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authorDavid Seifert <soap@gentoo.org>2016-04-03 18:29:28 +0200
committerDavid Seifert <soap@gentoo.org>2016-04-03 18:29:28 +0200
commit6b4151d6d2a91701e87a706fcdd896849698dea4 (patch)
tree9456dbfc15149fb94428247395db009205860d62 /sci-biology/cufflinks
parentsci-biology/cufflinks: Depend only on sci-biology/samtools:0.1-legacy (diff)
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sci-biology/cufflinks: Remove old
Package-Manager: portage-2.2.28
Diffstat (limited to 'sci-biology/cufflinks')
-rw-r--r--sci-biology/cufflinks/Manifest1
-rw-r--r--sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild40
-rw-r--r--sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild52
-rw-r--r--sci-biology/cufflinks/cufflinks-2.2.1.ebuild40
-rw-r--r--sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch38
-rw-r--r--sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch1320
-rw-r--r--sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch20
-rw-r--r--sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch16
8 files changed, 0 insertions, 1527 deletions
diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
index 017836ee07ad..88bfcfa10d11 100644
--- a/sci-biology/cufflinks/Manifest
+++ b/sci-biology/cufflinks/Manifest
@@ -1,2 +1 @@
-DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce
DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224
diff --git a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
deleted file mode 100644
index 36322f463de6..000000000000
--- a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
-HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
-SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="Artistic"
-IUSE="debug"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=sci-biology/samtools-0.1.18
- <sci-biology/samtools-1
- <dev-libs/boost-1.56:="
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/${P}-autotools.patch
- "${FILESDIR}"/${P}-boost.patch
- "${FILESDIR}"/${P}-gcc-4.7.patch
- )
-
-src_configure() {
- local myeconfargs=(
- --disable-optim
- --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
- --with-bam="${EPREFIX}/usr/"
- $(use_enable debug)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
deleted file mode 100644
index 66298cbc1972..000000000000
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic toolchain-funcs
-
-DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
-HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
-SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="Artistic"
-IUSE="debug"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- || (
- (
- >=sci-biology/samtools-0.1.18
- sci-libs/htslib
- )
- <sci-biology/samtools-1
- )
- >=dev-libs/boost-1.47.0:=
- <dev-libs/boost-1.56.0:=
- dev-cpp/eigen:3
-"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/${P}-hts.patch
- "${FILESDIR}"/${P}-flags.patch
- )
-
-src_prepare() {
- append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --disable-optim
- --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
- --with-bam="${EPREFIX}/usr/"
- $(use_enable debug)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild
deleted file mode 100644
index 5e7f763389f9..000000000000
--- a/sci-biology/cufflinks/cufflinks-2.2.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools-utils flag-o-matic toolchain-funcs
-
-DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
-HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
-SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="Artistic"
-IUSE="debug"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=sci-biology/samtools-0.1.18
- <sci-biology/samtools-1
- >=dev-libs/boost-1.47.0:=
- <dev-libs/boost-1.56.0:=
- dev-cpp/eigen:3
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --disable-optim
- --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
- --with-bam="${EPREFIX}/usr/"
- $(use_enable debug)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
deleted file mode 100644
index 73e52b4343a0..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -27,6 +27,7 @@ AC_PROG_AWK
- AC_PROG_CXX
- AC_PROG_CC
- AC_PROG_MAKE_SET
-+AM_PROG_AR
- AC_PROG_RANLIB
- AC_PROG_INSTALL
- AM_PATH_PYTHON([2.4])
-@@ -54,7 +55,7 @@ AC_CANONICAL_HOST
-
- # set CFLAGS and CXXFLAGS
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized"
- ext_CFLAGS=""
- debug_CFLAGS=""
- #echo "${host_cpu}-${host_os}"
-@@ -99,15 +100,15 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with
- [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
-
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
--CXXFLAGS="$CFLAGS"
-+CXXFLAGS="$CXXFLAGS"
- CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
--LDFLAGS="$ext_LDFLAGS"
-+LDFLAGS="$LDFLAGS $ext_LDFLAGS"
-
- # Checks for structures/functions that can be used to determine system memory
- AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>])
- AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>])
-
--AM_INIT_AUTOMAKE([-Wall -Werror tar-pax foreign])
-+AM_INIT_AUTOMAKE([-Wall tar-pax foreign subdir-objects])
-
- AC_CONFIG_FILES([Makefile
- src/Makefile])
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch
deleted file mode 100644
index d45391bf4f3a..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch
+++ /dev/null
@@ -1,1320 +0,0 @@
- ax_boost_thread.m4 | 6 +++---
- src/abundances.cpp | 56 +++++++++++++++++++++++++-------------------------
- src/biascorrection.cpp | 2 +-
- src/bundles.cpp | 10 ++++-----
- src/bundles.h | 10 ++++-----
- src/common.h | 4 ++--
- src/compress_gtf.cpp | 12 +++++------
- src/cuffdiff.cpp | 30 +++++++++++++--------------
- src/cufflinks.cpp | 34 +++++++++++++++---------------
- src/differential.cpp | 38 +++++++++++++++++-----------------
- src/filters.cpp | 8 ++++----
- src/genes.h | 6 +++---
- src/gtf_to_sam.cpp | 8 ++++----
- src/hits.cpp | 4 ++--
- src/replicates.cpp | 6 +++---
- src/replicates.h | 18 ++++++++--------
- src/scaffolds.cpp | 28 ++++++++++++-------------
- src/scaffolds.h | 2 +-
- 18 files changed, 141 insertions(+), 141 deletions(-)
-
-diff --git a/ax_boost_thread.m4 b/ax_boost_thread.m4
-index d1d42f6..6f99f1b 100644
---- a/ax_boost_thread.m4
-+++ b/ax_boost_thread.m4
-@@ -105,20 +105,20 @@ AC_DEFUN([AX_BOOST_THREAD],
- for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
-- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
-+ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- if test "x$link_thread" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
-- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
-+ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- fi
-
- else
-- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
-+ BOOST_THREAD_LIB="$ax_boost_user_thread_lib -lboost_system";
- AC_SUBST(BOOST_THREAD_LIB)
- link_thread="yes";
-
-diff --git a/src/abundances.cpp b/src/abundances.cpp
-index d8f81d0..6e717dc 100644
---- a/src/abundances.cpp
-+++ b/src/abundances.cpp
-@@ -140,7 +140,7 @@ AbundanceStatus AbundanceGroup::status() const
- {
- bool has_lowdata_member = false;
- bool has_ok_member = false;
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- if (ab->status() == NUMERIC_FAIL)
- {
-@@ -205,7 +205,7 @@ void TranscriptAbundance::FPKM_variance(double v)
-
- bool AbundanceGroup::has_member_with_status(AbundanceStatus member_status)
- {
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- if (ab->status() == member_status)
- {
-@@ -219,7 +219,7 @@ double AbundanceGroup::num_fragments() const
- {
- double num_f = 0;
-
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- num_f += ab->num_fragments();
- }
-@@ -231,7 +231,7 @@ double AbundanceGroup::mass_fraction() const
- {
- double mass = 0;
-
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- mass += ab->mass_fraction();
- }
-@@ -242,7 +242,7 @@ double AbundanceGroup::mass_variance() const
- {
- double mass_var = 0;
-
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- mass_var += ab->mass_variance();
- }
-@@ -253,7 +253,7 @@ double AbundanceGroup::FPKM() const
- {
- double fpkm = 0;
-
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- fpkm += ab->FPKM();
- }
-@@ -265,7 +265,7 @@ double AbundanceGroup::gamma() const
- {
- double gamma = 0;
-
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- gamma += ab->gamma();
- }
-@@ -281,7 +281,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep,
- assert (to_keep.size() == _abundances.size());
-
- size_t num_kept = 0;
-- foreach(bool keeper, to_keep)
-+ for_each(bool keeper, to_keep)
- {
- num_kept += keeper;
- }
-@@ -331,7 +331,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep,
- void AbundanceGroup::get_transfrags(vector<shared_ptr<Abundance> >& transfrags) const
- {
- transfrags.clear();
-- foreach(shared_ptr<Abundance> pA, _abundances)
-+ for_each(shared_ptr<Abundance> pA, _abundances)
- {
- shared_ptr<Scaffold> pS = pA->transfrag();
- if (pS)
-@@ -345,7 +345,7 @@ set<string> AbundanceGroup::gene_id() const
- {
- set<string> s;
-
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- set<string> sub = pA->gene_id();
- s.insert(sub.begin(), sub.end());
-@@ -358,7 +358,7 @@ set<string> AbundanceGroup::gene_name() const
- {
- set<string> s;
-
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- set<string> sub = pA->gene_name();
- s.insert(sub.begin(), sub.end());
-@@ -372,7 +372,7 @@ set<string> AbundanceGroup::tss_id() const
- {
- set<string> s;
-
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- set<string> sub = pA->tss_id();
- s.insert(sub.begin(), sub.end());
-@@ -385,7 +385,7 @@ set<string> AbundanceGroup::protein_id() const
- {
- set<string> s;
-
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- set<string> sub = pA->protein_id();
- s.insert(sub.begin(), sub.end());
-@@ -398,7 +398,7 @@ const string& AbundanceGroup::locus_tag() const
- {
- static string default_locus_tag = "-";
- const string* pLast = NULL;
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- if (pLast)
- {
-@@ -422,7 +422,7 @@ const string& AbundanceGroup::reference_tag() const
- {
- static string default_reference_tag = "-";
- const string* pLast = NULL;
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- if (pLast)
- {
-@@ -448,7 +448,7 @@ double AbundanceGroup::effective_length() const
- double group_fpkm = FPKM();
- if (group_fpkm == 0)
- return 0;
-- foreach (shared_ptr<Abundance> ab, _abundances)
-+ for_each (shared_ptr<Abundance> ab, _abundances)
- {
- eff_len += (ab->effective_length() * (ab->FPKM() / group_fpkm));
- }
-@@ -1216,7 +1216,7 @@ void AbundanceGroup::estimate_count_covariance()
- {
- // if the entire group is unstable, then set LOWDATA on all members of
- // it to reduce false positives in differential expression analysis.
-- foreach(shared_ptr<Abundance> ab, _abundances)
-+ for_each(shared_ptr<Abundance> ab, _abundances)
- {
- ab->status(NUMERIC_LOW_DATA);
- }
-@@ -1468,7 +1468,7 @@ void AbundanceGroup::calculate_conf_intervals()
- double sum_transfrag_FPKM_hi = 0;
- double max_fpkm = 0.0;
- //double min_fpkm = 1e100;
-- foreach(shared_ptr<Abundance> pA, _abundances)
-+ for_each(shared_ptr<Abundance> pA, _abundances)
- {
- double FPKM_hi;
- double FPKM_lo;
-@@ -1586,7 +1586,7 @@ void AbundanceGroup::calculate_conf_intervals()
- // double sum_transfrag_FPKM_hi = 0;
- // double max_fpkm = 0.0;
- // //double min_fpkm = 1e100;
--// foreach(shared_ptr<Abundance> pA, _abundances)
-+// for_each(shared_ptr<Abundance> pA, _abundances)
- // {
- // double FPKM_hi;
- // double FPKM_lo;
-@@ -1732,7 +1732,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments,
- if (mapped_transcripts.empty())
- {
- //gammas = vector<double>(transfrags.size(), 0.0);
-- foreach (shared_ptr<Abundance> ab, _abundances)
-+ for_each (shared_ptr<Abundance> ab, _abundances)
- {
- ab->gamma(0);
- }
-@@ -1783,7 +1783,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments,
- if (filtered_transcripts.empty())
- {
- //gammas = vector<double>(transfrags.size(), 0.0);
-- foreach (shared_ptr<Abundance> ab, _abundances)
-+ for_each (shared_ptr<Abundance> ab, _abundances)
- {
- ab->gamma(0);
- }
-@@ -2117,7 +2117,7 @@ void AbundanceGroup::calculate_kappas()
- double S_FPKM = 0.0;
- double Z_kappa = 0.0;
- double X_S = 0.0;
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- if (pA->effective_length() > 0)
- {
-@@ -2128,7 +2128,7 @@ void AbundanceGroup::calculate_kappas()
- }
-
- //fprintf (stderr, "*********\n");
-- foreach (shared_ptr<Abundance> pA, _abundances)
-+ for_each (shared_ptr<Abundance> pA, _abundances)
- {
- if (S_FPKM > 0)
- {
-@@ -2201,7 +2201,7 @@ void get_alignments_from_scaffolds(const vector<shared_ptr<Abundance> >& abundan
