[med-svn] [cufflinks] 03/10: New upstream version 2.2.1+dfsg.1
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Sep 5 21:59:19 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository cufflinks.
commit 5b2eb77e4c8fbb3b69e13f0651c47acfbb144f48
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Tue Sep 5 23:22:08 2017 +0200
New upstream version 2.2.1+dfsg.1
---
Makefile.in | 624 ---
aclocal.m4 | 1031 -----
autogen.sh | 21 +
ax_openmp.m4 | 101 +
boost.m4 | 87 +
build-aux/config.guess | 1463 -------
build-aux/config.sub | 1579 -------
build-aux/depcomp | 530 ---
build-aux/install-sh | 323 --
build-aux/missing | 360 --
config.h.in | 112 -
configure | 10836 -----------------------------------------------
make_bin.sh | 6 +-
src/LICENSE | 18 +
src/Makefile.in | 1624 -------
src/biascorrection.cpp | 2 +-
src/bundles.cpp | 39 +-
src/bundles.h | 25 +-
src/common.h | 10 +
src/compress_gtf.cpp | 6 -
src/cuffcluster.cpp | 942 ++++
src/cuffcompare.cpp | 7 -
src/cuffdiff.cpp | 12 +-
src/cuffdiff_to_gct.py | 108 +
src/cufflinks.cpp | 8 +-
src/cuffnorm.cpp | 701 +--
src/cuffquant.cpp | 10 +-
src/differential.cpp | 169 +-
src/differential.h | 729 +++-
src/gtf_reads.cpp | 187 +
src/gtf_to_sam.cpp | 6 -
src/hits.cpp | 8 +-
src/hits.h | 2 +-
src/replicates.cpp | 53 +-
src/replicates.h | 4 +-
version.m4 | 1 +
36 files changed, 2366 insertions(+), 19378 deletions(-)
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diff --git a/aclocal.m4 b/aclocal.m4
deleted file mode 100644
index 7f99a5a..0000000
--- a/aclocal.m4
+++ /dev/null
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-
diff --git a/autogen.sh b/autogen.sh
new file mode 100755
index 0000000..6a84d5e
--- /dev/null
+++ b/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
diff --git a/ax_openmp.m4 b/ax_openmp.m4
new file mode 100644
index 0000000..8c563b9
--- /dev/null
+++ b/ax_openmp.m4
@@ -0,0 +1,101 @@
+ # AC_C_OPENMP
+ # -----------
+ # Check which options need to be passed to the C compiler to support OpenMP.
+ # Set the OPENMP_CFLAGS variable to these options.
+ # The options are necessary at compile time (so the #pragmas are understood)
+ # and at link time (so the appropriate library is linked with).
+ # This macro takes care to not produce redundant options if $CC $CFLAGS
+already
+ # supports OpenMP. It also is careful to not pass options to compilers that
+ # misinterpret them; for example, most compilers accept "-openmp" and create
+ # an output file called 'penmp' rather than activating OpenMP support.
+ AC_DEFUN([AC_C_OPENMP],
+ [
+ AC_MSG_CHECKING([whether to use OpenMP])
+ AC_ARG_ENABLE(openmp,
+ [AS_HELP_STRING([--disable-openmp], [do not use OpenMP])],
+ [],
+ [enable_openmp=yes])
+ AC_MSG_RESULT([$enable_openmp])
+ OPENMP_CFLAGS=
+ if test "$enable_openmp" = yes; then
+ AC_MSG_CHECKING([for $CC option to support OpenMP])
+ AC_CACHE_VAL([ac_cv_prog_cc_openmp], [
+ ac_cv_prog_cc_openmp=unsupported
+ AC_LINK_IFELSE([
+ #ifndef _OPENMP
+ choke me
+ #endif
+ #include <omp.h>
+ int main () { return omp_get_num_threads (); }
+ ], [ac_cv_prog_cc_openmp="none needed"])
+ if test "$ac_cv_prog_cc_openmp" = unsupported; then
+ dnl Try these flags:
+ dnl GCC >= 4.2 -fopenmp
+ dnl SunPRO C -xopenmp
+ dnl Intel C -openmp
+ dnl SGI C, PGI C -mp
+ dnl Tru64 Compaq C -omp
+ dnl IBM C (AIX, Linux) -qsmp=omp
+ for brand in GCC SunPRO Intel SGI/PGI Compaq IBM; do
+ case $brand in
+ GCC)
+ ac_conditional='defined __GNUC__'
+ ac_option='-fopenmp' ;;
+ SunPRO)
+ ac_conditional='defined __SUNPRO_C || defined __SUNPRO_CC'
+ ac_option='-xopenmp' ;;
+ Intel)
+ ac_conditional='defined __INTEL_COMPILER'
+ ac_option='-openmp' ;;
+ SGI/PGI)
+ ac_conditional='defined __sgi || defined __PGI || defined
+__PGIC__'
+ ac_option='-mp' ;;
+ Compaq)
+ ac_conditional='defined __DECC || defined __DECCXX'
+ ac_option='-omp' ;;
+ IBM)
+ ac_conditional='defined __xlc__ || defined __xlC__'
+ ac_option='-qsmp=omp' ;;
+ esac
+ if test $brand = GCC; then
+ if test "$GCC" = yes; then
+ ac_openmp_result=yes
+ else
+ ac_openmp_result=no
+ fi
+ else
+ AC_EGREP_CPP([Brand], [
+ #if $ac_conditional
+ Brand
+ #endif
+ ], [ac_openmp_result=yes], [ac_openmp_result=no])
+ fi
+ if test $ac_openmp_result = yes; then
+ ac_save_CFLAGS=$CFLAGS
+ CFLAGS="$CFLAGS $ac_option"
+ AC_LINK_IFELSE([
+ #ifndef _OPENMP
+ choke me
+ #endif
+ #include <omp.h>
+ int main () { return omp_get_num_threads (); }
+ ], [ac_cv_prog_cc_openmp=$ac_option])
+ CFLAGS=$ac_save_CFLAGS
+ break
+ fi
+ done
+ fi
+ ])
+ AC_MSG_RESULT([$ac_cv_prog_cc_openmp])
+ case $ac_cv_prog_cc_openmp in
+ "none needed" | unsupported)
+ OPENMP_CFLAGS= ;;
+ *)
+ OPENMP_CFLAGS=$ac_cv_prog_cc_openmp ;;
+ esac
+ fi
+ AC_SUBST([OPENMP_CFLAGS])
+ ])
+
diff --git a/boost.m4 b/boost.m4
new file mode 100644
index 0000000..95190b9
--- /dev/null
+++ b/boost.m4
@@ -0,0 +1,87 @@
+dnl AC_PATH_BOOST([MINIMUM-VERSION], [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
+dnl Test for the Boost C++ libraries of a particular version (or newer)
+dnl Defines:
+dnl BOOST_CXXFLAGS to the set of flags required to compiled Boost
+AC_DEFUN([AC_PATH_BOOST],
+[
+ BOOST_CXXFLAGS=""
+ path_given="no"
+
+dnl Extract the path name from a --with-boost=PATH argument
+ AC_ARG_WITH(boost,
+ [ --with-boost=PATH absolute path name where the Boost C++ libraries
+ reside. Alternatively, the BOOST_ROOT environment variable will be used],
+ if test "$withval" = no ; then
+ path_given="no"
+ BOOST_CXXFLAGS=""
+ else
+ if test "$withval" != yes ; then
+ path_given="yes"
+ BOOST_CXXFLAGS="-I$withval"
+ BOOST_ROOT="$withval"
+ fi
+ fi
+ )
+
+dnl If no path with given and there is a BOOST_ROOT environment variable,
+dnl use it
+ if test "$path_given" = "no"; then
+ if test "x$BOOST_ROOT" = "x"; then
+ BOOST_CXXFLAGS=""
+ else
+ BOOST_CXXFLAGS="-I$BOOST_ROOT"
+ fi
+ fi
+
+ boost_min_version=ifelse([$1], ,1.20.0,$1)
+
+ AC_LANG_SAVE
+ AC_LANG_CPLUSPLUS
+ OLD_CXX_FLAGS=$CXXFLAGS
+ CXXFLAGS="$CXXFLAGS $BOOST_CXXFLAGS"
+ AC_MSG_CHECKING([for the Boost C++ libraries, version $boost_min_version or newer])
+ AC_TRY_COMPILE(
+ [
+#include <boost/version.hpp>
+],
+ [],
+ [
+ have_boost="yes"
+ ],
+ [
+ AC_MSG_RESULT(no)
+ have_boost="no"
+ ifelse([$3], , :, [$3])
+ ])
+
+ if test "$have_boost" = "yes"; then
+ WANT_BOOST_MAJOR=`expr $boost_min_version : '\([[0-9]]\+\)'`
+ WANT_BOOST_MINOR=`expr $boost_min_version : '[[0-9]]\+\.\([[0-9]]\+\)'`
+ WANT_BOOST_SUB_MINOR=`expr $boost_min_version : '[[0-9]]\+\.[[0-9]]\+\.\([[0-9]]\+\)'`
+ WANT_BOOST_VERSION=`expr $WANT_BOOST_MAJOR \* 100000 \+ $WANT_BOOST_MINOR \* 100 \+ $WANT_BOOST_SUB_MINOR`
+
+ AC_TRY_COMPILE(
+ [
+#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)
+ ifelse([$2], , :, [$2])
+ ],
+ [
+ AC_MSG_RESULT([no, version of installed Boost libraries is too old])
+ ifelse([$3], , :, [$3])
+ ])
+ fi
+ CXXFLAGS=$OLD_CXXFLAGS
+ AC_LANG_RESTORE
+])
+
diff --git a/build-aux/config.guess b/build-aux/config.guess
deleted file mode 100755
index 917bbc5..0000000
--- a/build-aux/config.guess
+++ /dev/null
@@ -1,1463 +0,0 @@
-#! /bin/sh
-# Attempt to guess a canonical system name.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
-
-timestamp='2005-07-08'
-
-# This file is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Originally written by Per Bothner <per at bothner.com>.
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
-#
-# This script attempts to guess a canonical system name similar to
-# config.sub. If it succeeds, it prints the system name on stdout, and
-# exits with 0. Otherwise, it exits with 1.
-#
-# The plan is that this can be called by configure scripts if you
-# don't specify an explicit build system type.
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION]
-
-Output the configuration name of the system \`$me' is run on.
-
-Operation modes:
- -h, --help print this help, then exit
- -t, --time-stamp print date of last modification, then exit
- -v, --version print version number, then exit
-
-Report bugs and patches to <config-patches at gnu.org>."
-
-version="\
-GNU config.guess ($timestamp)
-
-Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
- case $1 in
- --time-stamp | --time* | -t )
- echo "$timestamp" ; exit ;;
- --version | -v )
- echo "$version" ; exit ;;
- --help | --h* | -h )
- echo "$usage"; exit ;;
- -- ) # Stop option processing
- shift; break ;;
- - ) # Use stdin as input.
- break ;;
- -* )
- echo "$me: invalid option $1$help" >&2
- exit 1 ;;
- * )
- break ;;
- esac
-done
-
-if test $# != 0; then
- echo "$me: too many arguments$help" >&2
- exit 1
-fi
-
-trap 'exit 1' 1 2 15
-
-# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
-# compiler to aid in system detection is discouraged as it requires
-# temporary files to be created and, as you can see below, it is a
-# headache to deal with in a portable fashion.
-
-# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
-# use `HOST_CC' if defined, but it is deprecated.
-
-# Portable tmp directory creation inspired by the Autoconf team.
-
-set_cc_for_build='
-trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
-trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
-: ${TMPDIR=/tmp} ;
- { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
- { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
- { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
-dummy=$tmp/dummy ;
-tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
-case $CC_FOR_BUILD,$HOST_CC,$CC in
- ,,) echo "int x;" > $dummy.c ;
- for c in cc gcc c89 c99 ; do
- if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
- CC_FOR_BUILD="$c"; break ;
- fi ;
- done ;
- if test x"$CC_FOR_BUILD" = x ; then
- CC_FOR_BUILD=no_compiler_found ;
- fi
- ;;
- ,,*) CC_FOR_BUILD=$CC ;;
- ,*,*) CC_FOR_BUILD=$HOST_CC ;;
-esac ; set_cc_for_build= ;'
-
-# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
-# (ghazi at noc.rutgers.edu 1994-08-24)
-if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
- PATH=$PATH:/.attbin ; export PATH
-fi
-
-UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
-UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
-UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
-UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-
-# Note: order is significant - the case branches are not exclusive.
-
-case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
- *:NetBSD:*:*)
- # NetBSD (nbsd) targets should (where applicable) match one or
- # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
- # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
- # switched to ELF, *-*-netbsd* would select the old
- # object file format. This provides both forward
- # compatibility and a consistent mechanism for selecting the
- # object file format.
- #
- # Note: NetBSD doesn't particularly care about the vendor
- # portion of the name. We always set it to "unknown".
- sysctl="sysctl -n hw.machine_arch"
- UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
- /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
- case "${UNAME_MACHINE_ARCH}" in
- armeb) machine=armeb-unknown ;;
- arm*) machine=arm-unknown ;;
- sh3el) machine=shl-unknown ;;
- sh3eb) machine=sh-unknown ;;
- *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
- esac
- # The Operating System including object format, if it has switched
- # to ELF recently, or will in the future.
- case "${UNAME_MACHINE_ARCH}" in
- arm*|i386|m68k|ns32k|sh3*|sparc|vax)
- eval $set_cc_for_build
- if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
- | grep __ELF__ >/dev/null
- then
- # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
- # Return netbsd for either. FIX?
- os=netbsd
- else
- os=netbsdelf
- fi
- ;;
- *)
- os=netbsd
- ;;
- esac
- # The OS release
- # Debian GNU/NetBSD machines have a different userland, and
- # thus, need a distinct triplet. However, they do not need
- # kernel version information, so it can be replaced with a
- # suitable tag, in the style of linux-gnu.
