Moved trunk code to new trunk directory

AUTHORS

@@ -0,0 +1,13 @@
+Cufflinks authors
+Primary contact <cole@cs.umd.edu>
+
+Cole Trapnell designed and wrote Cufflinks, with substantial technical input 
+from Geo Pertea, Brian Williams, Ali Mortazavi, Jeltje van Baren, Steven Salzberg, Barbara Wold, 
+and Lior Pachter. Geo Pertea wrote Cuffcompare.
+
+"Tuxedo" Websites:
+ Cufflinks:			 http://cufflinks.cbcb.umd.edu
+ TopHat:			 http://tophat.cbcb.umd.edu
+ Bowtie:             http://bowtie-bio.sf.net
+
+September 2009

LICENSE

@@ -0,0 +1,29 @@
+Copyright (C) 2003-2009 Cole Trapnell et al
+
+===========================================================================
+Boost Software License, Version 1.0
+===========================================================================
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+

Makefile.am

@@ -0,0 +1,8 @@
+
+ALWAYS_BUILT = src
+SUBDIRS = $(ALWAYS_BUILT)
+DIST_SUBDIRS = $(ALWAYS_BUILT) 
+
+EXTRA_DIST = LICENSE
+
+.PHONY: FORCE

README

@@ -0,0 +1,74 @@
+CUFFLINKS
+----------------------------
+Cufflinks is a reference-guided assembler for RNA-Seq experiments. It
+simultaneously assembles transcripts from reads and estimates their relative
+abundances, without using a reference annotation.  The software expects as 
+input RNA-Seq read alignments in SAM format (http://samtools.sourceforge.net).
+
+Here's an example spliced read alignment record:
+s6.25mer.txt-913508	16	chr1	4482736	255	14M431N11M	*	0	0	CAAGATGCTAGGCAAGTCTTGGAAG	IIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	XS:A:-
+
+This record includes a custom tag used by Cufflinks to determine the strand 
+of the mRNA from which this read originated.  Often, RNA-Seq experiments lose
+strand information, and so reads will map to either strand of the genome.  
+However, strandedness of spliced alignments can often be inferred from the 
+orientation of consensus splice sites, and Cufflinks requires that spliced 
+aligments have the custom strand tag XS, which has SAM attribute type "A", and
+can take values of "+" or "-".  If your RNA-Seq protocol is strand specific,
+including this tag for all alignments, including unspliced alignments, will 
+improve the assembly quality.
+
+The SAM records MUST BE SORTED by reference coordinate, like so:
+
+sort -k 3,3 -k 4,4n hits.sam 
+
+The program is fully threaded, and when running with multiple threads, should
+be run on a machine with plenty of RAM. 4 GB per thread is probably reasonable
+for most experiments.  Since many experiments feature a handful of genes that
+are very abundantly transcribed, Cufflinks will spend much of its time 
+assembling" a few genes.  When using more than one thread, Cufflinks may 
+appear to "hang" while these genes are being assembled.
+
+Cufflinks assumes that library fragment lengths are size selected and normally
+distributed. When using paired end RNA-Seq reads, you must take care to supply
+Cufflinks with the mean and variance on the inner distances between mate 
+pairs. For the moment, Cufflinks doesn't support assembling mixtures of paired
+end reads from different fragment size distributions.  Mixtures of single 
+ended reads (of varying lengths) with paired ends are supported.
+
+Cufflinks also assumes that the donor does not contain major structural 
+variations with respect to the reference.  Tumor genomes are often highly 
+rearranged, and while Cufflinks may eventually identify gene fusions and 
+gracefully handle genome breakpoints, users are encouraged to be careful when
+using Cufflinks on tumor RNA-Seq experiments. 
+
+The full manual may be found at http://cufflinks.cbcb.umd.edu
+
+CUFFCOMPARE
+----------------------------
+Please see http://cufflinks.cbcb.umd.edu/manual.html
+
+REQUIREMENTS
+---------------------------
+
+Cufflinks is a standalone tool that requires gcc 4.0 or greater, and runs on
+Linux and OS X.  It depends on Boost (http://www.boost.org) version 1.38 or 
+higher.
+
+REFERENCES
+---------------------------
+Cufflinks builds on many ideas, including some
+proposed in the following papers:
+
+Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara 
+Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq",Nature 
+Methods, volume 5, 621 - 628 (2008)
+
+Hui Jiang and Wing Hung Wong, "Statistical Inferences for isoform expression", 
+Bioinformatics, 2009 25(8):1026-1032
+
+Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, 
+Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel, "Viral 
+population estimation using pyrosequencing", PLoS Computational Biology, 
+4(5):e1000074
+