- {
- set<const MateHit*> hits_in_gene_set;
-
-- foreach(shared_ptr<Abundance> pA, abundances)
-+ for_each(shared_ptr<Abundance> pA, abundances)
- {
- shared_ptr<Scaffold> pS = pA->transfrag();
- assert (pS);
-@@ -2787,7 +2787,7 @@ AbundanceStatus empirical_mean_replicate_gamma_mle(const vector<shared_ptr<Abund
- gamma_covariance = ublas::zero_matrix<double>(N,N);
- ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N);
- //
-- foreach(ublas::vector<double>& mle, mle_gammas)
-+ for_each(ublas::vector<double>& mle, mle_gammas)
- {
- expected_mle_gamma += mle;
- }
-@@ -3122,7 +3122,7 @@ AbundanceStatus bootstrap_gamma_mle(const vector<shared_ptr<Abundance> >& transc
- gamma_covariance = ublas::zero_matrix<double>(N,N);
- ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N);
-
-- foreach(ublas::vector<double>& mle, mle_gammas)
-+ for_each(ublas::vector<double>& mle, mle_gammas)
- {
- //cerr << "MLE # "<< MLENUM++ << endl;
- //cerr << mle << endl;
-@@ -3586,7 +3586,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts,
-
- double round_err = 0.0;
- double num_good = 0;
-- foreach (double& g, gammas)
-+ for_each (double& g, gammas)
- {
- if (g < min_isoform_fraction)
- {
-@@ -3598,7 +3598,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts,
- num_good += 1;
- }
- }
-- foreach (double& g, gammas)
-+ for_each (double& g, gammas)
- {
- if (g != 0)
- {
-diff --git a/src/biascorrection.cpp b/src/biascorrection.cpp
-index 0d49851..55884f4 100644
---- a/src/biascorrection.cpp
-+++ b/src/biascorrection.cpp
-@@ -207,7 +207,7 @@ void BiasLearner::preProcessTranscript(const Scaffold& transcript)
- vector<double> startHist(transcript.length()+1, 0.0); // +1 catches overhangs
- vector<double> endHist(transcript.length()+1, 0.0);
-
-- foreach (const MateHit* hit_p, transcript.mate_hits())
-+ for_each (const MateHit* hit_p, transcript.mate_hits())
- {
- const MateHit& hit = *hit_p;
- if (!hit.left_alignment() && !hit.right_alignment())
-diff --git a/src/bundles.cpp b/src/bundles.cpp
-index ead07f2..a392514 100644
---- a/src/bundles.cpp
-+++ b/src/bundles.cpp
-@@ -228,7 +228,7 @@ void load_ref_rnas(FILE* ref_mRNA_file,
- }
- }
-
-- foreach (shared_ptr<Scaffold> s, ref_mRNAs)
-+ for_each (shared_ptr<Scaffold> s, ref_mRNAs)
- {
- assert (s);
- }
-@@ -418,7 +418,7 @@ void HitBundle::finalize_open_mates()
-
- for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr)
- {
-- foreach (MateHit& hit, itr->second)
-+ for_each (MateHit& hit, itr->second)
- {
- delete hit.left_alignment();
- delete hit.right_alignment();
-@@ -438,7 +438,7 @@ void HitBundle::remove_hitless_scaffolds()
- void HitBundle::remove_unmapped_hits()
- {
-
-- foreach (MateHit& hit, _hits)
-+ for_each (MateHit& hit, _hits)
- {
- if (unmapped_hit(hit))
- {
-@@ -586,7 +586,7 @@ void HitBundle::finalize(bool is_combined)
- }
- else
- {
-- foreach (MateHit& hit, _hits)
-+ for_each (MateHit& hit, _hits)
- {
- hit.incr_collapse_mass(hit.common_scale_mass());
- }
-@@ -1316,7 +1316,7 @@ void identify_bad_splices(const HitBundle& bundle,
- ins_itr = bad_splice_ops.insert(make_pair(ref_id, vector<AugmentedCuffOp>()));
- vector<AugmentedCuffOp>& bad_introns = ins_itr.first->second;
-
-- foreach (const MateHit& hit, bundle.hits())
-+ for_each (const MateHit& hit, bundle.hits())
- {
- if (hit.left_alignment())
- {
-diff --git a/src/bundles.h b/src/bundles.h
-index 15f51ee..aec725e 100644
---- a/src/bundles.h
-+++ b/src/bundles.h
-@@ -57,7 +57,7 @@ public:
- ~HitBundle()
- {
- vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds();
-- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
-+ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
- {
- // This bundle and the factory that actually owns the ref_mRNAs
- // are the only objects that should have access to these scaffolds
-@@ -73,7 +73,7 @@ public:
- }
- }
-
-- foreach (MateHit& hit, _hits)
-+ for_each (MateHit& hit, _hits)
- {
- delete hit.left_alignment();
- delete hit.right_alignment();
-@@ -81,7 +81,7 @@ public:
-
- for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr)
- {
-- foreach (MateHit& hit, itr->second)
-+ for_each (MateHit& hit, itr->second)
- {
- delete hit.left_alignment();
- delete hit.right_alignment();
-@@ -113,7 +113,7 @@ public:
- _hits.clear();
- _non_redundant.clear();
- vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds();
-- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
-+ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs)
- {
- if (ref_scaff.use_count() <= 3)
- {
-@@ -250,7 +250,7 @@ public:
- next_ref_scaff = ref_mRNAs.begin();
- next_mask_scaff = mask_gtf_recs.begin();
-
-- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
-+ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
- {
- ref_scaff->clear_hits();
- }
-diff --git a/src/common.h b/src/common.h
-index b715e9c..1ed7d77 100644
---- a/src/common.h
-+++ b/src/common.h
-@@ -22,8 +22,8 @@
- using boost::math::normal;
-
- #include <boost/foreach.hpp>
--#define foreach BOOST_FOREACH
--#define reverse_foreach BOOST_REVERSE_FOREACH
-+#define for_each BOOST_FOREACH
-+#define reverse_for_each BOOST_REVERSE_FOREACH
-
- #include <boost/thread.hpp>
- #include <boost/shared_ptr.hpp>
-diff --git a/src/compress_gtf.cpp b/src/compress_gtf.cpp
-index a2cd10a..a3796fd 100644
---- a/src/compress_gtf.cpp
-+++ b/src/compress_gtf.cpp
-@@ -159,7 +159,7 @@ void compress_genes(FILE* ftranscripts,
- vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i];
- vector<Scaffold> gene_scaffs;
- string gene_id;
-- foreach (shared_ptr<Scaffold> s, gene)
-+ for_each (shared_ptr<Scaffold> s, gene)
- {
- if (gene_id == "")
- gene_id = s->annotated_gene_id();
-@@ -175,7 +175,7 @@ void compress_genes(FILE* ftranscripts,
- Scaffold smashed_gene;
- if (!proj_intersection && !proj_union)
- {
-- foreach (shared_ptr<Scaffold> s, gene)
-+ for_each (shared_ptr<Scaffold> s, gene)
- {
- /*
- *transfrag,
-@@ -224,7 +224,7 @@ void compress_genes(FILE* ftranscripts,
- int gmax = -1;
- int gmin = numeric_limits<int>::max();
-
-- foreach (shared_ptr<Scaffold> s, gene)
-+ for_each (shared_ptr<Scaffold> s, gene)
- {
- //iso_ops.push_back(s->augmented_ops());
- //sort (iso_ops.back().begin(), iso_ops.back().end());
-@@ -234,7 +234,7 @@ void compress_genes(FILE* ftranscripts,
- gmax = s->right();
- }
-
-- foreach (shared_ptr<Scaffold> s, gene)