- case "${UNAME_VERSION}" in
- Debian*)
- release='-gnu'
- ;;
- *)
- release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
- ;;
- esac
- # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
- # contains redundant information, the shorter form:
- # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
- echo "${machine}-${os}${release}"
- exit ;;
- *:OpenBSD:*:*)
- UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
- echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
- exit ;;
- *:ekkoBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
- exit ;;
- macppc:MirBSD:*:*)
- echo powerppc-unknown-mirbsd${UNAME_RELEASE}
- exit ;;
- *:MirBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
- exit ;;
- alpha:OSF1:*:*)
- case $UNAME_RELEASE in
- *4.0)
- UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
- ;;
- *5.*)
- UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
- ;;
- esac
- # According to Compaq, /usr/sbin/psrinfo has been available on
- # OSF/1 and Tru64 systems produced since 1995. I hope that
- # covers most systems running today. This code pipes the CPU
- # types through head -n 1, so we only detect the type of CPU 0.
- ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
- case "$ALPHA_CPU_TYPE" in
- "EV4 (21064)")
- UNAME_MACHINE="alpha" ;;
- "EV4.5 (21064)")
- UNAME_MACHINE="alpha" ;;
- "LCA4 (21066/21068)")
- UNAME_MACHINE="alpha" ;;
- "EV5 (21164)")
- UNAME_MACHINE="alphaev5" ;;
- "EV5.6 (21164A)")
- UNAME_MACHINE="alphaev56" ;;
- "EV5.6 (21164PC)")
- UNAME_MACHINE="alphapca56" ;;
- "EV5.7 (21164PC)")
- UNAME_MACHINE="alphapca57" ;;
- "EV6 (21264)")
- UNAME_MACHINE="alphaev6" ;;
- "EV6.7 (21264A)")
- UNAME_MACHINE="alphaev67" ;;
- "EV6.8CB (21264C)")
- UNAME_MACHINE="alphaev68" ;;
- "EV6.8AL (21264B)")
- UNAME_MACHINE="alphaev68" ;;
- "EV6.8CX (21264D)")
- UNAME_MACHINE="alphaev68" ;;
- "EV6.9A (21264/EV69A)")
- UNAME_MACHINE="alphaev69" ;;
- "EV7 (21364)")
- UNAME_MACHINE="alphaev7" ;;
- "EV7.9 (21364A)")
- UNAME_MACHINE="alphaev79" ;;
- esac
- # A Pn.n version is a patched version.
- # A Vn.n version is a released version.
- # A Tn.n version is a released field test version.
- # A Xn.n version is an unreleased experimental baselevel.
- # 1.2 uses "1.2" for uname -r.
- echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- exit ;;
- Alpha\ *:Windows_NT*:*)
- # How do we know it's Interix rather than the generic POSIX subsystem?
- # Should we change UNAME_MACHINE based on the output of uname instead
- # of the specific Alpha model?
- echo alpha-pc-interix
- exit ;;
- 21064:Windows_NT:50:3)
- echo alpha-dec-winnt3.5
- exit ;;
- Amiga*:UNIX_System_V:4.0:*)
- echo m68k-unknown-sysv4
- exit ;;
- *:[Aa]miga[Oo][Ss]:*:*)
- echo ${UNAME_MACHINE}-unknown-amigaos
- exit ;;
- *:[Mm]orph[Oo][Ss]:*:*)
- echo ${UNAME_MACHINE}-unknown-morphos
- exit ;;
- *:OS/390:*:*)
- echo i370-ibm-openedition
- exit ;;
- *:z/VM:*:*)
- echo s390-ibm-zvmoe
- exit ;;
- *:OS400:*:*)
- echo powerpc-ibm-os400
- exit ;;
- arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
- echo arm-acorn-riscix${UNAME_RELEASE}
- exit ;;
- arm:riscos:*:*|arm:RISCOS:*:*)
- echo arm-unknown-riscos
- exit ;;
- SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
- echo hppa1.1-hitachi-hiuxmpp
- exit ;;
- Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
- # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
- if test "`(/bin/universe) 2>/dev/null`" = att ; then
- echo pyramid-pyramid-sysv3
- else
- echo pyramid-pyramid-bsd
- fi
- exit ;;
- NILE*:*:*:dcosx)
- echo pyramid-pyramid-svr4
- exit ;;
- DRS?6000:unix:4.0:6*)
- echo sparc-icl-nx6
- exit ;;
- DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
- case `/usr/bin/uname -p` in
- sparc) echo sparc-icl-nx7; exit ;;
- esac ;;
- sun4H:SunOS:5.*:*)
- echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
- exit ;;
- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
- echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
- exit ;;
- i86pc:SunOS:5.*:*)
- echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
- exit ;;
- sun4*:SunOS:6*:*)
- # According to config.sub, this is the proper way to canonicalize
- # SunOS6. Hard to guess exactly what SunOS6 will be like, but
- # it's likely to be more like Solaris than SunOS4.
- echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
- exit ;;
- sun4*:SunOS:*:*)
- case "`/usr/bin/arch -k`" in
- Series*|S4*)
- UNAME_RELEASE=`uname -v`
- ;;
- esac
- # Japanese Language versions have a version number like `4.1.3-JL'.
- echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
- exit ;;
- sun3*:SunOS:*:*)
- echo m68k-sun-sunos${UNAME_RELEASE}
- exit ;;
- sun*:*:4.2BSD:*)
- UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
- test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
- case "`/bin/arch`" in
- sun3)
- echo m68k-sun-sunos${UNAME_RELEASE}
- ;;
- sun4)
- echo sparc-sun-sunos${UNAME_RELEASE}
- ;;
- esac
- exit ;;
- aushp:SunOS:*:*)
- echo sparc-auspex-sunos${UNAME_RELEASE}
- exit ;;
- # The situation for MiNT is a little confusing. The machine name
- # can be virtually everything (everything which is not
- # "atarist" or "atariste" at least should have a processor
- # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
- # to the lowercase version "mint" (or "freemint"). Finally
- # the system name "TOS" denotes a system which is actually not
- # MiNT. But MiNT is downward compatible to TOS, so this should
- # be no problem.
- atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
- exit ;;
- atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
- exit ;;
- *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
- exit ;;
- milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
- echo m68k-milan-mint${UNAME_RELEASE}
- exit ;;
- hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
- echo m68k-hades-mint${UNAME_RELEASE}
- exit ;;
- *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
- echo m68k-unknown-mint${UNAME_RELEASE}
- exit ;;
- m68k:machten:*:*)
- echo m68k-apple-machten${UNAME_RELEASE}
- exit ;;
- powerpc:machten:*:*)
- echo powerpc-apple-machten${UNAME_RELEASE}
- exit ;;
- RISC*:Mach:*:*)
- echo mips-dec-mach_bsd4.3
- exit ;;
- RISC*:ULTRIX:*:*)
- echo mips-dec-ultrix${UNAME_RELEASE}
- exit ;;
- VAX*:ULTRIX*:*:*)
- echo vax-dec-ultrix${UNAME_RELEASE}
- exit ;;
- 2020:CLIX:*:* | 2430:CLIX:*:*)
- echo clipper-intergraph-clix${UNAME_RELEASE}
- exit ;;
- mips:*:*:UMIPS | mips:*:*:RISCos)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
-#ifdef __cplusplus
-#include <stdio.h> /* for printf() prototype */
- int main (int argc, char *argv[]) {
-#else
- int main (argc, argv) int argc; char *argv[]; {
-#endif
- #if defined (host_mips) && defined (MIPSEB)
- #if defined (SYSTYPE_SYSV)
- printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
- #endif
- #if defined (SYSTYPE_SVR4)
- printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
- #endif
- #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
- printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
- #endif
- #endif
- exit (-1);
- }
-EOF
- $CC_FOR_BUILD -o $dummy $dummy.c &&
- dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
- SYSTEM_NAME=`$dummy $dummyarg` &&
- { echo "$SYSTEM_NAME"; exit; }
- echo mips-mips-riscos${UNAME_RELEASE}
- exit ;;
- Motorola:PowerMAX_OS:*:*)
- echo powerpc-motorola-powermax
- exit ;;
- Motorola:*:4.3:PL8-*)
- echo powerpc-harris-powermax
- exit ;;
- Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
- echo powerpc-harris-powermax
- exit ;;
- Night_Hawk:Power_UNIX:*:*)
- echo powerpc-harris-powerunix
- exit ;;
- m88k:CX/UX:7*:*)
- echo m88k-harris-cxux7
- exit ;;
- m88k:*:4*:R4*)
- echo m88k-motorola-sysv4
- exit ;;
- m88k:*:3*:R3*)
- echo m88k-motorola-sysv3
- exit ;;
- AViiON:dgux:*:*)
- # DG/UX returns AViiON for all architectures
- UNAME_PROCESSOR=`/usr/bin/uname -p`
- if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
- then
- if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
- [ ${TARGET_BINARY_INTERFACE}x = x ]
- then
- echo m88k-dg-dgux${UNAME_RELEASE}
- else
- echo m88k-dg-dguxbcs${UNAME_RELEASE}
- fi
- else
- echo i586-dg-dgux${UNAME_RELEASE}
- fi
- exit ;;
- M88*:DolphinOS:*:*) # DolphinOS (SVR3)
- echo m88k-dolphin-sysv3
- exit ;;
- M88*:*:R3*:*)
- # Delta 88k system running SVR3
- echo m88k-motorola-sysv3
- exit ;;
- XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
- echo m88k-tektronix-sysv3
- exit ;;
- Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
- echo m68k-tektronix-bsd
- exit ;;
- *:IRIX*:*:*)
- echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
- exit ;;
- ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
- echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
- exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
- i*86:AIX:*:*)
- echo i386-ibm-aix
- exit ;;
- ia64:AIX:*:*)
- if [ -x /usr/bin/oslevel ] ; then
- IBM_REV=`/usr/bin/oslevel`
- else
- IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
- fi
- echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
- exit ;;
- *:AIX:2:3)
- if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #include <sys/systemcfg.h>
-
- main()
- {
- if (!__power_pc())
- exit(1);
- puts("powerpc-ibm-aix3.2.5");
- exit(0);
- }
-EOF
- if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
- then
- echo "$SYSTEM_NAME"
- else
- echo rs6000-ibm-aix3.2.5
- fi
- elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
- echo rs6000-ibm-aix3.2.4
- else
- echo rs6000-ibm-aix3.2
- fi
- exit ;;
- *:AIX:*:[45])
- IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
- if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
- IBM_ARCH=rs6000
- else
- IBM_ARCH=powerpc
- fi
- if [ -x /usr/bin/oslevel ] ; then
- IBM_REV=`/usr/bin/oslevel`
- else
- IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
- fi
- echo ${IBM_ARCH}-ibm-aix${IBM_REV}
- exit ;;
- *:AIX:*:*)
- echo rs6000-ibm-aix
- exit ;;
- ibmrt:4.4BSD:*|romp-ibm:BSD:*)
- echo romp-ibm-bsd4.4
- exit ;;
- ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
- echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
- exit ;; # report: romp-ibm BSD 4.3
- *:BOSX:*:*)
- echo rs6000-bull-bosx
- exit ;;
- DPX/2?00:B.O.S.:*:*)
- echo m68k-bull-sysv3
- exit ;;
- 9000/[34]??:4.3bsd:1.*:*)
- echo m68k-hp-bsd
- exit ;;
- hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
- echo m68k-hp-bsd4.4
- exit ;;
- 9000/[34678]??:HP-UX:*:*)
- HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
- case "${UNAME_MACHINE}" in
- 9000/31? ) HP_ARCH=m68000 ;;
- 9000/[34]?? ) HP_ARCH=m68k ;;
- 9000/[678][0-9][0-9])
- if [ -x /usr/bin/getconf ]; then
- sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
- sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
- case "${sc_cpu_version}" in
- 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
- 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
- 532) # CPU_PA_RISC2_0
- case "${sc_kernel_bits}" in
- 32) HP_ARCH="hppa2.0n" ;;
- 64) HP_ARCH="hppa2.0w" ;;
- '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
- esac ;;
- esac
- fi
- if [ "${HP_ARCH}" = "" ]; then
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
-
- #define _HPUX_SOURCE
- #include <stdlib.h>
- #include <unistd.h>
-
- int main ()
- {
- #if defined(_SC_KERNEL_BITS)
- long bits = sysconf(_SC_KERNEL_BITS);
- #endif
- long cpu = sysconf (_SC_CPU_VERSION);
-
- switch (cpu)
- {
- case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
- case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
- case CPU_PA_RISC2_0:
- #if defined(_SC_KERNEL_BITS)
- switch (bits)
- {
- case 64: puts ("hppa2.0w"); break;
- case 32: puts ("hppa2.0n"); break;
- default: puts ("hppa2.0"); break;
- } break;
- #else /* !defined(_SC_KERNEL_BITS) */
- puts ("hppa2.0"); break;
- #endif
- default: puts ("hppa1.0"); break;
- }
- exit (0);
- }
-EOF
- (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
- test -z "$HP_ARCH" && HP_ARCH=hppa
- fi ;;
- esac
- if [ ${HP_ARCH} = "hppa2.0w" ]
- then
- eval $set_cc_for_build
-
- # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
- # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
- # generating 64-bit code. GNU and HP use different nomenclature:
- #
- # $ CC_FOR_BUILD=cc ./config.guess
- # => hppa2.0w-hp-hpux11.23
- # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
- # => hppa64-hp-hpux11.23
-
- if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
- grep __LP64__ >/dev/null
- then
- HP_ARCH="hppa2.0w"
- else
- HP_ARCH="hppa64"
- fi
- fi
- echo ${HP_ARCH}-hp-hpux${HPUX_REV}
- exit ;;
- ia64:HP-UX:*:*)
- HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
- echo ia64-hp-hpux${HPUX_REV}
- exit ;;
- 3050*:HI-UX:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #include <unistd.h>
- int
- main ()
- {
- long cpu = sysconf (_SC_CPU_VERSION);
- /* The order matters, because CPU_IS_HP_MC68K erroneously returns
- true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
- results, however. */
- if (CPU_IS_PA_RISC (cpu))
- {
- switch (cpu)
- {
- case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
- case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
- case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
- default: puts ("hppa-hitachi-hiuxwe2"); break;
- }
- }
- else if (CPU_IS_HP_MC68K (cpu))
- puts ("m68k-hitachi-hiuxwe2");
- else puts ("unknown-hitachi-hiuxwe2");
- exit (0);
- }
-EOF
- $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
- { echo "$SYSTEM_NAME"; exit; }
- echo unknown-hitachi-hiuxwe2
- exit ;;
- 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
- echo hppa1.1-hp-bsd
- exit ;;
- 9000/8??:4.3bsd:*:*)
- echo hppa1.0-hp-bsd
- exit ;;
- *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
- echo hppa1.0-hp-mpeix
- exit ;;
- hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
- echo hppa1.1-hp-osf
- exit ;;
- hp8??:OSF1:*:*)
- echo hppa1.0-hp-osf
- exit ;;
- i*86:OSF1:*:*)
- if [ -x /usr/sbin/sysversion ] ; then
- echo ${UNAME_MACHINE}-unknown-osf1mk
- else
- echo ${UNAME_MACHINE}-unknown-osf1
- fi
- exit ;;
- parisc*:Lites*:*:*)
- echo hppa1.1-hp-lites
- exit ;;
- C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
- echo c1-convex-bsd
- exit ;;
- C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
- if getsysinfo -f scalar_acc
- then echo c32-convex-bsd
- else echo c2-convex-bsd
- fi
- exit ;;
- C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
- echo c34-convex-bsd
- exit ;;
- C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
- echo c38-convex-bsd
- exit ;;
- C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
- echo c4-convex-bsd
- exit ;;
- CRAY*Y-MP:*:*:*)
- echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
- exit ;;
- CRAY*[A-Z]90:*:*:*)
- echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
- | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
- -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
- -e 's/\.[^.]*$/.X/'
- exit ;;
- CRAY*TS:*:*:*)
- echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
- exit ;;
- CRAY*T3E:*:*:*)
- echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
- exit ;;
- CRAY*SV1:*:*:*)
- echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
- exit ;;
- *:UNICOS/mp:*:*)
- echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
- exit ;;
- F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
- FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
- exit ;;
- 5000:UNIX_System_V:4.*:*)
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
- exit ;;
- i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
- echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
- exit ;;
- sparc*:BSD/OS:*:*)
- echo sparc-unknown-bsdi${UNAME_RELEASE}
- exit ;;
- *:BSD/OS:*:*)
- echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
- exit ;;
- *:FreeBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
- exit ;;
- i*:CYGWIN*:*)
- echo ${UNAME_MACHINE}-pc-cygwin
- exit ;;
- i*:MINGW*:*)
- echo ${UNAME_MACHINE}-pc-mingw32
- exit ;;
- i*:windows32*:*)
- # uname -m includes "-pc" on this system.
