commit: 6b4151d6d2a91701e87a706fcdd896849698dea4 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 3 16:29:28 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Apr 3 16:29:28 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6b4151d6
sci-biology/cufflinks: Remove old Package-Manager: portage-2.2.28 sci-biology/cufflinks/Manifest | 1 - sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild | 40 - sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild | 52 - sci-biology/cufflinks/cufflinks-2.2.1.ebuild | 40 - .../files/cufflinks-1.3.0-autotools.patch | 38 - .../cufflinks/files/cufflinks-1.3.0-boost.patch | 1320 -------------------- .../cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch | 20 - .../cufflinks/files/cufflinks-2.2.1-hts.patch | 16 - 8 files changed, 1527 deletions(-) diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest index 017836e..88bfcfa 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 36322f4..0000000 --- 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 66298cb..0000000 --- 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 5e7f763..0000000 --- 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/" - $(use_enable debug) - ) - autotools-utils_src_configure -} diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch deleted file mode 100644 index 73e52b4..0000000 --- a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch +++ /dev/null @@ -1,38 +0,0 @@ ---- a/configure.ac -+++ b/configure.ac -@@ -27,6 +27,7 @@ AC_PROG_AWK - AC_PROG_CXX - AC_PROG_CC - AC_PROG_MAKE_SET -+AM_PROG_AR - AC_PROG_RANLIB - AC_PROG_INSTALL - AM_PATH_PYTHON([2.4]) -@@ -54,7 +55,7 @@ AC_CANONICAL_HOST - - # set CFLAGS and CXXFLAGS - user_CFLAGS=${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 d45391b..0000000 --- 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 360e9c1..0000000 --- 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 3b9abd8..0000000 --- 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)