-+ for_each (shared_ptr<Scaffold> s, gene)
- {
- if (s->left() > gmin)
- {
-@@ -347,7 +347,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* gtf_out)
- vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table;
- vector<pair<string, vector<double> > > sample_count_table;
-
-- foreach (FILE* ref_gtf, ref_gtf_files)
-+ for_each (FILE* ref_gtf, ref_gtf_files)
- {
- vector<shared_ptr<Scaffold> > ref_mRNAs;
- ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true);
-@@ -393,7 +393,7 @@ int main(int argc, char** argv)
-
- vector<FILE*> ref_gtf_files;
-
-- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames)
-+ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames)
- {
- FILE* ref_gtf = NULL;
- if (ref_gtf_in_filename != "")
-diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp
-index 575b064..7725910 100644
---- a/src/cuffdiff.cpp
-+++ b/src/cuffdiff.cpp
-@@ -490,7 +490,7 @@ void print_FPKM_tracking(FILE* fout,
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- AbundanceStatus status = NUMERIC_OK;
-- foreach (const FPKMContext& c, fpkms)
-+ for_each (const FPKMContext& c, fpkms)
- {
- if (c.status == NUMERIC_FAIL)
- status = NUMERIC_FAIL;
-@@ -811,7 +811,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- ::load_ref_rnas(mask_gtf, rt, mask_rnas, false, false);
- }
-
-- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
- {
- fac->set_ref_rnas(ref_mRNAs);
- if (mask_gtf)
-@@ -826,7 +826,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- int tmp_max_frag_len = 0;
-
- ProgressBar p_bar("Inspecting maps and determining fragment length distributions.",0);
-- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
- {
- #if ENABLE_THREADS
- while(1)
-@@ -877,7 +877,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- {
- long double total_mass = 0.0;
- long double total_norm_mass = 0.0;
-- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups)
-+ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups)
- {
- total_mass += rg->total_map_mass();
- total_norm_mass += rg->normalized_map_mass();
-@@ -886,7 +886,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- if (total_mass > 0)
- {
- double scaling_factor = total_mass / total_norm_mass;
-- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups)
-+ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups)
- {
- double scaled_mass = scaling_factor * rg->normalized_map_mass();
-
-@@ -916,7 +916,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
-
- if (most_reps != 1 && poisson_dispersion == false)
- {
-- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
- {
- if (fac->num_replicates() == 1)
- {
-@@ -990,7 +990,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- shared_ptr<MassDispersionModel const> disperser;
- disperser = fit_dispersion_model("pooled", scale_factors, sample_count_table);
-
-- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
-+ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
- {
- rg_props->mass_dispersion_model(disperser);
- }
-@@ -999,7 +999,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
-
- long double total_norm_mass = 0.0;
- long double total_mass = 0.0;
-- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
-+ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
- {
- total_norm_mass += rg_props->normalized_map_mass();
- total_mass += rg_props->total_map_mass();
-@@ -1007,7 +1007,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
-
- // scale the normalized masses so that both quantile total count normalization
- // are roughly on the same numerical scale
-- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
-+ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
- {
- long double new_norm = rg_props->normalized_map_mass() * (total_mass / total_norm_mass);
- rg_props->normalized_map_mass(new_norm);
-@@ -1039,7 +1039,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >());
- quantitate_next_locus(rt, bundle_factories, test_launcher);
- bool more_loci_remain = false;
-- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
- {
- if (rep_fac->bundles_remain())
- {
-@@ -1071,7 +1071,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- }
- }
-
-- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
- {
- rep_fac->reset();
- }
-@@ -1081,9 +1081,9 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- if (corr_bias)
- {
- p_bar = ProgressBar("Learning bias parameters.", 0);
-- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
- {
-- foreach (shared_ptr<BundleFactory> fac, rep_fac->factories())
-+ for_each (shared_ptr<BundleFactory> fac, rep_fac->factories())
- {
- #if ENABLE_THREADS
- while(1)
-@@ -1124,7 +1124,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- boost::this_thread::sleep(boost::posix_time::milliseconds(5));
- }
- #endif
-- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
- {
- rep_fac->reset();
- }
-@@ -1167,7 +1167,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list
- //shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >());
- quantitate_next_locus(rt, bundle_factories, test_launcher);
- bool more_loci_remain = false;
-- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
-+ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
- {
- if (rep_fac->bundles_remain())
- {
-diff --git a/src/cufflinks.cpp b/src/cufflinks.cpp
-index 796af98..1030ae8 100644
---- a/src/cufflinks.cpp
-+++ b/src/cufflinks.cpp
-@@ -471,7 +471,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs,
- {
- for(size_t l = 0; l < lhs.size(); ++l)
- {
-- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
-+ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
- {
- // if we're past all the overlaps, just stop
- if (ref_scaff->left() >= lhs[l].right() + overhang_3)
-@@ -504,7 +504,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs,
- }
- for(size_t r = 0; r < rhs.size(); ++r)
- {
-- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
-+ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs)
- {
- if (ref_scaff->left() >= rhs[r].right() + overhang_3)
- {
-@@ -665,7 +665,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle,
- if (ref_guided && enable_faux_reads && !hits.empty())
- {
- vector<Scaffold> pseudohits;
-- foreach(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
-+ for_each(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
- {