- echo ${UNAME_MACHINE}-mingw32
- exit ;;
- i*:PW*:*)
- echo ${UNAME_MACHINE}-pc-pw32
- exit ;;
- x86:Interix*:[34]*)
- echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//'
- exit ;;
- [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
- echo i${UNAME_MACHINE}-pc-mks
- exit ;;
- i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
- # How do we know it's Interix rather than the generic POSIX subsystem?
- # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
- # UNAME_MACHINE based on the output of uname instead of i386?
- echo i586-pc-interix
- exit ;;
- i*:UWIN*:*)
- echo ${UNAME_MACHINE}-pc-uwin
- exit ;;
- amd64:CYGWIN*:*:*)
- echo x86_64-unknown-cygwin
- exit ;;
- p*:CYGWIN*:*)
- echo powerpcle-unknown-cygwin
- exit ;;
- prep*:SunOS:5.*:*)
- echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
- exit ;;
- *:GNU:*:*)
- # the GNU system
- echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
- exit ;;
- *:GNU/*:*:*)
- # other systems with GNU libc and userland
- echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
- exit ;;
- i*86:Minix:*:*)
- echo ${UNAME_MACHINE}-pc-minix
- exit ;;
- arm*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- cris:Linux:*:*)
- echo cris-axis-linux-gnu
- exit ;;
- crisv32:Linux:*:*)
- echo crisv32-axis-linux-gnu
- exit ;;
- frv:Linux:*:*)
- echo frv-unknown-linux-gnu
- exit ;;
- ia64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- m32r*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- m68*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- mips:Linux:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #undef CPU
- #undef mips
- #undef mipsel
- #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mipsel
- #else
- #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips
- #else
- CPU=
- #endif
- #endif
-EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
- ;;
- mips64:Linux:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #undef CPU
- #undef mips64
- #undef mips64el
- #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mips64el
- #else
- #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips64
- #else
- CPU=
- #endif
- #endif
-EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
- ;;
- ppc:Linux:*:*)
- echo powerpc-unknown-linux-gnu
- exit ;;
- ppc64:Linux:*:*)
- echo powerpc64-unknown-linux-gnu
- exit ;;
- alpha:Linux:*:*)
- case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
- EV5) UNAME_MACHINE=alphaev5 ;;
- EV56) UNAME_MACHINE=alphaev56 ;;
- PCA56) UNAME_MACHINE=alphapca56 ;;
- PCA57) UNAME_MACHINE=alphapca56 ;;
- EV6) UNAME_MACHINE=alphaev6 ;;
- EV67) UNAME_MACHINE=alphaev67 ;;
- EV68*) UNAME_MACHINE=alphaev68 ;;
- esac
- objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
- if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
- echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
- exit ;;
- parisc:Linux:*:* | hppa:Linux:*:*)
- # Look for CPU level
- case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
- PA7*) echo hppa1.1-unknown-linux-gnu ;;
- PA8*) echo hppa2.0-unknown-linux-gnu ;;
- *) echo hppa-unknown-linux-gnu ;;
- esac
- exit ;;
- parisc64:Linux:*:* | hppa64:Linux:*:*)
- echo hppa64-unknown-linux-gnu
- exit ;;
- s390:Linux:*:* | s390x:Linux:*:*)
- echo ${UNAME_MACHINE}-ibm-linux
- exit ;;
- sh64*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- sh*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- sparc:Linux:*:* | sparc64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
- exit ;;
- x86_64:Linux:*:*)
- echo x86_64-unknown-linux-gnu
- exit ;;
- i*86:Linux:*:*)
- # The BFD linker knows what the default object file format is, so
- # first see if it will tell us. cd to the root directory to prevent
- # problems with other programs or directories called `ld' in the path.
- # Set LC_ALL=C to ensure ld outputs messages in English.
- ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
- | sed -ne '/supported targets:/!d
- s/[ ][ ]*/ /g
- s/.*supported targets: *//
- s/ .*//
- p'`
- case "$ld_supported_targets" in
- elf32-i386)
- TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
- ;;
- a.out-i386-linux)
- echo "${UNAME_MACHINE}-pc-linux-gnuaout"
- exit ;;
- coff-i386)
- echo "${UNAME_MACHINE}-pc-linux-gnucoff"
- exit ;;
- "")
- # Either a pre-BFD a.out linker (linux-gnuoldld) or
- # one that does not give us useful --help.
- echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
- exit ;;
- esac
- # Determine whether the default compiler is a.out or elf
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #include <features.h>
- #ifdef __ELF__
- # ifdef __GLIBC__
- # if __GLIBC__ >= 2
- LIBC=gnu
- # else
- LIBC=gnulibc1
- # endif
- # else
- LIBC=gnulibc1
- # endif
- #else
- #ifdef __INTEL_COMPILER
- LIBC=gnu
- #else
- LIBC=gnuaout
- #endif
- #endif
- #ifdef __dietlibc__
- LIBC=dietlibc
- #endif
-EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=`
- test x"${LIBC}" != x && {
- echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
- exit
- }
- test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
- ;;
- i*86:DYNIX/ptx:4*:*)
- # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
- # earlier versions are messed up and put the nodename in both
- # sysname and nodename.
- echo i386-sequent-sysv4
- exit ;;
- i*86:UNIX_SV:4.2MP:2.*)
- # Unixware is an offshoot of SVR4, but it has its own version
- # number series starting with 2...
- # I am not positive that other SVR4 systems won't match this,
- # I just have to hope. -- rms.
- # Use sysv4.2uw... so that sysv4* matches it.
- echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
- exit ;;
- i*86:OS/2:*:*)
- # If we were able to find `uname', then EMX Unix compatibility
- # is probably installed.
- echo ${UNAME_MACHINE}-pc-os2-emx
- exit ;;
- i*86:XTS-300:*:STOP)
- echo ${UNAME_MACHINE}-unknown-stop
- exit ;;
- i*86:atheos:*:*)
- echo ${UNAME_MACHINE}-unknown-atheos
- exit ;;
- i*86:syllable:*:*)
- echo ${UNAME_MACHINE}-pc-syllable
- exit ;;
- i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
- echo i386-unknown-lynxos${UNAME_RELEASE}
- exit ;;
- i*86:*DOS:*:*)
- echo ${UNAME_MACHINE}-pc-msdosdjgpp
- exit ;;
- i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
- UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
- echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
- else
- echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
- fi
- exit ;;
- i*86:*:5:[678]*)
- # UnixWare 7.x, OpenUNIX and OpenServer 6.
- case `/bin/uname -X | grep "^Machine"` in
- *486*) UNAME_MACHINE=i486 ;;
- *Pentium) UNAME_MACHINE=i586 ;;
- *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
- esac
- echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
- exit ;;
- i*86:*:3.2:*)
- if test -f /usr/options/cb.name; then
- UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
- echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
- elif /bin/uname -X 2>/dev/null >/dev/null ; then
- UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
- (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
- (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
- && UNAME_MACHINE=i586
- (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
- && UNAME_MACHINE=i686
- (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
- && UNAME_MACHINE=i686
- echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
- else
- echo ${UNAME_MACHINE}-pc-sysv32
- fi
- exit ;;
- pc:*:*:*)
- # Left here for compatibility:
- # uname -m prints for DJGPP always 'pc', but it prints nothing about
- # the processor, so we play safe by assuming i386.
- echo i386-pc-msdosdjgpp
- exit ;;
- Intel:Mach:3*:*)
- echo i386-pc-mach3
- exit ;;
- paragon:*:*:*)
- echo i860-intel-osf1
- exit ;;
- i860:*:4.*:*) # i860-SVR4
- if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
- echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
- else # Add other i860-SVR4 vendors below as they are discovered.
- echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
- fi
- exit ;;
- mini*:CTIX:SYS*5:*)
- # "miniframe"
- echo m68010-convergent-sysv
- exit ;;
- mc68k:UNIX:SYSTEM5:3.51m)
- echo m68k-convergent-sysv
- exit ;;
- M680?0:D-NIX:5.3:*)
- echo m68k-diab-dnix
- exit ;;
- M68*:*:R3V[5678]*:*)
- test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
- 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
- OS_REL=''
- test -r /etc/.relid \
- && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
- /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
- /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
- && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
- 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
- /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4; exit; } ;;
- m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
- echo m68k-unknown-lynxos${UNAME_RELEASE}
- exit ;;
- mc68030:UNIX_System_V:4.*:*)
- echo m68k-atari-sysv4
- exit ;;
- TSUNAMI:LynxOS:2.*:*)
- echo sparc-unknown-lynxos${UNAME_RELEASE}
- exit ;;
- rs6000:LynxOS:2.*:*)
- echo rs6000-unknown-lynxos${UNAME_RELEASE}
- exit ;;
- PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
- echo powerpc-unknown-lynxos${UNAME_RELEASE}
- exit ;;
- SM[BE]S:UNIX_SV:*:*)
- echo mips-dde-sysv${UNAME_RELEASE}
- exit ;;
- RM*:ReliantUNIX-*:*:*)
- echo mips-sni-sysv4
- exit ;;
- RM*:SINIX-*:*:*)
- echo mips-sni-sysv4
- exit ;;
- *:SINIX-*:*:*)
- if uname -p 2>/dev/null >/dev/null ; then
- UNAME_MACHINE=`(uname -p) 2>/dev/null`
- echo ${UNAME_MACHINE}-sni-sysv4
- else
- echo ns32k-sni-sysv
- fi
- exit ;;
- PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
- # says <Richard.M.Bartel at ccMail.Census.GOV>
- echo i586-unisys-sysv4
- exit ;;
- *:UNIX_System_V:4*:FTX*)
- # From Gerald Hewes <hewes at openmarket.com>.
- # How about differentiating between stratus architectures? -djm
- echo hppa1.1-stratus-sysv4
- exit ;;
- *:*:*:FTX*)
- # From seanf at swdc.stratus.com.
- echo i860-stratus-sysv4
- exit ;;
- i*86:VOS:*:*)
- # From Paul.Green at stratus.com.
- echo ${UNAME_MACHINE}-stratus-vos
- exit ;;
- *:VOS:*:*)
- # From Paul.Green at stratus.com.
- echo hppa1.1-stratus-vos
- exit ;;
- mc68*:A/UX:*:*)
- echo m68k-apple-aux${UNAME_RELEASE}
- exit ;;
- news*:NEWS-OS:6*:*)
- echo mips-sony-newsos6
- exit ;;
- R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
- if [ -d /usr/nec ]; then
- echo mips-nec-sysv${UNAME_RELEASE}
- else
- echo mips-unknown-sysv${UNAME_RELEASE}
- fi
- exit ;;
- BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
- echo powerpc-be-beos
- exit ;;
- BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
- echo powerpc-apple-beos
- exit ;;
- BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
- echo i586-pc-beos
- exit ;;
- SX-4:SUPER-UX:*:*)
- echo sx4-nec-superux${UNAME_RELEASE}
- exit ;;
- SX-5:SUPER-UX:*:*)
- echo sx5-nec-superux${UNAME_RELEASE}
- exit ;;
- SX-6:SUPER-UX:*:*)
- echo sx6-nec-superux${UNAME_RELEASE}
- exit ;;
- Power*:Rhapsody:*:*)
- echo powerpc-apple-rhapsody${UNAME_RELEASE}
- exit ;;
- *:Rhapsody:*:*)
- echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
- exit ;;
- *:Darwin:*:*)
- UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
- case $UNAME_PROCESSOR in
- *86) UNAME_PROCESSOR=i686 ;;
- unknown) UNAME_PROCESSOR=powerpc ;;
- esac
- echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
- exit ;;
- *:procnto*:*:* | *:QNX:[0123456789]*:*)
- UNAME_PROCESSOR=`uname -p`
- if test "$UNAME_PROCESSOR" = "x86"; then
- UNAME_PROCESSOR=i386
- UNAME_MACHINE=pc
- fi
- echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
- exit ;;
- *:QNX:*:4*)
- echo i386-pc-qnx
- exit ;;
- NSE-?:NONSTOP_KERNEL:*:*)
- echo nse-tandem-nsk${UNAME_RELEASE}
- exit ;;
- NSR-?:NONSTOP_KERNEL:*:*)
- echo nsr-tandem-nsk${UNAME_RELEASE}
- exit ;;
- *:NonStop-UX:*:*)
- echo mips-compaq-nonstopux
- exit ;;
- BS2000:POSIX*:*:*)
- echo bs2000-siemens-sysv
- exit ;;
- DS/*:UNIX_System_V:*:*)
- echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
- exit ;;
- *:Plan9:*:*)
- # "uname -m" is not consistent, so use $cputype instead. 386
- # is converted to i386 for consistency with other x86
- # operating systems.