autogen.sh

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+submodule_init ( ) {
+    local SUBMODULES=$(git submodule | awk '{print $2}')
+    for submodule in $SUBMODULES; do
+	echo "Initializing submodule $submodule"
+	git submodule init $submodule
+	git submodule update $submodule
+	cd $submodule
+	if test -f version.sh
+	then
+	    ./version.sh
+	fi
+	submodule_init
+	cd ..
+    done
+}
+
+./version.sh
+submodule_init
+autoreconf --install

ax_boost_base.m4

@@ -0,0 +1,219 @@
+# ===========================================================================
+#             http://autoconf-archive.cryp.to/ax_boost_base.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_BOOST_BASE([MINIMUM-VERSION])
+#
+# DESCRIPTION
+#
+#   Test for the Boost C++ libraries of a particular version (or newer)
+#
+#   If no path to the installed boost library is given the macro searchs
+#   under /usr, /usr/local, /opt and /opt/local and evaluates the
+#   $BOOST_ROOT environment variable. Further documentation is available at
+#   <http://randspringer.de/boost/index.html>.
+#
+#   This macro calls:
+#
+#     AC_SUBST(BOOST_CPPFLAGS) / AC_SUBST(BOOST_LDFLAGS)
+#
+#   And sets:
+#
+#     HAVE_BOOST
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Thomas Porschberg <thomas@randspringer.de>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved.
+
+AC_DEFUN([AX_BOOST_BASE],
+[
+AC_ARG_WITH([boost],
+	AS_HELP_STRING([--with-boost@<:@=DIR@:>@], [use boost (default is yes) - it is possible to specify the root directory for boost (optional)]),
+	[
+    if test "$withval" = "no"; then
+		want_boost="no"
+    elif test "$withval" = "yes"; then
+        want_boost="yes"
+        ac_boost_path=""
+    else
+	    want_boost="yes"
+        ac_boost_path="$withval"
+	fi
+    ],
+    [want_boost="yes"])
+
+
+AC_ARG_WITH([boost-libdir],
+        AS_HELP_STRING([--with-boost-libdir=LIB_DIR],
+        [Force given directory for boost libraries. Note that this will overwrite library path detection, so use this parameter only if default library detection fails and you know exactly where your boost libraries are located.]),
+        [
+        if test -d $withval
+        then
+                ac_boost_lib_path="$withval"
+        else
+                AC_MSG_ERROR(--with-boost-libdir expected directory name)
+        fi
+        ],
+        [ac_boost_lib_path=""]
+)
+
+if test "x$want_boost" = "xyes"; then
+	boost_lib_version_req=ifelse([$1], ,1.20.0,$1)
+	boost_lib_version_req_shorten=`expr $boost_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
+	boost_lib_version_req_major=`expr $boost_lib_version_req : '\([[0-9]]*\)'`
+	boost_lib_version_req_minor=`expr $boost_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
+	boost_lib_version_req_sub_minor=`expr $boost_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
+	if test "x$boost_lib_version_req_sub_minor" = "x" ; then
+		boost_lib_version_req_sub_minor="0"
+    	fi
+	WANT_BOOST_VERSION=`expr $boost_lib_version_req_major \* 100000 \+  $boost_lib_version_req_minor \* 100 \+ $boost_lib_version_req_sub_minor`
+	AC_MSG_CHECKING(for boostlib >= $boost_lib_version_req)
+	succeeded=no
+
+	dnl first we check the system location for boost libraries
+	dnl this location ist chosen if boost libraries are installed with the --layout=system option
+	dnl or if you install boost with RPM
+	if test "$ac_boost_path" != ""; then
+		BOOST_LDFLAGS="-L$ac_boost_path/lib"
+		BOOST_CPPFLAGS="-I$ac_boost_path/include"
+	else
+		for ac_boost_path_tmp in /usr /usr/local /opt /opt/local ; do
+			if test -d "$ac_boost_path_tmp/include/boost" && test -r "$ac_boost_path_tmp/include/boost"; then
+				BOOST_LDFLAGS="-L$ac_boost_path_tmp/lib"
+				BOOST_CPPFLAGS="-I$ac_boost_path_tmp/include"
+				break;
+			fi
+		done
+	fi
+
+    dnl overwrite ld flags if we have required special directory with