- ref_scaff->tile_with_scaffs(pseudohits, tile_len, tile_off);
- }
-@@ -842,7 +842,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle,
- }
- if (assembled_successfully)
- {
-- foreach(Scaffold& scaff, tmp_scaffs)
-+ for_each(Scaffold& scaff, tmp_scaffs)
- {
- scaffolds.push_back(shared_ptr<Scaffold>(new Scaffold(scaff)));
- }
-@@ -886,7 +886,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
-
- // need the avg read length for depth of coverage calculation
- double avg_read_length = 0;
-- foreach (MateHit& hit, hits_in_cluster)
-+ for_each (MateHit& hit, hits_in_cluster)
- {
- if (hit.left_alignment())
- avg_read_length += hit.left_alignment()->read_len();
-@@ -905,7 +905,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- }
- else
- {
-- foreach(shared_ptr<Abundance> ab, transfrag_cluster.abundances())
-+ for_each(shared_ptr<Abundance> ab, transfrag_cluster.abundances())
- {
- ab->status(NUMERIC_HI_DATA);
- }
-@@ -939,7 +939,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- {
- shared_ptr<Abundance> ab_i = abundances[i];
- bool found = false;
-- foreach (shared_ptr<Abundance> ab_j, filtered_transcripts)
-+ for_each (shared_ptr<Abundance> ab_j, filtered_transcripts)
- {
- if (ab_i == ab_j)
- {
-@@ -961,7 +961,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- transfrags_by_strand);
-
-
-- foreach (const AbundanceGroup& strand_group, transfrags_by_strand)
-+ for_each (const AbundanceGroup& strand_group, transfrags_by_strand)
- {
- vector<AbundanceGroup> transfrags_by_gene;
-
-@@ -974,7 +974,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- cluster_transcripts<ConnectByExonOverlap>(strand_group, transfrags_by_gene);
- }
-
-- foreach(const AbundanceGroup& gene, transfrags_by_gene)
-+ for_each(const AbundanceGroup& gene, transfrags_by_gene)
- {
- const vector<shared_ptr<Abundance> >& iso_abundances = gene.abundances();
- vector<Isoform> isoforms;
-@@ -985,7 +985,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- string ref_gene_id = "";
-
- double major_isoform_FPKM = 0;
-- foreach (shared_ptr<Abundance> iso_ab, iso_abundances)
-+ for_each (shared_ptr<Abundance> iso_ab, iso_abundances)
- {
- if (iso_ab->transfrag()->is_ref())
- {
-@@ -1002,7 +1002,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
- major_isoform_FPKM = max(iso_ab->FPKM(), major_isoform_FPKM);
- }
-
-- foreach (shared_ptr<Abundance> iso_ab, iso_abundances)
-+ for_each (shared_ptr<Abundance> iso_ab, iso_abundances)
- {
- // Calculate transcript depth of coverage and FMI from FPKM
- double FPKM = iso_ab->FPKM();
-@@ -1067,7 +1067,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
- {
- vector<Scaffold> c;
- scaffolds[i]->get_complete_subscaffolds(c);
-- foreach (Scaffold& s, c)
-+ for_each (Scaffold& s, c)
- {
- split_partials.push_back(shared_ptr<Scaffold>(new Scaffold(s)));
- }
-@@ -1076,7 +1076,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
- scaffolds = split_partials;
-
- vector<shared_ptr<Abundance> > abundances;
-- foreach(shared_ptr<Scaffold> s, scaffolds)
-+ for_each(shared_ptr<Scaffold> s, scaffolds)
- {
- TranscriptAbundance* pT = new TranscriptAbundance;
- pT->transfrag(s);
-@@ -1091,7 +1091,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds,
- cluster_transcripts<ConnectByExonOverlap>(transfrags,
- transfrags_by_cluster);
-
-- foreach(AbundanceGroup& cluster, transfrags_by_cluster)
-+ for_each(AbundanceGroup& cluster, transfrags_by_cluster)
- {
- quantitate_transcript_cluster(cluster, total_map_mass, genes, bundle_too_large);
- }
-@@ -1233,10 +1233,10 @@ void assemble_bundle(const RefSequenceTable& rt,
- if (init_bundle_mode == REF_GUIDED)
- {
- hit_introns = new set<AugmentedCuffOp>();
-- foreach(const MateHit& h, bundle.non_redundant_hits())
-+ for_each(const MateHit& h, bundle.non_redundant_hits())
- {
- Scaffold s(h);
-- foreach (AugmentedCuffOp a, s.augmented_ops())
-+ for_each (AugmentedCuffOp a, s.augmented_ops())
- {
- if (a.opcode == CUFF_INTRON)
- {
-@@ -1567,7 +1567,7 @@ void driver(const string& hit_file_name, FILE* ref_gtf, FILE* mask_gtf)
- verbose_msg("%d ReadHits still live\n", num_deleted);
- verbose_msg("Found %lu reference contigs\n", rt.size());
-
-- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
-+ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs)
- {
- ref_scaff->clear_hits();
- }
-diff --git a/src/differential.cpp b/src/differential.cpp
-index 3e5cff0..6b108cb 100644
---- a/src/differential.cpp
-+++ b/src/differential.cpp
-@@ -84,7 +84,7 @@ void TestLauncher::abundance_avail(const string& locus_id,
- // acquire the lock itself.
- bool TestLauncher::all_samples_reported_in(vector<shared_ptr<SampleAbundances> >& abundances)
- {
-- foreach (shared_ptr<SampleAbundances> ab, abundances)
-+ for_each (shared_ptr<SampleAbundances> ab, abundances)
- {
- if (!ab)
- {
-@@ -436,7 +436,7 @@ pair<int, SampleDiffs::iterator> get_de_tests(const string& description,
- // ublas::vector<double> null_kappa_mean;
- // null_kappa_mean = ublas::zero_vector<double>(curr_kappa_cov.size1());
- //
--// foreach(ublas::vector<double>& sample, samples)
-+// for_each(ublas::vector<double>& sample, samples)
- // {
- // null_kappa_mean += sample;
- // }
-@@ -1056,7 +1056,7 @@ void sample_abundance_worker(const string& locus_tag,
- {
- vector<shared_ptr<Abundance> > abundances;
-
-- foreach(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds())
-+ for_each(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds())
- {
- TranscriptAbundance* pT = new TranscriptAbundance;
- pT->transfrag(s);
-@@ -1082,7 +1082,7 @@ void sample_abundance_worker(const string& locus_tag,
- }
- else
- {
-- foreach(shared_ptr<Abundance> ab, abundances)
-+ for_each(shared_ptr<Abundance> ab, abundances)
- {
- ab->status(NUMERIC_HI_DATA);
- }
-@@ -1093,7 +1093,7 @@ void sample_abundance_worker(const string& locus_tag,
- cluster_transcripts<ConnectByAnnotatedGeneId>(sample.transcripts,
- transcripts_by_gene_id);
-
-- foreach(AbundanceGroup& ab_group, transcripts_by_gene_id)
-+ for_each(AbundanceGroup& ab_group, transcripts_by_gene_id)
- {
- ab_group.locus_tag(locus_tag);
- set<string> gene_ids = ab_group.gene_id();
-@@ -1119,7 +1119,7 @@ void sample_abundance_worker(const string& locus_tag,
- &cds_count_cov,
- &cds_fpkm_cov,
- &cds_gamma_boot_cov);
-- foreach(AbundanceGroup& ab_group, transcripts_by_cds)