- if test "$cputype" = "386"; then
- UNAME_MACHINE=i386
- else
- UNAME_MACHINE="$cputype"
- fi
- echo ${UNAME_MACHINE}-unknown-plan9
- exit ;;
- *:TOPS-10:*:*)
- echo pdp10-unknown-tops10
- exit ;;
- *:TENEX:*:*)
- echo pdp10-unknown-tenex
- exit ;;
- KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
- echo pdp10-dec-tops20
- exit ;;
- XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
- echo pdp10-xkl-tops20
- exit ;;
- *:TOPS-20:*:*)
- echo pdp10-unknown-tops20
- exit ;;
- *:ITS:*:*)
- echo pdp10-unknown-its
- exit ;;
- SEI:*:*:SEIUX)
- echo mips-sei-seiux${UNAME_RELEASE}
- exit ;;
- *:DragonFly:*:*)
- echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
- exit ;;
- *:*VMS:*:*)
- UNAME_MACHINE=`(uname -p) 2>/dev/null`
- case "${UNAME_MACHINE}" in
- A*) echo alpha-dec-vms ; exit ;;
- I*) echo ia64-dec-vms ; exit ;;
- V*) echo vax-dec-vms ; exit ;;
- esac ;;
- *:XENIX:*:SysV)
- echo i386-pc-xenix
- exit ;;
- i*86:skyos:*:*)
- echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
- exit ;;
-esac
-
-#echo '(No uname command or uname output not recognized.)' 1>&2
-#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
-
-eval $set_cc_for_build
-cat >$dummy.c <<EOF
-#ifdef _SEQUENT_
-# include <sys/types.h>
-# include <sys/utsname.h>
-#endif
-main ()
-{
-#if defined (sony)
-#if defined (MIPSEB)
- /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
- I don't know.... */
- printf ("mips-sony-bsd\n"); exit (0);
-#else
-#include <sys/param.h>
- printf ("m68k-sony-newsos%s\n",
-#ifdef NEWSOS4
- "4"
-#else
- ""
-#endif
- ); exit (0);
-#endif
-#endif
-
-#if defined (__arm) && defined (__acorn) && defined (__unix)
- printf ("arm-acorn-riscix\n"); exit (0);
-#endif
-
-#if defined (hp300) && !defined (hpux)
- printf ("m68k-hp-bsd\n"); exit (0);
-#endif
-
-#if defined (NeXT)
-#if !defined (__ARCHITECTURE__)
-#define __ARCHITECTURE__ "m68k"
-#endif
- int version;
- version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
- if (version < 4)
- printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
- else
- printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
- exit (0);
-#endif
-
-#if defined (MULTIMAX) || defined (n16)
-#if defined (UMAXV)
- printf ("ns32k-encore-sysv\n"); exit (0);
-#else
-#if defined (CMU)
- printf ("ns32k-encore-mach\n"); exit (0);
-#else
- printf ("ns32k-encore-bsd\n"); exit (0);
-#endif
-#endif
-#endif
-
-#if defined (__386BSD__)
- printf ("i386-pc-bsd\n"); exit (0);
-#endif
-
-#if defined (sequent)
-#if defined (i386)
- printf ("i386-sequent-dynix\n"); exit (0);
-#endif
-#if defined (ns32000)
- printf ("ns32k-sequent-dynix\n"); exit (0);
-#endif
-#endif
-
-#if defined (_SEQUENT_)
- struct utsname un;
-
- uname(&un);
-
- if (strncmp(un.version, "V2", 2) == 0) {
- printf ("i386-sequent-ptx2\n"); exit (0);
- }
- if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
- printf ("i386-sequent-ptx1\n"); exit (0);
- }
- printf ("i386-sequent-ptx\n"); exit (0);
-
-#endif
-
-#if defined (vax)
-# if !defined (ultrix)
-# include <sys/param.h>
-# if defined (BSD)
-# if BSD == 43
- printf ("vax-dec-bsd4.3\n"); exit (0);
-# else
-# if BSD == 199006
- printf ("vax-dec-bsd4.3reno\n"); exit (0);
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# endif
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# else
- printf ("vax-dec-ultrix\n"); exit (0);
-# endif
-#endif
-
-#if defined (alliant) && defined (i860)
- printf ("i860-alliant-bsd\n"); exit (0);
-#endif
-
- exit (1);
-}
-EOF
-
-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
- { echo "$SYSTEM_NAME"; exit; }
-
-# Apollos put the system type in the environment.
-
-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
-
-# Convex versions that predate uname can use getsysinfo(1)
-
-if [ -x /usr/convex/getsysinfo ]
-then
- case `getsysinfo -f cpu_type` in
- c1*)
- echo c1-convex-bsd
- exit ;;
- c2*)
- if getsysinfo -f scalar_acc
- then echo c32-convex-bsd
- else echo c2-convex-bsd
- fi
- exit ;;
- c34*)
- echo c34-convex-bsd
- exit ;;
- c38*)
- echo c38-convex-bsd
- exit ;;
- c4*)
- echo c4-convex-bsd
- exit ;;
- esac
-fi
-
-cat >&2 <<EOF
-$0: unable to guess system type
-
-This script, last modified $timestamp, has failed to recognize
-the operating system you are using. It is advised that you
-download the most up to date version of the config scripts from
-
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
-and
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
-
-If the version you run ($0) is already up to date, please
-send the following data and any information you think might be
-pertinent to <config-patches at gnu.org> in order to provide the needed
-information to handle your system.
-
-config.guess timestamp = $timestamp
-
-uname -m = `(uname -m) 2>/dev/null || echo unknown`
-uname -r = `(uname -r) 2>/dev/null || echo unknown`
-uname -s = `(uname -s) 2>/dev/null || echo unknown`
-uname -v = `(uname -v) 2>/dev/null || echo unknown`
-
-/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
-/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
-
-hostinfo = `(hostinfo) 2>/dev/null`
-/bin/universe = `(/bin/universe) 2>/dev/null`
-/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
-/bin/arch = `(/bin/arch) 2>/dev/null`
-/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
-/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
-
-UNAME_MACHINE = ${UNAME_MACHINE}
-UNAME_RELEASE = ${UNAME_RELEASE}
-UNAME_SYSTEM = ${UNAME_SYSTEM}
-UNAME_VERSION = ${UNAME_VERSION}
-EOF
-
-exit 1
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/build-aux/config.sub b/build-aux/config.sub
deleted file mode 100755
index 1c366df..0000000
--- a/build-aux/config.sub
+++ /dev/null
@@ -1,1579 +0,0 @@
-#! /bin/sh
-# Configuration validation subroutine script.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
-
-timestamp='2005-07-08'
-
-# This file is (in principle) common to ALL GNU software.
-# The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine. It does not imply ALL GNU software can.
-#
-# This file is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
-#
-# Configuration subroutine to validate and canonicalize a configuration type.
-# Supply the specified configuration type as an argument.
-# If it is invalid, we print an error message on stderr and exit with code 1.
-# Otherwise, we print the canonical config type on stdout and succeed.
-
-# This file is supposed to be the same for all GNU packages
-# and recognize all the CPU types, system types and aliases
-# that are meaningful with *any* GNU software.
-# Each package is responsible for reporting which valid configurations
-# it does not support. The user should be able to distinguish
-# a failure to support a valid configuration from a meaningless
-# configuration.
-
-# The goal of this file is to map all the various variations of a given
-# machine specification into a single specification in the form:
-# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
-# or in some cases, the newer four-part form:
-# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
-# It is wrong to echo any other type of specification.
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
- $0 [OPTION] ALIAS
-
-Canonicalize a configuration name.
-
-Operation modes:
- -h, --help print this help, then exit
- -t, --time-stamp print date of last modification, then exit
- -v, --version print version number, then exit
-
-Report bugs and patches to <config-patches at gnu.org>."
-
-version="\
-GNU config.sub ($timestamp)
-
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
- case $1 in
- --time-stamp | --time* | -t )
- echo "$timestamp" ; exit ;;
- --version | -v )
- echo "$version" ; exit ;;
- --help | --h* | -h )
- echo "$usage"; exit ;;
- -- ) # Stop option processing
- shift; break ;;
- - ) # Use stdin as input.
- break ;;
- -* )
- echo "$me: invalid option $1$help"
- exit 1 ;;
-
- *local*)
- # First pass through any local machine types.
- echo $1
- exit ;;
-
- * )
- break ;;
- esac
-done
-
-case $# in
- 0) echo "$me: missing argument$help" >&2
- exit 1;;
- 1) ;;
- *) echo "$me: too many arguments$help" >&2
- exit 1;;
-esac
-
-# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
-# Here we must recognize all the valid KERNEL-OS combinations.
-maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
-case $maybe_os in
- nto-qnx* | linux-gnu* | linux-dietlibc | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | \
- kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*)
- os=-$maybe_os
- basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
- ;;
- *)
- basic_machine=`echo $1 | sed 's/-[^-]*$//'`
- if [ $basic_machine != $1 ]
- then os=`echo $1 | sed 's/.*-/-/'`
- else os=; fi
- ;;
-esac
-
-### Let's recognize common machines as not being operating systems so
-### that things like config.sub decstation-3100 work. We also
-### recognize some manufacturers as not being operating systems, so we
-### can provide default operating systems below.
-case $os in
- -sun*os*)
- # Prevent following clause from handling this invalid input.
- ;;
- -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
- -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
- -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
- -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
- -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
- -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
- -apple | -axis | -knuth | -cray)
- os=
- basic_machine=$1
- ;;
- -sim | -cisco | -oki | -wec | -winbond)
- os=
- basic_machine=$1
- ;;
- -scout)
- ;;
- -wrs)
- os=-vxworks
- basic_machine=$1
- ;;
- -chorusos*)
- os=-chorusos
- basic_machine=$1
- ;;
- -chorusrdb)
- os=-chorusrdb
- basic_machine=$1
- ;;
- -hiux*)
- os=-hiuxwe2
- ;;
- -sco5)
- os=-sco3.2v5
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -sco4)
- os=-sco3.2v4
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -sco3.2.[4-9]*)
- os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -sco3.2v[4-9]*)
- # Don't forget version if it is 3.2v4 or newer.
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -sco*)
- os=-sco3.2v2
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -udk*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -isc)
- os=-isc2.2
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -clix*)
- basic_machine=clipper-intergraph
- ;;
- -isc*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
- ;;
- -lynx*)
- os=-lynxos
- ;;
- -ptx*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
- ;;
- -windowsnt*)
- os=`echo $os | sed -e 's/windowsnt/winnt/'`
- ;;
- -psos*)
- os=-psos
- ;;
- -mint | -mint[0-9]*)
- basic_machine=m68k-atari
- os=-mint
- ;;
-esac
-
-# Decode aliases for certain CPU-COMPANY combinations.
-case $basic_machine in
- # Recognize the basic CPU types without company name.
- # Some are omitted here because they have special meanings below.
- 1750a | 580 \
- | a29k \
- | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
- | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
- | am33_2.0 \
- | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \
- | bfin \
- | c4x | clipper \
- | d10v | d30v | dlx | dsp16xx \
- | fr30 | frv \
- | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
- | i370 | i860 | i960 | ia64 \
- | ip2k | iq2000 \
- | m32r | m32rle | m68000 | m68k | m88k | maxq | mcore \
- | mips | mipsbe | mipseb | mipsel | mipsle \
- | mips16 \
- | mips64 | mips64el \
- | mips64vr | mips64vrel \
- | mips64orion | mips64orionel \
- | mips64vr4100 | mips64vr4100el \
- | mips64vr4300 | mips64vr4300el \
- | mips64vr5000 | mips64vr5000el \
- | mips64vr5900 | mips64vr5900el \
- | mipsisa32 | mipsisa32el \
- | mipsisa32r2 | mipsisa32r2el \
- | mipsisa64 | mipsisa64el \
- | mipsisa64r2 | mipsisa64r2el \
- | mipsisa64sb1 | mipsisa64sb1el \
- | mipsisa64sr71k | mipsisa64sr71kel \
- | mipstx39 | mipstx39el \
- | mn10200 | mn10300 \
- | ms1 \
- | msp430 \
- | ns16k | ns32k \
- | or32 \
- | pdp10 | pdp11 | pj | pjl \
- | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
- | pyramid \
- | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \
- | sh64 | sh64le \
- | sparc | sparc64 | sparc64b | sparc86x | sparclet | sparclite \
- | sparcv8 | sparcv9 | sparcv9b \
- | strongarm \
- | tahoe | thumb | tic4x | tic80 | tron \
- | v850 | v850e \
- | we32k \
- | x86 | xscale | xscalee[bl] | xstormy16 | xtensa \
- | z8k)
- basic_machine=$basic_machine-unknown
- ;;
- m32c)
- basic_machine=$basic_machine-unknown
- ;;
- m6811 | m68hc11 | m6812 | m68hc12)
- # Motorola 68HC11/12.
- basic_machine=$basic_machine-unknown
- os=-none
- ;;
- m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
- ;;
-
- # We use `pc' rather than `unknown'
- # because (1) that's what they normally are, and
- # (2) the word "unknown" tends to confuse beginning users.
- i*86 | x86_64)
- basic_machine=$basic_machine-pc
- ;;
- # Object if more than one company name word.