+    dnl --with-boost-libdir parameter
+    if test "$ac_boost_lib_path" != ""; then
+       BOOST_LDFLAGS="-L$ac_boost_lib_path"
+    fi
+
+	CPPFLAGS_SAVED="$CPPFLAGS"
+	CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+	export CPPFLAGS
+
+	LDFLAGS_SAVED="$LDFLAGS"
+	LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+	export LDFLAGS
+
+	AC_LANG_PUSH(C++)
+     	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+	@%:@include <boost/version.hpp>
+	]], [[
+	#if BOOST_VERSION >= $WANT_BOOST_VERSION
+	// Everything is okay
+	#else
+	#  error Boost version is too old
+	#endif
+	]])],[
+        AC_MSG_RESULT(yes)
+	succeeded=yes
+	found_system=yes
+       	],[
+       	])
+	AC_LANG_POP([C++])
+
+
+
+	dnl if we found no boost with system layout we search for boost libraries
+	dnl built and installed without the --layout=system option or for a staged(not installed) version
+	if test "x$succeeded" != "xyes"; then
+		_version=0
+		if test "$ac_boost_path" != ""; then
+			if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
+				for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
+					_version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+					V_CHECK=`expr $_version_tmp \> $_version`
+					if test "$V_CHECK" = "1" ; then
+						_version=$_version_tmp
+					fi
+					VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+					BOOST_CPPFLAGS="-I$ac_boost_path/include/boost-$VERSION_UNDERSCORE"
+				done
+			fi
+		else
+			for ac_boost_path in /usr /usr/local /opt /opt/local ; do
+				if test -d "$ac_boost_path" && test -r "$ac_boost_path"; then
+					for i in `ls -d $ac_boost_path/include/boost-* 2>/dev/null`; do
+						_version_tmp=`echo $i | sed "s#$ac_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+						V_CHECK=`expr $_version_tmp \> $_version`
+						if test "$V_CHECK" = "1" ; then
+							_version=$_version_tmp
+	               					best_path=$ac_boost_path
+						fi
+					done
+				fi
+			done
+
+			VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+			BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
+            if test "$ac_boost_lib_path" = ""
+            then
+               BOOST_LDFLAGS="-L$best_path/lib"
+            fi
+
+	    		if test "x$BOOST_ROOT" != "x"; then
+				if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/lib" && test -r "$BOOST_ROOT/stage/lib"; then
+					version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
+					stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
+			        	stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
+					V_CHECK=`expr $stage_version_shorten \>\= $_version`
+                    if test "$V_CHECK" = "1" -a "$ac_boost_lib_path" = "" ; then
+						AC_MSG_NOTICE(We will use a staged boost library from $BOOST_ROOT)
+						BOOST_CPPFLAGS="-I$BOOST_ROOT"
+						BOOST_LDFLAGS="-L$BOOST_ROOT/stage/lib"
+					fi
+				fi
+	    		fi
+		fi
+
+		CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+		export CPPFLAGS
+		LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+		export LDFLAGS
+
+		AC_LANG_PUSH(C++)
+	     	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+		@%:@include <boost/version.hpp>
+		]], [[
+		#if BOOST_VERSION >= $WANT_BOOST_VERSION
+		// Everything is okay
+		#else
+		#  error Boost version is too old
+		#endif
+		]])],[
+        	AC_MSG_RESULT(yes)
+		succeeded=yes
+		found_system=yes
+       		],[
+	       	])
+		AC_LANG_POP([C++])
+	fi
+
+	if test "$succeeded" != "yes" ; then
+		if test "$_version" = "0" ; then
+			AC_MSG_ERROR([[We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.]])
+		else
+			AC_MSG_NOTICE([Your boost libraries seems to old (version $_version).])
+		fi
+	else
+		AC_SUBST(BOOST_CPPFLAGS)
+		AC_SUBST(BOOST_LDFLAGS)
+		AC_DEFINE(HAVE_BOOST,,[define if the Boost library is available])
+	fi
+
+        CPPFLAGS="$CPPFLAGS_SAVED"
+       	LDFLAGS="$LDFLAGS_SAVED"
+fi
+
+])