-+ for_each(AbundanceGroup& ab_group, transcripts_by_cds)
- {
- ab_group.locus_tag(locus_tag);
- set<string> protein_ids = ab_group.protein_id();
-@@ -1135,7 +1135,7 @@ void sample_abundance_worker(const string& locus_tag,
- vector<shared_ptr<Abundance> > cds_abundances;
- double max_cds_mass_variance = 0.0;
- set<shared_ptr<ReadGroupProperties const> > rg_props;
-- foreach (AbundanceGroup& ab_group, sample.cds)
-+ for_each (AbundanceGroup& ab_group, sample.cds)
- {
- cds_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group)));
- max_cds_mass_variance = max(ab_group.max_mass_variance(), max_cds_mass_variance);
-@@ -1155,7 +1155,7 @@ void sample_abundance_worker(const string& locus_tag,
- cluster_transcripts<ConnectByAnnotatedGeneId>(cds,
- cds_by_gene);
-
-- foreach(AbundanceGroup& ab_group, cds_by_gene)
-+ for_each(AbundanceGroup& ab_group, cds_by_gene)
- {
- ab_group.locus_tag(locus_tag);
- set<string> gene_ids = ab_group.gene_id();
-@@ -1185,7 +1185,7 @@ void sample_abundance_worker(const string& locus_tag,
- &tss_gamma_boot_cov);
-
-
-- foreach(AbundanceGroup& ab_group, transcripts_by_tss)
-+ for_each(AbundanceGroup& ab_group, transcripts_by_tss)
- {
- ab_group.locus_tag(locus_tag);
- set<string> tss_ids = ab_group.tss_id();
-@@ -1202,7 +1202,7 @@ void sample_abundance_worker(const string& locus_tag,
- // Group TSS clusters by gene
- vector<shared_ptr<Abundance> > primary_transcript_abundances;
- set<shared_ptr<ReadGroupProperties const> > rg_props;
-- foreach (AbundanceGroup& ab_group, sample.primary_transcripts)
-+ for_each (AbundanceGroup& ab_group, sample.primary_transcripts)
- {
- primary_transcript_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group)));
- max_tss_mass_variance = max(max_tss_mass_variance, ab_group.max_mass_variance());
-@@ -1223,13 +1223,13 @@ void sample_abundance_worker(const string& locus_tag,
- cluster_transcripts<ConnectByAnnotatedGeneId>(primary_transcripts,
- primary_transcripts_by_gene);
-
-- foreach(AbundanceGroup& ab_group, primary_transcripts_by_gene)
-+ for_each(AbundanceGroup& ab_group, primary_transcripts_by_gene)
- {
- ab_group.locus_tag(locus_tag);
- set<string> gene_ids = ab_group.gene_id();
- // if (gene_ids.size() > 1)
- // {
--// foreach (string st, gene_ids)
-+// for_each (string st, gene_ids)
- // {
- // fprintf(stderr, "%s\n", st.c_str());
- // }
-@@ -1314,7 +1314,7 @@ void sample_worker(const RefSequenceTable& rt,
- bool perform_cds_analysis = final_est_run;
- bool perform_tss_analysis = final_est_run;
-
-- foreach(shared_ptr<Scaffold> s, bundle.ref_scaffolds())
-+ for_each(shared_ptr<Scaffold> s, bundle.ref_scaffolds())
- {
- if (s->annotated_tss_id() == "")
- {
-@@ -1439,7 +1439,7 @@ void sample_worker(const RefSequenceTable& rt,
- ///////////////////////////////////////////////
-
-
-- foreach(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds())
-+ for_each(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds())
- {
- ref_scaff->clear_hits();
- }
-@@ -1465,7 +1465,7 @@ void dump_locus_variance_info(const string& filename)
-
- fprintf(fdump,
- "condition\tdescription\tlocus_counts\tempir_var\tlocus_fit_var\tsum_iso_fit_var\tcross_replicate_js\tnum_transcripts\tbayes_gamma_trace\tempir_gamma_trace\tcount_mean\tgamma_var\tgamma_bootstrap_var\tlocus_salient_frags\tlocus_total_frags\tcount_sharing\n");
-- foreach (LocusVarianceInfo& L, locus_variance_info_table)
-+ for_each (LocusVarianceInfo& L, locus_variance_info_table)
- {
- for (size_t i = 0; i < L.gamma.size(); ++i)
- {
-@@ -1503,22 +1503,22 @@ void test_differential(const string& locus_tag,
- for (size_t i = 0; i < samples.size(); ++i)
- {
- const AbundanceGroup& ab_group = samples[i]->transcripts;
-- foreach (shared_ptr<Abundance> ab, ab_group.abundances())
-+ for_each (shared_ptr<Abundance> ab, ab_group.abundances())
- {
- add_to_tracking_table(i, *ab, tracking.isoform_fpkm_tracking);
- }
-
-- foreach (AbundanceGroup& ab, samples[i]->cds)
-+ for_each (AbundanceGroup& ab, samples[i]->cds)
- {
- add_to_tracking_table(i, ab, tracking.cds_fpkm_tracking);
- }
-
-- foreach (AbundanceGroup& ab, samples[i]->primary_transcripts)
-+ for_each (AbundanceGroup& ab, samples[i]->primary_transcripts)
- {
- add_to_tracking_table(i, ab, tracking.tss_group_fpkm_tracking);
- }
-
-- foreach (AbundanceGroup& ab, samples[i]->genes)
-+ for_each (AbundanceGroup& ab, samples[i]->genes)
- {
- add_to_tracking_table(i, ab, tracking.gene_fpkm_tracking);
- }
-diff --git a/src/filters.cpp b/src/filters.cpp
-index 0a10b50..5ab31e0 100644
---- a/src/filters.cpp
-+++ b/src/filters.cpp
-@@ -752,7 +752,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
-
- if (library_type != "transfrags")
- {
-- foreach (Scaffold& scaff, scaffolds)
-+ for_each (Scaffold& scaff, scaffolds)
- {
- if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV))
- continue;
-@@ -761,7 +761,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
- vector<double> coverage(scaff_len, 0.0);
-
- double total = 0;
-- foreach(const MateHit* hit, scaff.mate_hits())
-+ for_each(const MateHit* hit, scaff.mate_hits())
- {
- int start, end, frag_len;
- if (!scaff.map_frag(*hit, start, end, frag_len)) continue;
-@@ -906,7 +906,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
- }
- else
- {
-- foreach (Scaffold& scaff, scaffolds)
-+ for_each (Scaffold& scaff, scaffolds)
- {
- if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV))
- continue;
-@@ -915,7 +915,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)
- vector<double> coverage(scaff_len, 0.0);
-
- double total = 0;
-- foreach(const MateHit* hit, scaff.mate_hits())
-+ for_each(const MateHit* hit, scaff.mate_hits())
- {
- int start, end, frag_len;
- if (!scaff.map_frag(*hit, start, end, frag_len)) continue;
-diff --git a/src/genes.h b/src/genes.h
-index 4dfa996..eb48a14 100644
---- a/src/genes.h
-+++ b/src/genes.h
-@@ -169,7 +169,7 @@ public:
-
- bool has_ref_trans() const
- {
-- foreach (const Isoform& iso, _isoforms)
-+ for_each (const Isoform& iso, _isoforms)
- {
- if (iso.is_ref_trans())
- return true;
-@@ -180,7 +180,7 @@ public:
- double estimated_count() const
- {
- double est = 0.0;
-- foreach (const Isoform& iso, _isoforms)
-+ for_each (const Isoform& iso, _isoforms)
- {
- est += iso.estimated_count();
- }
-@@ -191,7 +191,7 @@ public:
- {
- double eff = 0.0;