- *-*-*)
- echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
- exit 1
- ;;
- # Recognize the basic CPU types with company name.
- 580-* \
- | a29k-* \
- | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
- | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
- | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
- | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
- | avr-* \
- | bfin-* | bs2000-* \
- | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
- | clipper-* | craynv-* | cydra-* \
- | d10v-* | d30v-* | dlx-* \
- | elxsi-* \
- | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
- | h8300-* | h8500-* \
- | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
- | i*86-* | i860-* | i960-* | ia64-* \
- | ip2k-* | iq2000-* \
- | m32r-* | m32rle-* \
- | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* \
- | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
- | mips16-* \
- | mips64-* | mips64el-* \
- | mips64vr-* | mips64vrel-* \
- | mips64orion-* | mips64orionel-* \
- | mips64vr4100-* | mips64vr4100el-* \
- | mips64vr4300-* | mips64vr4300el-* \
- | mips64vr5000-* | mips64vr5000el-* \
- | mips64vr5900-* | mips64vr5900el-* \
- | mipsisa32-* | mipsisa32el-* \
- | mipsisa32r2-* | mipsisa32r2el-* \
- | mipsisa64-* | mipsisa64el-* \
- | mipsisa64r2-* | mipsisa64r2el-* \
- | mipsisa64sb1-* | mipsisa64sb1el-* \
- | mipsisa64sr71k-* | mipsisa64sr71kel-* \
- | mipstx39-* | mipstx39el-* \
- | mmix-* \
- | ms1-* \
- | msp430-* \
- | none-* | np1-* | ns16k-* | ns32k-* \
- | orion-* \
- | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
- | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
- | pyramid-* \
- | romp-* | rs6000-* \
- | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | shbe-* \
- | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
- | sparc-* | sparc64-* | sparc64b-* | sparc86x-* | sparclet-* \
- | sparclite-* \
- | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \
- | tahoe-* | thumb-* \
- | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
- | tron-* \
- | v850-* | v850e-* | vax-* \
- | we32k-* \
- | x86-* | x86_64-* | xps100-* | xscale-* | xscalee[bl]-* \
- | xstormy16-* | xtensa-* \
- | ymp-* \
- | z8k-*)
- ;;
- m32c-*)
- ;;
- # Recognize the various machine names and aliases which stand
- # for a CPU type and a company and sometimes even an OS.
- 386bsd)
- basic_machine=i386-unknown
- os=-bsd
- ;;
- 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
- basic_machine=m68000-att
- ;;
- 3b*)
- basic_machine=we32k-att
- ;;
- a29khif)
- basic_machine=a29k-amd
- os=-udi
- ;;
- abacus)
- basic_machine=abacus-unknown
- ;;
- adobe68k)
- basic_machine=m68010-adobe
- os=-scout
- ;;
- alliant | fx80)
- basic_machine=fx80-alliant
- ;;
- altos | altos3068)
- basic_machine=m68k-altos
- ;;
- am29k)
- basic_machine=a29k-none
- os=-bsd
- ;;
- amd64)
- basic_machine=x86_64-pc
- ;;
- amd64-*)
- basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- amdahl)
- basic_machine=580-amdahl
- os=-sysv
- ;;
- amiga | amiga-*)
- basic_machine=m68k-unknown
- ;;
- amigaos | amigados)
- basic_machine=m68k-unknown
- os=-amigaos
- ;;
- amigaunix | amix)
- basic_machine=m68k-unknown
- os=-sysv4
- ;;
- apollo68)
- basic_machine=m68k-apollo
- os=-sysv
- ;;
- apollo68bsd)
- basic_machine=m68k-apollo
- os=-bsd
- ;;
- aux)
- basic_machine=m68k-apple
- os=-aux
- ;;
- balance)
- basic_machine=ns32k-sequent
- os=-dynix
- ;;
- c90)
- basic_machine=c90-cray
- os=-unicos
- ;;
- convex-c1)
- basic_machine=c1-convex
- os=-bsd
- ;;
- convex-c2)
- basic_machine=c2-convex
- os=-bsd
- ;;
- convex-c32)
- basic_machine=c32-convex
- os=-bsd
- ;;
- convex-c34)
- basic_machine=c34-convex
- os=-bsd
- ;;
- convex-c38)
- basic_machine=c38-convex
- os=-bsd
- ;;
- cray | j90)
- basic_machine=j90-cray
- os=-unicos
- ;;
- craynv)
- basic_machine=craynv-cray
- os=-unicosmp
- ;;
- cr16c)
- basic_machine=cr16c-unknown
- os=-elf
- ;;
- crds | unos)
- basic_machine=m68k-crds
- ;;
- crisv32 | crisv32-* | etraxfs*)
- basic_machine=crisv32-axis
- ;;
- cris | cris-* | etrax*)
- basic_machine=cris-axis
- ;;
- crx)
- basic_machine=crx-unknown
- os=-elf
- ;;
- da30 | da30-*)
- basic_machine=m68k-da30
- ;;
- decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
- basic_machine=mips-dec
- ;;
- decsystem10* | dec10*)
- basic_machine=pdp10-dec
- os=-tops10
- ;;
- decsystem20* | dec20*)
- basic_machine=pdp10-dec
- os=-tops20
- ;;
- delta | 3300 | motorola-3300 | motorola-delta \
- | 3300-motorola | delta-motorola)
- basic_machine=m68k-motorola
- ;;
- delta88)
- basic_machine=m88k-motorola
- os=-sysv3
- ;;
- djgpp)
- basic_machine=i586-pc
- os=-msdosdjgpp
- ;;
- dpx20 | dpx20-*)
- basic_machine=rs6000-bull
- os=-bosx
- ;;
- dpx2* | dpx2*-bull)
- basic_machine=m68k-bull
- os=-sysv3
- ;;
- ebmon29k)
- basic_machine=a29k-amd
- os=-ebmon
- ;;
- elxsi)
- basic_machine=elxsi-elxsi
- os=-bsd
- ;;
- encore | umax | mmax)
- basic_machine=ns32k-encore
- ;;
- es1800 | OSE68k | ose68k | ose | OSE)
- basic_machine=m68k-ericsson
- os=-ose
- ;;
- fx2800)
- basic_machine=i860-alliant
- ;;
- genix)
- basic_machine=ns32k-ns
- ;;
- gmicro)
- basic_machine=tron-gmicro
- os=-sysv
- ;;
- go32)
- basic_machine=i386-pc
- os=-go32
- ;;
- h3050r* | hiux*)
- basic_machine=hppa1.1-hitachi
- os=-hiuxwe2
- ;;
- h8300hms)
- basic_machine=h8300-hitachi
- os=-hms
- ;;
- h8300xray)
- basic_machine=h8300-hitachi
- os=-xray
- ;;
- h8500hms)
- basic_machine=h8500-hitachi
- os=-hms
- ;;
- harris)
- basic_machine=m88k-harris
- os=-sysv3
- ;;
- hp300-*)
- basic_machine=m68k-hp
- ;;
- hp300bsd)
- basic_machine=m68k-hp
- os=-bsd
- ;;
- hp300hpux)
- basic_machine=m68k-hp
- os=-hpux
- ;;
- hp3k9[0-9][0-9] | hp9[0-9][0-9])
- basic_machine=hppa1.0-hp
- ;;
- hp9k2[0-9][0-9] | hp9k31[0-9])
- basic_machine=m68000-hp
- ;;
- hp9k3[2-9][0-9])
- basic_machine=m68k-hp
- ;;
- hp9k6[0-9][0-9] | hp6[0-9][0-9])
- basic_machine=hppa1.0-hp
- ;;
- hp9k7[0-79][0-9] | hp7[0-79][0-9])
- basic_machine=hppa1.1-hp
- ;;
- hp9k78[0-9] | hp78[0-9])
- # FIXME: really hppa2.0-hp
- basic_machine=hppa1.1-hp
- ;;
- hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
- # FIXME: really hppa2.0-hp
- basic_machine=hppa1.1-hp
- ;;
- hp9k8[0-9][13679] | hp8[0-9][13679])
- basic_machine=hppa1.1-hp
- ;;
- hp9k8[0-9][0-9] | hp8[0-9][0-9])
- basic_machine=hppa1.0-hp
- ;;
- hppa-next)
- os=-nextstep3
- ;;
- hppaosf)
- basic_machine=hppa1.1-hp
- os=-osf
- ;;
- hppro)
- basic_machine=hppa1.1-hp
- os=-proelf
- ;;
- i370-ibm* | ibm*)
- basic_machine=i370-ibm
- ;;
-# I'm not sure what "Sysv32" means. Should this be sysv3.2?
- i*86v32)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
- os=-sysv32
- ;;
- i*86v4*)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
- os=-sysv4
- ;;
- i*86v)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
- os=-sysv
- ;;
- i*86sol2)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
- os=-solaris2
- ;;
- i386mach)
- basic_machine=i386-mach
- os=-mach
- ;;
- i386-vsta | vsta)
- basic_machine=i386-unknown
- os=-vsta
- ;;
- iris | iris4d)
- basic_machine=mips-sgi
- case $os in
- -irix*)
- ;;
- *)
- os=-irix4
- ;;
- esac
- ;;
- isi68 | isi)
- basic_machine=m68k-isi
- os=-sysv
- ;;
- m88k-omron*)
- basic_machine=m88k-omron
- ;;
- magnum | m3230)
- basic_machine=mips-mips
- os=-sysv
- ;;
- merlin)
- basic_machine=ns32k-utek
- os=-sysv
- ;;
- mingw32)
- basic_machine=i386-pc
- os=-mingw32
- ;;
- miniframe)
- basic_machine=m68000-convergent
- ;;
- *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
- basic_machine=m68k-atari
- os=-mint
- ;;
- mips3*-*)
- basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
- ;;
- mips3*)
- basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
- ;;
- monitor)
- basic_machine=m68k-rom68k
- os=-coff
- ;;
- morphos)
- basic_machine=powerpc-unknown
- os=-morphos
- ;;
- msdos)
- basic_machine=i386-pc
- os=-msdos
- ;;
- mvs)
- basic_machine=i370-ibm
- os=-mvs
- ;;
- ncr3000)
- basic_machine=i486-ncr
- os=-sysv4
- ;;
- netbsd386)
- basic_machine=i386-unknown
- os=-netbsd
- ;;
- netwinder)
- basic_machine=armv4l-rebel
- os=-linux
- ;;
- news | news700 | news800 | news900)
- basic_machine=m68k-sony
- os=-newsos
- ;;
- news1000)
- basic_machine=m68030-sony
- os=-newsos
- ;;
- news-3600 | risc-news)
- basic_machine=mips-sony
- os=-newsos
- ;;
- necv70)
- basic_machine=v70-nec
- os=-sysv
- ;;
- next | m*-next )
- basic_machine=m68k-next
- case $os in
- -nextstep* )
- ;;
- -ns2*)
- os=-nextstep2
- ;;
- *)
- os=-nextstep3
- ;;
- esac
- ;;
- nh3000)
- basic_machine=m68k-harris
- os=-cxux
- ;;
- nh[45]000)
- basic_machine=m88k-harris
- os=-cxux
- ;;
- nindy960)
- basic_machine=i960-intel
- os=-nindy
- ;;
- mon960)
- basic_machine=i960-intel
- os=-mon960
- ;;
- nonstopux)
- basic_machine=mips-compaq
- os=-nonstopux
- ;;
- np1)
- basic_machine=np1-gould
- ;;
- nsr-tandem)
- basic_machine=nsr-tandem
- ;;
- op50n-* | op60c-*)
- basic_machine=hppa1.1-oki
- os=-proelf
- ;;
- openrisc | openrisc-*)
- basic_machine=or32-unknown
- ;;
- os400)
- basic_machine=powerpc-ibm
- os=-os400
- ;;
- OSE68000 | ose68000)
- basic_machine=m68000-ericsson
- os=-ose
- ;;
- os68k)
- basic_machine=m68k-none
- os=-os68k
- ;;
- pa-hitachi)
- basic_machine=hppa1.1-hitachi
- os=-hiuxwe2
- ;;
- paragon)
- basic_machine=i860-intel
- os=-osf
- ;;
- pbd)
- basic_machine=sparc-tti
- ;;
- pbb)
- basic_machine=m68k-tti
- ;;
- pc532 | pc532-*)
- basic_machine=ns32k-pc532
- ;;
- pentium | p5 | k5 | k6 | nexgen | viac3)
- basic_machine=i586-pc
- ;;
- pentiumpro | p6 | 6x86 | athlon | athlon_*)
- basic_machine=i686-pc
- ;;
- pentiumii | pentium2 | pentiumiii | pentium3)
- basic_machine=i686-pc
- ;;
- pentium4)
- basic_machine=i786-pc
- ;;
- pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
- basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- pentiumpro-* | p6-* | 6x86-* | athlon-*)
- basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
- basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- pentium4-*)
- basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- pn)
- basic_machine=pn-gould
- ;;
- power) basic_machine=power-ibm
- ;;
- ppc) basic_machine=powerpc-unknown
- ;;
- ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- ppcle | powerpclittle | ppc-le | powerpc-little)
- basic_machine=powerpcle-unknown
- ;;
- ppcle-* | powerpclittle-*)
- basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- ppc64) basic_machine=powerpc64-unknown
- ;;
- ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- ppc64le | powerpc64little | ppc64-le | powerpc64-little)
- basic_machine=powerpc64le-unknown
- ;;
- ppc64le-* | powerpc64little-*)
- basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
- ;;
- ps2)
- basic_machine=i386-ibm
- ;;
- pw32)
- basic_machine=i586-unknown
- os=-pw32
- ;;
- rom68k)
- basic_machine=m68k-rom68k
- os=-coff
- ;;
- rm[46]00)
- basic_machine=mips-siemens
- ;;
- rtpc | rtpc-*)
- basic_machine=romp-ibm
- ;;
- s390 | s390-*)
- basic_machine=s390-ibm
- ;;
- s390x | s390x-*)
- basic_machine=s390x-ibm
- ;;
- sa29200)
- basic_machine=a29k-amd
- os=-udi
- ;;
- sb1)
- basic_machine=mipsisa64sb1-unknown
- ;;
- sb1el)
- basic_machine=mipsisa64sb1el-unknown
- ;;
- sei)
- basic_machine=mips-sei
- os=-seiux
- ;;
- sequent)
- basic_machine=i386-sequent
- ;;
- sh)
- basic_machine=sh-hitachi
- os=-hms
- ;;
- sh64)
- basic_machine=sh64-unknown
- ;;
- sparclite-wrs | simso-wrs)
- basic_machine=sparclite-wrs
- os=-vxworks
- ;;
- sps7)
- basic_machine=m68k-bull
- os=-sysv2
- ;;
- spur)
- basic_machine=spur-unknown
- ;;
- st2000)
- basic_machine=m68k-tandem
- ;;
- stratus)
- basic_machine=i860-stratus
- os=-sysv4
- ;;
- sun2)
- basic_machine=m68000-sun
- ;;
- sun2os3)
- basic_machine=m68000-sun
- os=-sunos3
- ;;
- sun2os4)
- basic_machine=m68000-sun
- os=-sunos4
- ;;
- sun3os3)
- basic_machine=m68k-sun
- os=-sunos3
- ;;
- sun3os4)
- basic_machine=m68k-sun
- os=-sunos4
- ;;
- sun4os3)
- basic_machine=sparc-sun
- os=-sunos3
- ;;
- sun4os4)
- basic_machine=sparc-sun
- os=-sunos4
- ;;
- sun4sol2)
- basic_machine=sparc-sun
- os=-solaris2
- ;;
- sun3 | sun3-*)
- basic_machine=m68k-sun
- ;;
- sun4)
- basic_machine=sparc-sun
- ;;
- sun386 | sun386i | roadrunner)
- basic_machine=i386-sun
- ;;
- sv1)
- basic_machine=sv1-cray
- os=-unicos
- ;;
- symmetry)
- basic_machine=i386-sequent
- os=-dynix
- ;;
- t3e)
- basic_machine=alphaev5-cray
- os=-unicos
- ;;
- t90)
- basic_machine=t90-cray
- os=-unicos
- ;;
- tic54x | c54x*)
- basic_machine=tic54x-unknown
- os=-coff
- ;;
- tic55x | c55x*)
- basic_machine=tic55x-unknown
- os=-coff
- ;;
- tic6x | c6x*)
- basic_machine=tic6x-unknown
- os=-coff
- ;;
- tx39)
- basic_machine=mipstx39-unknown
- ;;
- tx39el)
- basic_machine=mipstx39el-unknown
- ;;
- toad1)
- basic_machine=pdp10-xkl
- os=-tops20
- ;;
- tower | tower-32)
- basic_machine=m68k-ncr
- ;;
- tpf)
- basic_machine=s390x-ibm
- os=-tpf
- ;;
- udi29k)
- basic_machine=a29k-amd
- os=-udi
- ;;
- ultra3)
- basic_machine=a29k-nyu
- os=-sym1
- ;;
- v810 | necv810)
- basic_machine=v810-nec
- os=-none
- ;;
- vaxv)
- basic_machine=vax-dec
- os=-sysv
- ;;
- vms)
- basic_machine=vax-dec
- os=-vms
- ;;
- vpp*|vx|vx-*)
- basic_machine=f301-fujitsu
- ;;
- vxworks960)
- basic_machine=i960-wrs
- os=-vxworks
- ;;
- vxworks68)
- basic_machine=m68k-wrs
- os=-vxworks
- ;;
- vxworks29k)
- basic_machine=a29k-wrs
- os=-vxworks
- ;;
- w65*)
- basic_machine=w65-wdc
- os=-none
- ;;
- w89k-*)
- basic_machine=hppa1.1-winbond
- os=-proelf
- ;;
- xbox)
- basic_machine=i686-pc
- os=-mingw32
- ;;
- xps | xps100)
- basic_machine=xps100-honeywell
- ;;
- ymp)
- basic_machine=ymp-cray
- os=-unicos
- ;;
- z8k-*-coff)
- basic_machine=z8k-unknown
- os=-sim
- ;;
- none)
- basic_machine=none-none
- os=-none
- ;;
-
-# Here we handle the default manufacturer of certain CPU types. It is in
-# some cases the only manufacturer, in others, it is the most popular.
