proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

10 files changed, 1561 insertions, 0 deletions

diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
new file mode 100644
index 000000000000..017836ee07ad
--- /dev/null
+++ b/sci-biology/cufflinks/Manifest
@@ -0,0 +1,2 @@
+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
new file mode 100644
index 000000000000..36322f463de6
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
@@ -0,0 +1,40 @@
+# 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
new file mode 100644
index 000000000000..66298cbc1972
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
@@ -0,0 +1,52 @@
+# 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
new file mode 100644
index 000000000000..5e7f763389f9
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild
@@ -0,0 +1,40 @@
+# 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/"
+		$(use_enable debug)
+	)
+	autotools-utils_src_configure
+}
diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
new file mode 100644
index 000000000000..73e52b4343a0
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch
@@ -0,0 +1,38 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -27,6 +27,7 @@ AC_PROG_AWK
+ AC_PROG_CXX
+ AC_PROG_CC
+ AC_PROG_MAKE_SET
++AM_PROG_AR
+ AC_PROG_RANLIB
+ AC_PROG_INSTALL
+ AM_PATH_PYTHON([2.4])
+@@ -54,7 +55,7 @@ AC_CANONICAL_HOST
+ 
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${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
new file mode 100644
index 000000000000..d45391bf4f3a
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch
@@ -0,0 +1,1320 @@
+ 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
new file mode 100644
index 000000000000..360e9c1a11b8
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch
@@ -0,0 +1,20 @@
+ 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-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
new file mode 100644
index 000000000000..47784088fab9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
@@ -0,0 +1,28 @@
+ configure.ac | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 96ffbac..e88b8e4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
+ 
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ #echo "${host_cpu}-${host_os}"
+@@ -106,8 +107,8 @@ 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} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
+ user_LDFLAGS="$LDFLAGS"
+ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+ 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
new file mode 100644
index 000000000000..3b9abd812680
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch
@@ -0,0 +1,16 @@
+ ax_bam.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ax_bam.m4 b/ax_bam.m4
+index 7d463b7..95f1bed 100644
+--- a/ax_bam.m4
++++ b/ax_bam.m4
+@@ -189,7 +189,7 @@ if test "x$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)
diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/cufflinks/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>