- double total_fpkm = 0;
-- foreach (const Isoform& iso, _isoforms)
-+ for_each (const Isoform& iso, _isoforms)
- {
- eff += iso.FPKM() * iso.effective_length();
- total_fpkm += iso.FPKM();
-diff --git a/src/gtf_to_sam.cpp b/src/gtf_to_sam.cpp
-index 12f70c1..f52d40a 100644
---- a/src/gtf_to_sam.cpp
-+++ b/src/gtf_to_sam.cpp
-@@ -241,13 +241,13 @@ void set_relative_fpkms(vector<shared_ptr<Scaffold> >& ref_mRNAs)
- vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i];
-
- double total_fpkm = 0.0;
-- foreach(shared_ptr<Scaffold> scaff, gene)
-+ for_each(shared_ptr<Scaffold> scaff, gene)
- {
- total_fpkm += scaff->fpkm();
- }
- if (total_fpkm > 0)
- {
-- foreach (shared_ptr<Scaffold> scaff, gene)
-+ for_each (shared_ptr<Scaffold> scaff, gene)
- {
- scaff->fpkm(scaff->fpkm() / total_fpkm);
- }
-@@ -263,7 +263,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* sam_out)
- vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table;
- vector<pair<string, vector<double> > > sample_count_table;
-
-- foreach (FILE* ref_gtf, ref_gtf_files)
-+ for_each (FILE* ref_gtf, ref_gtf_files)
- {
- vector<shared_ptr<Scaffold> > ref_mRNAs;
- ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true);
-@@ -314,7 +314,7 @@ int main(int argc, char** argv)
-
- vector<FILE*> ref_gtf_files;
-
-- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames)
-+ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames)
- {
- FILE* ref_gtf = NULL;
- if (ref_gtf_in_filename != "")
-diff --git a/src/hits.cpp b/src/hits.cpp
-index 910ba0f..dc81813 100644
---- a/src/hits.cpp
-+++ b/src/hits.cpp
-@@ -233,7 +233,7 @@ void collapse_hits(const vector<MateHit>& hits,
- non_redundant.erase(new_end, non_redundant.end());
- non_redundant.resize(non_redundant.size());
-
-- foreach(MateHit& hit, non_redundant)
-+ for_each(MateHit& hit, non_redundant)
- hit.collapse_mass(0);
-
- size_t curr_aln = 0;
-@@ -252,7 +252,7 @@ void collapse_hits(const vector<MateHit>& hits,
- ++curr_aln;
- }
-
-- //foreach(MateHit& hit, non_redundant)
-+ //for_each(MateHit& hit, non_redundant)
- //assert(hit.collapse_mass() <= 1 || !hit.is_multi());
-
- //non_redundant.erase(remove_if(non_redundant.begin(),non_redundant.end(),has_no_collapse_mass), non_redundant.end());
-diff --git a/src/replicates.cpp b/src/replicates.cpp
-index 634f209..ec8ce9c 100644
---- a/src/replicates.cpp
-+++ b/src/replicates.cpp
-@@ -236,7 +236,7 @@ fit_dispersion_model_helper(const string& condition_name,
- mean /= p.counts.size();
-
- double var = 0.0;
-- foreach (double d, p.counts)
-+ for_each (double d, p.counts)
- {
- var += (d - mean) * (d - mean);
- }
-@@ -363,7 +363,7 @@ fit_dispersion_model(const string& condition_name,
- ProgressBar p_bar("Modeling fragment count overdispersion.",0);
-
- int max_transcripts = 0;
-- foreach(const LocusCountList& L, sample_count_table)
-+ for_each(const LocusCountList& L, sample_count_table)
- {
- if (L.num_transcripts > max_transcripts)
- {
-@@ -382,7 +382,7 @@ fit_dispersion_model(const string& condition_name,
- if (i != 0)
- {
- // vector<LocusCountList> sample_count_subtable;
--// foreach(const LocusCountList& L, sample_count_table)
-+// for_each(const LocusCountList& L, sample_count_table)
- // {
- // if (L.num_transcripts == i)
- // {
-diff --git a/src/replicates.h b/src/replicates.h
-index ca4484f..73d339c 100644
---- a/src/replicates.h
-+++ b/src/replicates.h
-@@ -99,7 +99,7 @@ public:
- #if ENABLE_THREADS
- boost::mutex::scoped_lock lock(_rep_factory_lock);
- #endif
-- foreach (boost::shared_ptr<BundleFactory> fac, _factories)
-+ for_each (boost::shared_ptr<BundleFactory> fac, _factories)
- {
- if (fac->bundles_remain())
- return true;
-@@ -115,7 +115,7 @@ public:
- std::vector<HitBundle*> bundles;
-
- bool non_empty_bundle = false;
-- foreach (boost::shared_ptr<BundleFactory> fac, _factories)
-+ for_each (boost::shared_ptr<BundleFactory> fac, _factories)
- {
- bundles.push_back(new HitBundle());
- if (fac->next_bundle(*(bundles.back())))
-@@ -126,7 +126,7 @@ public:
-
- if (non_empty_bundle == false)
- {
-- foreach (HitBundle* in_bundle, bundles)
-+ for_each (HitBundle* in_bundle, bundles)
- {
- in_bundle->ref_scaffolds().clear();
- in_bundle->clear_hits();
-@@ -149,7 +149,7 @@ public:
- // Merge the replicates into a combined bundle of hits.
- HitBundle::combine(bundles, bundle_out);
-
-- foreach (HitBundle* in_bundle, bundles)
-+ for_each (HitBundle* in_bundle, bundles)
- {
- in_bundle->ref_scaffolds().clear();
- in_bundle->clear_hits();
-@@ -163,7 +163,7 @@ public:
- #if ENABLE_THREADS
- boost::mutex::scoped_lock lock(_rep_factory_lock);
- #endif
-- foreach (shared_ptr<BundleFactory> fac, _factories)
-+ for_each (shared_ptr<BundleFactory> fac, _factories)
- {
- fac->reset();
- }
-@@ -246,7 +246,7 @@ public:
- shared_ptr<MassDispersionModel const> disperser;
- disperser = fit_dispersion_model(_condition_name,scale_factors, sample_count_table);
-
-- foreach (shared_ptr<BundleFactory> fac, _factories)
-+ for_each (shared_ptr<BundleFactory> fac, _factories)
- {
- shared_ptr<ReadGroupProperties> rg_props = fac->read_group_properties();
- rg_props->mass_dispersion_model(disperser);
-@@ -260,7 +260,7 @@ public:
- #if ENABLE_THREADS
- boost::mutex::scoped_lock lock(_rep_factory_lock);
- #endif
-- foreach(shared_ptr<BundleFactory> fac, _factories)
-+ for_each(shared_ptr<BundleFactory> fac, _factories)
- {
- fac->set_ref_rnas(mRNAs);
- }
-@@ -271,7 +271,7 @@ public:
- #if ENABLE_THREADS
- boost::mutex::scoped_lock lock(_rep_factory_lock);
- #endif
-- foreach(shared_ptr<BundleFactory> fac, _factories)
-+ for_each(shared_ptr<BundleFactory> fac, _factories)
- {
- fac->set_mask_rnas(mRNAs);
- }
-@@ -284,7 +284,7 @@ public:
- #if ENABLE_THREADS
- boost::mutex::scoped_lock lock(_rep_factory_lock);
- #endif
-- foreach(shared_ptr<BundleFactory>& fac, _factories)
-+ for_each(shared_ptr<BundleFactory>& fac, _factories)
- {
- fac->read_group_properties()->mass_dispersion_model(disperser);
- }
-diff --git a/src/scaffolds.cpp b/src/scaffolds.cpp
-index 096f58a..c12118e 100644
---- a/src/scaffolds.cpp
-+++ b/src/scaffolds.cpp
-@@ -620,7 +620,7 @@ void Scaffold::tile_with_scaffs(vector<Scaffold>& tile_scaffs, int max_len, int
-
- // genomic_offset actually could be zero - from an exon starting at coord
- // 1 in some chromosome of the ref.