- w89k)
- basic_machine=hppa1.1-winbond
- ;;
- op50n)
- basic_machine=hppa1.1-oki
- ;;
- op60c)
- basic_machine=hppa1.1-oki
- ;;
- romp)
- basic_machine=romp-ibm
- ;;
- mmix)
- basic_machine=mmix-knuth
- ;;
- rs6000)
- basic_machine=rs6000-ibm
- ;;
- vax)
- basic_machine=vax-dec
- ;;
- pdp10)
- # there are many clones, so DEC is not a safe bet
- basic_machine=pdp10-unknown
- ;;
- pdp11)
- basic_machine=pdp11-dec
- ;;
- we32k)
- basic_machine=we32k-att
- ;;
- sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
- basic_machine=sh-unknown
- ;;
- sparc | sparcv8 | sparcv9 | sparcv9b)
- basic_machine=sparc-sun
- ;;
- cydra)
- basic_machine=cydra-cydrome
- ;;
- orion)
- basic_machine=orion-highlevel
- ;;
- orion105)
- basic_machine=clipper-highlevel
- ;;
- mac | mpw | mac-mpw)
- basic_machine=m68k-apple
- ;;
- pmac | pmac-mpw)
- basic_machine=powerpc-apple
- ;;
- *-unknown)
- # Make sure to match an already-canonicalized machine name.
- ;;
- *)
- echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
- exit 1
- ;;
-esac
-
-# Here we canonicalize certain aliases for manufacturers.
-case $basic_machine in
- *-digital*)
- basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
- ;;
- *-commodore*)
- basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
- ;;
- *)
- ;;
-esac
-
-# Decode manufacturer-specific aliases for certain operating systems.
-
-if [ x"$os" != x"" ]
-then
-case $os in
- # First match some system type aliases
- # that might get confused with valid system types.
- # -solaris* is a basic system type, with this one exception.
- -solaris1 | -solaris1.*)
- os=`echo $os | sed -e 's|solaris1|sunos4|'`
- ;;
- -solaris)
- os=-solaris2
- ;;
- -svr4*)
- os=-sysv4
- ;;
- -unixware*)
- os=-sysv4.2uw
- ;;
- -gnu/linux*)
- os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
- ;;
- # First accept the basic system types.
- # The portable systems comes first.
- # Each alternative MUST END IN A *, to match a version number.
- # -sysv* is not here because it comes later, after sysvr4.
- -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
- | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
- | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
- | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
- | -aos* \
- | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
- | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
- | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* | -openbsd* \
- | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
- | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
- | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
- | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* \
- | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -mingw32* | -linux-gnu* | -linux-uclibc* | -uxpv* | -beos* | -mpeix* | -udk* \
- | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
- | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
- | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
- | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
- | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
- | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku*)
- # Remember, each alternative MUST END IN *, to match a version number.
- ;;
- -qnx*)
- case $basic_machine in
- x86-* | i*86-*)
- ;;
- *)
- os=-nto$os
- ;;
- esac
- ;;
- -nto-qnx*)
- ;;
- -nto*)
- os=`echo $os | sed -e 's|nto|nto-qnx|'`
- ;;
- -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
- | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
- | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
- ;;
- -mac*)
- os=`echo $os | sed -e 's|mac|macos|'`
- ;;
- -linux-dietlibc)
- os=-linux-dietlibc
- ;;
- -linux*)
- os=`echo $os | sed -e 's|linux|linux-gnu|'`
- ;;
- -sunos5*)
- os=`echo $os | sed -e 's|sunos5|solaris2|'`
- ;;
- -sunos6*)
- os=`echo $os | sed -e 's|sunos6|solaris3|'`
- ;;
- -opened*)
- os=-openedition
- ;;
- -os400*)
- os=-os400
- ;;
- -wince*)
- os=-wince
- ;;
- -osfrose*)
- os=-osfrose
- ;;
- -osf*)
- os=-osf
- ;;
- -utek*)
- os=-bsd
- ;;
- -dynix*)
- os=-bsd
- ;;
- -acis*)
- os=-aos
- ;;
- -atheos*)
- os=-atheos
- ;;
- -syllable*)
- os=-syllable
- ;;
- -386bsd)
- os=-bsd
- ;;
- -ctix* | -uts*)
- os=-sysv
- ;;
- -nova*)
- os=-rtmk-nova
- ;;
- -ns2 )
- os=-nextstep2
- ;;
- -nsk*)
- os=-nsk
- ;;
- # Preserve the version number of sinix5.
- -sinix5.*)
- os=`echo $os | sed -e 's|sinix|sysv|'`
- ;;
- -sinix*)
- os=-sysv4
- ;;
- -tpf*)
- os=-tpf
- ;;
- -triton*)
- os=-sysv3
- ;;
- -oss*)
- os=-sysv3
- ;;
- -svr4)
- os=-sysv4
- ;;
- -svr3)
- os=-sysv3
- ;;
- -sysvr4)
- os=-sysv4
- ;;
- # This must come after -sysvr4.
- -sysv*)
- ;;
- -ose*)
- os=-ose
- ;;
- -es1800*)
- os=-ose
- ;;
- -xenix)
- os=-xenix
- ;;
- -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
- os=-mint
- ;;
- -aros*)
- os=-aros
- ;;
- -kaos*)
- os=-kaos
- ;;
- -zvmoe)
- os=-zvmoe
- ;;
- -none)
- ;;
- *)
- # Get rid of the `-' at the beginning of $os.
- os=`echo $os | sed 's/[^-]*-//'`
- echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
- exit 1
- ;;
-esac
-else
-
-# Here we handle the default operating systems that come with various machines.
-# The value should be what the vendor currently ships out the door with their
-# machine or put another way, the most popular os provided with the machine.
-
-# Note that if you're going to try to match "-MANUFACTURER" here (say,
-# "-sun"), then you have to tell the case statement up towards the top
-# that MANUFACTURER isn't an operating system. Otherwise, code above
-# will signal an error saying that MANUFACTURER isn't an operating
-# system, and we'll never get to this point.
-
-case $basic_machine in
- *-acorn)
- os=-riscix1.2
- ;;
- arm*-rebel)
- os=-linux
- ;;
- arm*-semi)
- os=-aout
- ;;
- c4x-* | tic4x-*)
- os=-coff
- ;;
- # This must come before the *-dec entry.
- pdp10-*)
- os=-tops20
- ;;
- pdp11-*)
- os=-none
- ;;
- *-dec | vax-*)
- os=-ultrix4.2
- ;;
- m68*-apollo)
- os=-domain
- ;;
- i386-sun)
- os=-sunos4.0.2
- ;;
- m68000-sun)
- os=-sunos3
- # This also exists in the configure program, but was not the
- # default.
- # os=-sunos4
- ;;
- m68*-cisco)
- os=-aout
- ;;
- mips*-cisco)
- os=-elf
- ;;
- mips*-*)
- os=-elf
- ;;
- or32-*)
- os=-coff
- ;;
- *-tti) # must be before sparc entry or we get the wrong os.
- os=-sysv3
- ;;
- sparc-* | *-sun)
- os=-sunos4.1.1
- ;;
- *-be)
- os=-beos
- ;;
- *-haiku)
- os=-haiku
- ;;
- *-ibm)
- os=-aix
- ;;
- *-knuth)
- os=-mmixware
- ;;
- *-wec)
- os=-proelf
- ;;
- *-winbond)
- os=-proelf
- ;;
- *-oki)
- os=-proelf
- ;;
- *-hp)
- os=-hpux
- ;;
- *-hitachi)
- os=-hiux
- ;;
- i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
- os=-sysv
- ;;
- *-cbm)
- os=-amigaos
- ;;
- *-dg)
- os=-dgux
- ;;
- *-dolphin)
- os=-sysv3
- ;;
- m68k-ccur)
- os=-rtu
- ;;
- m88k-omron*)
- os=-luna
- ;;
- *-next )
- os=-nextstep
- ;;
- *-sequent)
- os=-ptx
- ;;
- *-crds)
- os=-unos
- ;;
- *-ns)
- os=-genix
- ;;
- i370-*)
- os=-mvs
- ;;
- *-next)
- os=-nextstep3
- ;;
- *-gould)
- os=-sysv
- ;;
- *-highlevel)
- os=-bsd
- ;;
- *-encore)
- os=-bsd
- ;;
- *-sgi)
- os=-irix
- ;;
- *-siemens)
- os=-sysv4
- ;;
- *-masscomp)
- os=-rtu
- ;;
- f30[01]-fujitsu | f700-fujitsu)
- os=-uxpv
- ;;
- *-rom68k)
- os=-coff
- ;;
- *-*bug)
- os=-coff
- ;;
- *-apple)
- os=-macos
- ;;
- *-atari*)
- os=-mint
- ;;
- *)
- os=-none
- ;;
-esac
-fi
-
-# Here we handle the case where we know the os, and the CPU type, but not the
-# manufacturer. We pick the logical manufacturer.
-vendor=unknown
-case $basic_machine in
- *-unknown)
- case $os in
- -riscix*)
- vendor=acorn
- ;;
- -sunos*)
- vendor=sun
- ;;
- -aix*)
- vendor=ibm
- ;;
- -beos*)
- vendor=be
- ;;
- -hpux*)
- vendor=hp
- ;;
- -mpeix*)
- vendor=hp
- ;;
- -hiux*)
- vendor=hitachi
- ;;
- -unos*)
- vendor=crds
- ;;
- -dgux*)
- vendor=dg
- ;;
- -luna*)
- vendor=omron
- ;;
- -genix*)
- vendor=ns
- ;;
- -mvs* | -opened*)
- vendor=ibm
- ;;
- -os400*)
- vendor=ibm
- ;;
- -ptx*)
- vendor=sequent
- ;;
- -tpf*)
- vendor=ibm
- ;;
- -vxsim* | -vxworks* | -windiss*)
- vendor=wrs
- ;;
- -aux*)
- vendor=apple
- ;;
- -hms*)
- vendor=hitachi
- ;;
- -mpw* | -macos*)
- vendor=apple
- ;;
- -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
- vendor=atari
- ;;
- -vos*)
- vendor=stratus
- ;;
- esac
- basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
- ;;
-esac
-
-echo $basic_machine$os
-exit
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/build-aux/depcomp b/build-aux/depcomp
deleted file mode 100755
index 04701da..0000000
--- a/build-aux/depcomp
+++ /dev/null
@@ -1,530 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2005-07-09.11
-
-# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
-
-case $1 in
- '')
- echo "$0: No command. Try \`$0 --help' for more information." 1>&2
- exit 1;
- ;;
- -h | --h*)
- cat <<\EOF
-Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-
-Run PROGRAMS ARGS to compile a file, generating dependencies
-as side-effects.
