sci-biology/cufflinks: Remove old

Package-Manager: portage-2.2.28

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)