--// foreach(const AugmentedCuffOp& op, ops)
-+// for_each(const AugmentedCuffOp& op, ops)
- // {
- // assert (op.genomic_offset != 0);
- // }
-@@ -819,7 +819,7 @@ void Scaffold::merge(const vector<Scaffold>& s,
- if (library_type == "transfrags")
- {
- double avg_fpkm = 0.0;
-- foreach (const Scaffold& sc, s)
-+ for_each (const Scaffold& sc, s)
- {
- avg_fpkm += sc.fpkm();
- }
-@@ -871,7 +871,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler)
-
- vector<AugmentedCuffOp> tmp_filler = filler;
-
-- foreach(const AugmentedCuffOp& op, orig_ops)
-+ for_each(const AugmentedCuffOp& op, orig_ops)
- {
- assert (op.g_left() < op.g_right());
-
-@@ -888,7 +888,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler)
- AugmentedCuffOp::merge_ops(tmp_filler, padded_filler, false);
-
- vector<AugmentedCuffOp> overlapping;
-- foreach (const AugmentedCuffOp& op, padded_filler)
-+ for_each (const AugmentedCuffOp& op, padded_filler)
- {
- //if (left() <= op.g_left() && right() >= op.g_right()
- if(::overlap_in_genome(op.g_left(),op.g_right(), left(), right())
-@@ -1630,7 +1630,7 @@ void Scaffold::get_complete_subscaffolds(vector<Scaffold>& complete)
-
- // const vector<const MateHit*>& hits = known.mate_hits();
- // bool contains_spliced_hit = false;
-- // foreach (const MateHit* h, hits)
-+ // for_each (const MateHit* h, hits)
- // {
- // const ReadHit* left = h->left_alignment();
- // const ReadHit* right = h->right_alignment();
-@@ -1670,7 +1670,7 @@ double Scaffold::internal_exon_coverage() const
- int left = augmented_ops()[2].g_left();
- int right = augmented_ops()[augmented_ops().size() - 3].g_right();
- vector<bool> covered(right-left, 0);
-- foreach(const MateHit* h, mate_hits())
-+ for_each(const MateHit* h, mate_hits())
- {
- if (::overlap_in_genome(h->left(),h->right(), left, right))
- {
-@@ -1694,7 +1694,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con
- if (has_intron())
- return true;
-
-- foreach (const MateHit* h, mate_hits())
-+ for_each (const MateHit* h, mate_hits())
- {
- if (h->strand() == strand())
- return true;
-@@ -1704,7 +1704,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con
- if (ref_scaffs == NULL)
- return false;
-
-- foreach (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
-+ for_each (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
- {
- if (ref_scaff->strand() == strand() && exons_overlap(*this, *ref_scaff))
- return true;
-@@ -1729,10 +1729,10 @@ bool Scaffold::hits_support_introns() const
- {
- set<AugmentedCuffOp> hit_introns;
- set<AugmentedCuffOp> scaffold_introns;
-- foreach(const MateHit* h, _mates_in_scaff)
-+ for_each(const MateHit* h, _mates_in_scaff)
- {
- Scaffold s(*h);
-- foreach (AugmentedCuffOp a, s.augmented_ops())
-+ for_each (AugmentedCuffOp a, s.augmented_ops())
- {
- if (a.opcode == CUFF_INTRON)
- {
-@@ -1740,7 +1740,7 @@ bool Scaffold::hits_support_introns() const
- }
- }
- }
-- foreach (AugmentedCuffOp a, _augmented_ops)
-+ for_each (AugmentedCuffOp a, _augmented_ops)
- {
- if (a.opcode == CUFF_INTRON)
- {
-@@ -1751,13 +1751,13 @@ bool Scaffold::hits_support_introns() const
- if (hit_introns != scaffold_introns)
- {
- fprintf(stderr, "********************\n");
-- foreach(const AugmentedCuffOp& a, hit_introns)
-+ for_each(const AugmentedCuffOp& a, hit_introns)
- {
- fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right());
- }
-
- fprintf(stderr, "####################\n");
-- foreach(const AugmentedCuffOp& a, scaffold_introns)
-+ for_each(const AugmentedCuffOp& a, scaffold_introns)
- {
- fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right());
- }
-@@ -1770,7 +1770,7 @@ bool Scaffold::hits_support_introns(set<AugmentedCuffOp>& hit_introns) const
- {
- set<AugmentedCuffOp> scaffold_introns;
-
-- foreach (AugmentedCuffOp a, _augmented_ops)
-+ for_each (AugmentedCuffOp a, _augmented_ops)
- {
- if (a.opcode == CUFF_INTRON)
- {
-diff --git a/src/scaffolds.h b/src/scaffolds.h
-index 0f29e80..f8410f7 100644
---- a/src/scaffolds.h
-+++ b/src/scaffolds.h
-@@ -314,7 +314,7 @@ public:
- if (library_type == "transfrags")
- {
- double avg_fpkm = 0.0;
-- foreach (const Scaffold& sc, hits)
-+ for_each (const Scaffold& sc, hits)
- {
- avg_fpkm += sc.fpkm();
- }
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch
deleted file mode 100644
index 360e9c1a11b8..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch
+++ /dev/null
@@ -1,20 +0,0 @@
- src/lemon/bits/base_extender.h | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/lemon/bits/base_extender.h b/src/lemon/bits/base_extender.h
-index 84bb242..b812247 100644
---- a/src/lemon/bits/base_extender.h
-+++ b/src/lemon/bits/base_extender.h
-@@ -359,10 +359,10 @@ namespace lemon {
- }
-
- Node source(const UEdge& edge) const {
-- return aNode(edge);
-+ return this->aNode(edge);
- }
- Node target(const UEdge& edge) const {
-- return bNode(edge);
-+ return this->bNode(edge);
- }
-
- void firstInc(UEdge& edge, bool& dir, const Node& node) const {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
deleted file mode 100644
index 3b9abd812680..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- ax_bam.m4 | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ax_bam.m4 b/ax_bam.m4
-index 7d463b7..95f1bed 100644
---- a/ax_bam.m4
-+++ b/ax_bam.m4
-@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then
- AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
- fi
- else
-- BAM_LIB="-lbam"
-+ BAM_LIB="-lbam -lhts"
- AC_SUBST(BAM_CPPFLAGS)
- AC_SUBST(BAM_LDFLAGS)
- AC_SUBST(BAM_LIB)