-
-Environment variables:
- depmode Dependency tracking mode.
- source Source file read by `PROGRAMS ARGS'.
- object Object file output by `PROGRAMS ARGS'.
- DEPDIR directory where to store dependencies.
- depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputing dependencies.
- libtool Whether libtool is used (yes/no).
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "depcomp $scriptversion"
- exit $?
- ;;
-esac
-
-if test -z "$depmode" || test -z "$source" || test -z "$object"; then
- echo "depcomp: Variables source, object and depmode must be set" 1>&2
- exit 1
-fi
-
-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-depfile=${depfile-`echo "$object" |
- sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-
-rm -f "$tmpdepfile"
-
-# Some modes work just like other modes, but use different flags. We
-# parameterize here, but still list the modes in the big case below,
-# to make depend.m4 easier to write. Note that we *cannot* use a case
-# here, because this file can only contain one case statement.
-if test "$depmode" = hp; then
- # HP compiler uses -M and no extra arg.
- gccflag=-M
- depmode=gcc
-fi
-
-if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
-fi
-
-case "$depmode" in
-gcc3)
-## gcc 3 implements dependency tracking that does exactly what
-## we want. Yay! Note: for some reason libtool 1.4 doesn't like
-## it if -MD -MP comes after the -MF stuff. Hmm.
- "$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- mv "$tmpdepfile" "$depfile"
- ;;
-
-gcc)
-## There are various ways to get dependency output from gcc. Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-## up in a subdir. Having to rename by hand is ugly.
-## (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say).
-## - Using -M directly means running the compiler twice (even worse
-## than renaming).
- if test -z "$gccflag"; then
- gccflag=-MD,
- fi
- "$@" -Wp,"$gccflag$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
- sed -e 's/^[^:]*: / /' \
- -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
-## The problem is that when a header file which appears in a .P file
-## is deleted, the dependency causes make to die (because there is
-## typically no way to rebuild the header). We avoid this by adding
-## dummy dependencies for each header file. Too bad gcc doesn't do
-## this for us directly.
- tr ' ' '
-' < "$tmpdepfile" |
-## Some versions of gcc put a space before the `:'. On the theory
-## that the space means something, we add a space to the output as
-## well.
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-sgi)
- if test "$libtool" = yes; then
- "$@" "-Wp,-MDupdate,$tmpdepfile"
- else
- "$@" -MDupdate "$tmpdepfile"
- fi
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
-
- if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
- echo "$object : \\" > "$depfile"
-
- # Clip off the initial element (the dependent). Don't try to be
- # clever and replace this with sed code, as IRIX sed won't handle
- # lines with more than a fixed number of characters (4096 in
- # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like `#:fec' to the end of the
- # dependency line.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
- tr '
-' ' ' >> $depfile
- echo >> $depfile
-
- # The second pass generates a dummy entry for each header file.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> $depfile
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-aix)
- # The C for AIX Compiler uses -M and outputs the dependencies
- # in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts `$object:' at the
- # start of each line; $object doesn't have directory information.
- # Version 6 uses the directory in both cases.
- stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
- tmpdepfile="$stripped.u"
- if test "$libtool" = yes; then
- "$@" -Wc,-M
- else
- "$@" -M
- fi
- stat=$?
-
- if test -f "$tmpdepfile"; then :
- else
- stripped=`echo "$stripped" | sed 's,^.*/,,'`
- tmpdepfile="$stripped.u"
- fi
-
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
-
- if test -f "$tmpdepfile"; then
- outname="$stripped.o"
- # Each line is of the form `foo.o: dependent.h'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
- sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-icc)
- # Intel's C compiler understands `-MD -MF file'. However on
- # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
- # ICC 7.0 will fill foo.d with something like
- # foo.o: sub/foo.c
- # foo.o: sub/foo.h
- # which is wrong. We want:
- # sub/foo.o: sub/foo.c
- # sub/foo.o: sub/foo.h
- # sub/foo.c:
- # sub/foo.h:
- # ICC 7.1 will output
- # foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using \ :
- # foo.o: sub/foo.c ... \
- # sub/foo.h ... \
- # ...
-
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each line is of the form `foo.o: dependent.h',
- # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
- sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in `foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
- if test "$libtool" = yes; then
- # With Tru64 cc, shared objects can also be used to make a
- # static library. This mecanism is used in libtool 1.4 series to
- # handle both shared and static libraries in a single compilation.
- # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
- #
- # With libtool 1.5 this exception was removed, and libtool now
- # generates 2 separate objects for the 2 libraries. These two
- # compilations output dependencies in in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
- tmpdepfile2=$dir$base.o.d # libtool 1.5
- tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
- tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.o.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- tmpdepfile4=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- # That's a tab and a space in the [].
- sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-#nosideeffect)
- # This comment above is used by automake to tell side-effect
- # dependency tracking mechanisms from slower ones.
-
-dashmstdout)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove `-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for `:'
- # in the target name. This is to cope with DOS-style filenames:
- # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
- "$@" $dashmflag |
- sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
- rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- tr ' ' '
-' < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-dashXmstdout)
- # This case only exists to satisfy depend.m4. It is never actually
- # run, as this mode is specially recognized in the preamble.
- exit 1
- ;;
-
-makedepend)
- "$@" || exit $?
- # Remove any Libtool call
- if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
- shift
- done
- shift
- fi
- # X makedepend
- shift
- cleared=no
- for arg in "$@"; do
- case $cleared in
- no)
- set ""; shift
- cleared=yes ;;
- esac
- case "$arg" in
- -D*|-I*)
- set fnord "$@" "$arg"; shift ;;
- # Strip any option that makedepend may not understand. Remove
- # the object too, otherwise makedepend will parse it as a source file.
- -*|$object)
- ;;
- *)
- set fnord "$@" "$arg"; shift ;;
- esac
- done
- obj_suffix="`echo $object | sed 's/^.*\././'`"
- touch "$tmpdepfile"
- ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
- rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- sed '1,2d' "$tmpdepfile" | tr ' ' '
-' | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile" "$tmpdepfile".bak
- ;;
-
-cpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove `-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- "$@" -E |
- sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
- sed '$ s: \\$::' > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- cat < "$tmpdepfile" >> "$depfile"
- sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvisualcpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o,
- # because we must use -o when running libtool.
- "$@" || exit $?
- IFS=" "
- for arg
- do
- case "$arg" in
- "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
- esac
- done
- "$@" -E |
- sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
- echo " " >> "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-none)
- exec "$@"
- ;;
-
-*)
- echo "Unknown depmode $depmode" 1>&2
- exit 1
- ;;
-esac
-
-exit 0
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
-# End:
diff --git a/build-aux/install-sh b/build-aux/install-sh
deleted file mode 100755
index 4d4a951..0000000
--- a/build-aux/install-sh
+++ /dev/null
@@ -1,323 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2005-05-14.22
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# 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 AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-# Except as contained in this notice, the name of the X Consortium shall not
-# be used in advertising or otherwise to promote the sale, use or other deal-
-# ings in this Software without prior written authorization from the X Consor-
-# tium.
-#
-#
-# FSF changes to this file are in the public domain.
-#
-# Calling this script install-sh is preferred over install.sh, to prevent
-# `make' implicit rules from creating a file called install from it
-# when there is no Makefile.
-#
-# This script is compatible with the BSD install script, but was written
-# from scratch. It can only install one file at a time, a restriction
-# shared with many OS's install programs.
-
-# set DOITPROG to echo to test this script
-
-# Don't use :- since 4.3BSD and earlier shells don't like it.
-doit="${DOITPROG-}"
-
-# put in absolute paths if you don't have them in your path; or use env. vars.
-
-mvprog="${MVPROG-mv}"
-cpprog="${CPPROG-cp}"
-chmodprog="${CHMODPROG-chmod}"
-chownprog="${CHOWNPROG-chown}"
-chgrpprog="${CHGRPPROG-chgrp}"
-stripprog="${STRIPPROG-strip}"
-rmprog="${RMPROG-rm}"
-mkdirprog="${MKDIRPROG-mkdir}"
-
-chmodcmd="$chmodprog 0755"
-chowncmd=
-chgrpcmd=
-stripcmd=
-rmcmd="$rmprog -f"
-mvcmd="$mvprog"
-src=
-dst=
-dir_arg=
-dstarg=
-no_target_directory=
-
-usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
- or: $0 [OPTION]... SRCFILES... DIRECTORY
- or: $0 [OPTION]... -t DIRECTORY SRCFILES...
- or: $0 [OPTION]... -d DIRECTORIES...
-
-In the 1st form, copy SRCFILE to DSTFILE.
-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
-In the 4th, create DIRECTORIES.
-
-Options:
--c (ignored)
--d create directories instead of installing files.
--g GROUP $chgrpprog installed files to GROUP.
--m MODE $chmodprog installed files to MODE.
--o USER $chownprog installed files to USER.
--s $stripprog installed files.
--t DIRECTORY install into DIRECTORY.
--T report an error if DSTFILE is a directory.
---help display this help and exit.
---version display version info and exit.
-
-Environment variables override the default commands:
- CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
-"
-
-while test -n "$1"; do
- case $1 in
- -c) shift
- continue;;
-
- -d) dir_arg=true
- shift
- continue;;
-
- -g) chgrpcmd="$chgrpprog $2"
- shift
- shift
- continue;;
-
- --help) echo "$usage"; exit $?;;
-
- -m) chmodcmd="$chmodprog $2"
- shift
- shift
- continue;;
-
- -o) chowncmd="$chownprog $2"
- shift
- shift
- continue;;
-
- -s) stripcmd=$stripprog
- shift
- continue;;
-
- -t) dstarg=$2
- shift
- shift
- continue;;
-
- -T) no_target_directory=true
- shift
- continue;;
-
- --version) echo "$0 $scriptversion"; exit $?;;
-
- *) # When -d is used, all remaining arguments are directories to create.
- # When -t is used, the destination is already specified.
- test -n "$dir_arg$dstarg" && break
- # Otherwise, the last argument is the destination. Remove it from $@.
- for arg
- do
- if test -n "$dstarg"; then
- # $@ is not empty: it contains at least $arg.
- set fnord "$@" "$dstarg"
- shift # fnord
- fi
- shift # arg
- dstarg=$arg
- done
- break;;
- esac
-done
-
-if test -z "$1"; then
- if test -z "$dir_arg"; then
- echo "$0: no input file specified." >&2
- exit 1
- fi
- # It's OK to call `install-sh -d' without argument.
- # This can happen when creating conditional directories.
- exit 0
-fi
-
-for src
-do
- # Protect names starting with `-'.
- case $src in
- -*) src=./$src ;;
- esac
-
- if test -n "$dir_arg"; then
- dst=$src
- src=
-
- if test -d "$dst"; then
- mkdircmd=:
- chmodcmd=
- else
- mkdircmd=$mkdirprog
- fi
- else
- # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
- # might cause directories to be created, which would be especially bad
- # if $src (and thus $dsttmp) contains '*'.
- if test ! -f "$src" && test ! -d "$src"; then
- echo "$0: $src does not exist." >&2
- exit 1
- fi
-
- if test -z "$dstarg"; then
- echo "$0: no destination specified." >&2
- exit 1
- fi
-
- dst=$dstarg
- # Protect names starting with `-'.
- case $dst in
- -*) dst=./$dst ;;
- esac
-
- # If destination is a directory, append the input filename; won't work
- # if double slashes aren't ignored.
- if test -d "$dst"; then
- if test -n "$no_target_directory"; then
- echo "$0: $dstarg: Is a directory" >&2
- exit 1
- fi
- dst=$dst/`basename "$src"`
- fi
- fi
-
- # This sed command emulates the dirname command.
- dstdir=`echo "$dst" | sed -e 's,/*$,,;s,[^/]*$,,;s,/*$,,;s,^$,.,'`
-
- # Make sure that the destination directory exists.
-
- # Skip lots of stat calls in the usual case.
- if test ! -d "$dstdir"; then
- defaultIFS='
- '
- IFS="${IFS-$defaultIFS}"
-
- oIFS=$IFS
- # Some sh's can't handle IFS=/ for some reason.
- IFS='%'
- set x `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
- shift
- IFS=$oIFS
-
- pathcomp=
-
- while test $# -ne 0 ; do
- pathcomp=$pathcomp$1
- shift
- if test ! -d "$pathcomp"; then
- $mkdirprog "$pathcomp"
- # mkdir can fail with a `File exist' error in case several
- # install-sh are creating the directory concurrently. This
- # is OK.
- test -d "$pathcomp" || exit
- fi
- pathcomp=$pathcomp/
- done
- fi
-
- if test -n "$dir_arg"; then
- $doit $mkdircmd "$dst" \
- && { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
- && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
- && { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
- && { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
-
- else
- dstfile=`basename "$dst"`
-
- # Make a couple of temp file names in the proper directory.
- dsttmp=$dstdir/_inst.$$_
- rmtmp=$dstdir/_rm.$$_
-
- # Trap to clean up those temp files at exit.
- trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
- trap '(exit $?); exit' 1 2 13 15
-
- # Copy the file name to the temp name.
- $doit $cpprog "$src" "$dsttmp" &&
-
- # and set any options; do chmod last to preserve setuid bits.
- #
- # If any of these fail, we abort the whole thing. If we want to
- # ignore errors from any of these, just make sure not to ignore
- # errors from the above "$doit $cpprog $src $dsttmp" command.
- #
- { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
- && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
- && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
- && { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
-
- # Now rename the file to the real destination.
- { $doit $mvcmd -f "$dsttmp" "$dstdir/$dstfile" 2>/dev/null \
- || {
- # The rename failed, perhaps because mv can't rename something else
- # to itself, or perhaps because mv is so ancient that it does not
- # support -f.
