.2/seqan/system/system_thread.h \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SeqAn-1.4.2/seqan/version.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SAMDIR = ./samtools-0.1.18
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SAMLIB = libbam.a
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SAMPROG = samtools_0.1.18
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-BAM_LIB = -lbam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-BAM_CPPFLAGS = -I$(SAMDIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-BAM_LDFLAGS = -L$(SAMDIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++BAM_LIB = -lbam.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++BAM_CPPFLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #-- progs to be installed in $prefix/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bin_PROGRAMS = \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- $(SAMPROG) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ prep_reads \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ gtf_to_fasta \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fix_map_ordering \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -730,7 +725,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #-- tophat library for linking convienence
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++noinst_LIBRARIES = libgc.a libtophat.a
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ noinst_HEADERS = \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reads.h \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -844,15 +839,5 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-libbam_a_SOURCES =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-samtools_0_1_18_SOURCES =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-$(SAMPROG): $(SAMLIB)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- true
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-$(SAMLIB):
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- echo "ZORG!"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ install-data-hook:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/tophat.py.orig 2019-01-27 00:19:36.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/tophat.py 2019-01-27 00:45:30.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -182,7 +182,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ unmapped_reads_fifo = None # if use_BWT_FIFO is True, this tricks bowtie into writing the
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # unmapped reads into a compressed file
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-samtools_path = "samtools_0.1.18"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++samtools_path = "samtools_0.1"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie_path = None
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fail_str = "\t[FAILED]\n"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ gtf_juncs = None #file name with junctions extracted from given GFF file
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1569,7 +1569,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ def check_samtools():
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #th_log("Checking for Samtools")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ global samtools_path
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- samtools_path=prog_path("samtools_0.1.18")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ samtools_path=prog_path("samtools_0.1")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #samtools_version_str, samtools_version_arr = get_samtools_version()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #if samtools_version_str == None:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if not samtools_path:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/common.cpp.orig 2018-05-24 08:24:31.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/common.cpp 2019-01-27 00:46:14.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -151,7 +151,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ string sam_header = "";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ string sam_readgroup_id = "";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ string zpacker = "";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-string samtools_path = "samtools_0.1.18";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++string samtools_path = "samtools_0.1";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool solexa_quals = false;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool phred64_quals = false;
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/tophat/files/src_GList.hh.patch b/science/tophat/files/src_GList.hh.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0611d53..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/tophat/files/src_GList.hh.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,29 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/GList.hh.orig 2010-12-10 07:25:09.000000000 +1100
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/GList.hh 2012-09-12 14:04:37.000000000 +1000
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -504,7 +504,7 @@ template <class OBJ> int GArray<OBJ>::Ad
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (Found(*item, result))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (fUnique) return -1; //cannot add a duplicate!
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //Found sets result to the position where the item should be!
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- idxInsert(result, *item);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ this->idxInsert(result, *item);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (fUnique && Found(*item,result)) return -1; //set behaviour
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -534,7 +534,7 @@ template <class OBJ> void GArray<OBJ>::A
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for (int i=0;i<list.fCount;i++) Add(&list[i]);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else { //simply copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- setCapacity(this->fCapacity+list.fCount);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ this->setCapacity(this->fCapacity+list.fCount);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int s=this->fCount;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for (int i=0;i<list.fCount;i++)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- this->fArray[s+i]=list.fArray[i];
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -769,7 +769,7 @@ template <class OBJ> void GList<OBJ>::Ad
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for (int i=0;i<list.Count();i++) Add(list[i]);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else { //simply copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- setCapacity(this->fCapacity+list.fCount);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ this->setCapacity(this->fCapacity+list.fCount);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- memcpy( & (this->fList[this->fCount]), list.fList, list.fCount*sizeof(OBJ*));
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- this->fCount+=list.fCount;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
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