-
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- if test -f "$dstdir/$dstfile"; then
- $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
- || $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
- || {
- echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
- (exit 1); exit 1
- }
- else
- :
- fi
- } &&
-
- # Now rename the file to the real destination.
- $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
- }
- }
- fi || { (exit 1); exit 1; }
-done
-
-# The final little trick to "correctly" pass the exit status to the exit trap.
-{
- (exit 0); exit 0
-}
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
-# End:
diff --git a/build-aux/missing b/build-aux/missing
deleted file mode 100755
index 894e786..0000000
--- a/build-aux/missing
+++ /dev/null
@@ -1,360 +0,0 @@
-#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
-
-scriptversion=2005-06-08.21
-
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005
-# Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-if test $# -eq 0; then
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
-fi
-
-run=:
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
- configure_ac=configure.ac
-else
- configure_ac=configure.in
-fi
-
-msg="missing on your system"
-
-case "$1" in
---run)
- # Try to run requested program, and just exit if it succeeds.
- run=
- shift
- "$@" && exit 0
- # Exit code 63 means version mismatch. This often happens
- # when the user try to use an ancient version of a tool on
- # a file that requires a minimum version. In this case we
- # we should proceed has if the program had been absent, or
- # if --run hadn't been passed.
- if test $? = 63; then
- run=:
- msg="probably too old"
- fi
- ;;
-
- -h|--h|--he|--hel|--help)
- echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
-
-Options:
- -h, --help display this help and exit
- -v, --version output version information and exit
- --run try to run the given command, and emulate it if it fails
-
-Supported PROGRAM values:
- aclocal touch file \`aclocal.m4'
- autoconf touch file \`configure'
- autoheader touch file \`config.h.in'
- automake touch all \`Makefile.in' files
- bison create \`y.tab.[ch]', if possible, from existing .[ch]
- flex create \`lex.yy.c', if possible, from existing .c
- help2man touch the output file
- lex create \`lex.yy.c', if possible, from existing .c
- makeinfo touch the output file
- tar try tar, gnutar, gtar, then tar without non-portable flags
- yacc create \`y.tab.[ch]', if possible, from existing .[ch]
-
-Send bug reports to <bug-automake at gnu.org>."
- exit $?
- ;;
-
- -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
- echo "missing $scriptversion (GNU Automake)"
- exit $?
- ;;
-
- -*)
- echo 1>&2 "$0: Unknown \`$1' option"
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
- ;;
-
-esac
-
-# Now exit if we have it, but it failed. Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program).
-case "$1" in
- lex|yacc)
- # Not GNU programs, they don't have --version.
- ;;
-
- tar)
- if test -n "$run"; then
- echo 1>&2 "ERROR: \`tar' requires --run"
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- exit 1
- fi
- ;;
-
- *)
- if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
- # We have it, but it failed.
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- # Could not run --version or --help. This is probably someone
- # running `$TOOL --version' or `$TOOL --help' to check whether
- # $TOOL exists and not knowing $TOOL uses missing.
- exit 1
- fi
- ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case "$1" in
- aclocal*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acinclude.m4' or \`${configure_ac}'. You might want
- to install the \`Automake' and \`Perl' packages. Grab them from
- any GNU archive site."
- touch aclocal.m4
- ;;
-
- autoconf)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`${configure_ac}'. You might want to install the
- \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
- archive site."
- touch configure
- ;;
-
- autoheader)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acconfig.h' or \`${configure_ac}'. You might want
- to install the \`Autoconf' and \`GNU m4' packages. Grab them
- from any GNU archive site."
- files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
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- *) touch_files="$touch_files $f.in";;
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- touch $touch_files
- ;;
-
- automake*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
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- ;;
-
- autom4te)
- echo 1>&2 "\
-WARNING: \`$1' is needed, but is $msg.
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- archive site."
-
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- fi
- ;;
-
- bison|yacc)
- echo 1>&2 "\
-WARNING: \`$1' $msg. You should only need it if
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- in order for those modifications to take effect. You can get
- \`Bison' from any GNU archive site."
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- *.y)
- SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
- if [ -f "$SRCFILE" ]; then
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- fi
- SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
- if [ -f "$SRCFILE" ]; then
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- fi
- ;;
- esac
- fi
- if [ ! -f y.tab.h ]; then
- echo >y.tab.h
- fi
- if [ ! -f y.tab.c ]; then
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- fi
- ;;
-
- lex|flex)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
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- rm -f lex.yy.c
- if [ $# -ne 1 ]; then
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- case "$LASTARG" in
- *.l)
- SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
- if [ -f "$SRCFILE" ]; then
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- fi
- ;;
- esac
- fi
- if [ ! -f lex.yy.c ]; then
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- fi
- ;;
-
- help2man)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a dependency of a manual page. You may need the
- \`Help2man' package in order for those modifications to take
- effect. You can get \`Help2man' from any GNU archive site."
-
- file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
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-
-exit 0
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-# Local variables:
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-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
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diff --git a/config.h.in b/config.h.in
deleted file mode 100644
index 71a19ef..0000000
--- a/config.h.in
+++ /dev/null
@@ -1,112 +0,0 @@
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-
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-/* define if the Boost library is available */
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-/* define if the Boost::Serialization library is available */
-#undef HAVE_BOOST_SERIALIZATION
-
-/* define if the Boost::System library is available */
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-
-/* define if the Boost::Thread library is available */
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-
-/* Define to 1 if you have the declaration of `CTL_HW', and to 0 if you don't.
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-
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-/* Define to 1 if you have the `z' library (-lz). */
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-/* Define to 1 if you have the <memory.h> header file. */
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-/* Define to 1 if the system has the type `ptrdiff_t'. */
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-/* Define to 1 if stdbool.h conforms to C99. */
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-/* Define to 1 if you have the <stdint.h> header file. */
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-/* Define to 1 if you have the <stdlib.h> header file. */
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-/* Define to 1 if you have the <strings.h> header file. */
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-/* Define to 1 if you have the <string.h> header file. */
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-/* Define to 1 if you have the <sys/stat.h> header file. */
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-
-/* Define to 1 if you have the <sys/types.h> header file. */
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-
-/* Define to 1 if you have the <unistd.h> header file. */
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-
-/* Define to 1 if the system has the type `_Bool'. */
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-
-/* Name of package */
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-/* Define to the address where bug reports for this package should be sent. */
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-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
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-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* SVN Revision */
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-
-/* Version number of package */
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-
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-/* Define to `int' if <sys/types.h> does not define. */
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-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
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diff --git a/configure b/configure
deleted file mode 100755
index b9cb412..0000000
--- a/configure
+++ /dev/null
@@ -1,10836 +0,0 @@
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- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SET_MAKE=
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- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- SET_MAKE="MAKE=${MAKE-make}"
-fi
-
-if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
-set dummy ${ac_tool_prefix}ranlib; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_RANLIB+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test -n "$RANLIB"; then
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-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
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-do
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- ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
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-done
-IFS=$as_save_IFS
-
-fi
-fi
-RANLIB=$ac_cv_prog_RANLIB
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-$as_echo "$RANLIB" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
-fi
-if test -z "$ac_cv_prog_RANLIB"; then
- ac_ct_RANLIB=$RANLIB
- # Extract the first word of "ranlib", so it can be a program name with args.
-set dummy ranlib; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test -n "$ac_ct_RANLIB"; then
- ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
-else
-as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_ac_ct_RANLIB="ranlib"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-IFS=$as_save_IFS
-
-fi
-fi
-ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
-if test -n "$ac_ct_RANLIB"; then
- { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
-$as_echo "$ac_ct_RANLIB" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
- if test "x$ac_ct_RANLIB" = x; then
- RANLIB=":"
- else
- case $cross_compiling:$ac_tool_warned in
-yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
-$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
-ac_tool_warned=yes ;;
-esac
- RANLIB=$ac_ct_RANLIB
- fi
-else
- RANLIB="$ac_cv_prog_RANLIB"
-fi
-
-# Find a good install program. We prefer a C program (faster),
-# so one script is as good as another. But avoid the broken or
-# incompatible versions:
-# SysV /etc/install, /usr/sbin/install
-# SunOS /usr/etc/install
-# IRIX /sbin/install
-# AIX /bin/install
-# AmigaOS /C/install, which installs bootblocks on floppy discs
-# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
-# AFS /usr/afsws/bin/install, which mishandles nonexistent args
-# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
-# OS/2's system install, which has a completely different semantic
-# ./install, which can be erroneously created by make from ./install.sh.
-# Reject install programs that cannot install multiple files.
-{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
-$as_echo_n "checking for a BSD-compatible install... " >&6; }
-if test -z "$INSTALL"; then
-if test "${ac_cv_path_install+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in
- ./ | .// | /cC/* | \
- /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
- /usr/ucb/* ) ;;
- *)
- # OSF1 and SCO ODT 3.0 have their own names for install.
- # Don't use installbsd from OSF since it installs stuff as root
- # by default.
- for ac_prog in ginstall scoinst install; do
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
- if test $ac_prog = install &&
- grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # AIX install. It has an incompatible calling convention.
- :
- elif test $ac_prog = install &&
- grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # program-specific install script used by HP pwplus--don't use.
- :
- else
- rm -rf conftest.one conftest.two conftest.dir
- echo one > conftest.one
- echo two > conftest.two
- mkdir conftest.dir
- if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
- test -s conftest.one && test -s conftest.two &&
- test -s conftest.dir/conftest.one &&
- test -s conftest.dir/conftest.two
- then
- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
- break 3
- fi
- fi
- fi
- done
- done
- ;;
-esac
-
-done
-IFS=$as_save_IFS
-
-rm -rf conftest.one conftest.two conftest.dir
-
-fi
- if test "${ac_cv_path_install+set}" = set; then
- INSTALL=$ac_cv_path_install
- else
- # As a last resort, use the slow shell script. Don't cache a
- # value for INSTALL within a source directory, because that will
- # break other packages using the cache if that directory is
- # removed, or if the value is a relative name.
- INSTALL=$ac_install_sh
- fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
-$as_echo "$INSTALL" >&6; }
-
-# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
-# It thinks the first close brace ends the variable substitution.
-test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
-
-test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
-
-test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-
-
-
-
-
-
- if test -n "$PYTHON"; then
- # If the user set $PYTHON, use it and don't search something else.
- { $as_echo "$as_me:$LINENO: checking whether $PYTHON version >= 2.4" >&5
-$as_echo_n "checking whether $PYTHON version >= 2.4... " >&6; }
- prog="import sys, string
-# split strings by '.' and convert to numeric. Append some zeros
-# because we need at least 4 digits for the hex conversion.
-minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
-minverhex = 0
-for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
-sys.exit(sys.hexversion < minverhex)"
- if { echo "$as_me:$LINENO: $PYTHON -c "$prog"" >&5
- ($PYTHON -c "$prog") >&5 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- { { $as_echo "$as_me:$LINENO: error: too old" >&5
-$as_echo "$as_me: error: too old" >&2;}
- { (exit 1); exit 1; }; }
-fi
-
- am_display_PYTHON=$PYTHON
- else
- # Otherwise, try each interpreter until we find one that satisfies
- # VERSION.
- { $as_echo "$as_me:$LINENO: checking for a Python interpreter with version >= 2.4" >&5
-$as_echo_n "checking for a Python interpreter with version >= 2.4... " >&6; }
-if test "${am_cv_pathless_PYTHON+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- for am_cv_pathless_PYTHON in python python2 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 python1.6 python1.5 none; do
- test "$am_cv_pathless_PYTHON" = none && break
- prog="import sys, string
-# split strings by '.' and convert to numeric. Append some zeros
-# because we need at least 4 digits for the hex conversion.
-minver = map(int, string.split('2.4', '.')) + [0, 0, 0]
-minverhex = 0
-for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
-sys.exit(sys.hexversion < minverhex)"
- if { echo "$as_me:$LINENO: $am_cv_pathless_PYTHON -c "$prog"" >&5
- ($am_cv_pathless_PYTHON -c "$prog") >&5 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
- break
-fi
-
- done
-fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_pathless_PYTHON" >&5
-$as_echo "$am_cv_pathless_PYTHON" >&6; }
- # Set $PYTHON to the absolute path of $am_cv_pathless_PYTHON.
- if test "$am_cv_pathless_PYTHON" = none; then
- PYTHON=:
- else
- # Extract the first word of "$am_cv_pathless_PYTHON", so it can be a program name with args.
-set dummy $am_cv_pathless_PYTHON; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_path_PYTHON+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- case $PYTHON in
- [\\/]* | ?:[\\/]*)
- ac_cv_path_PYTHON="$PYTHON" # Let the user override the test with a path.
- ;;
- *)
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
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- ac_cv_path_PYTHON="$as_dir/$ac_word$ac_exec_ext"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
-done
-IFS=$as_save_IFS
-
- ;;
-esac
-fi
-PYTHON=$ac_cv_path_PYTHON
-if test -n "$PYTHON"; then
- { $as_echo "$as_me:$LINENO: result: $PYTHON" >&5
-$as_echo "$PYTHON" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
- fi
- am_display_PYTHON=$am_cv_pathless_PYTHON
- fi
-
-
- if test "$PYTHON" = :; then
- { { $as_echo "$as_me:$LINENO: error: no suitable Python interpreter found" >&5
-$as_echo "$as_me: error: no suitable Python interpreter found" >&2;}
- { (exit 1); exit 1; }; }
- else
-
-
- { $as_echo "$as_me:$LINENO: checking for $am_display_PYTHON version" >&5
-$as_echo_n "checking for $am_display_PYTHON version... " >&6; }
-if test "${am_cv_python_version+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- am_cv_python_version=`$PYTHON -c "import sys; print sys.version[:3]"`
-fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_python_version" >&5
-$as_echo "$am_cv_python_version" >&6; }
- PYTHON_VERSION=$am_cv_python_version
-
-
-
- PYTHON_PREFIX='${prefix}'
-
- PYTHON_EXEC_PREFIX='${exec_prefix}'
-
-
-
- { $as_echo "$as_me:$LINENO: checking for $am_display_PYTHON platform" >&5
-$as_echo_n "checking for $am_display_PYTHON platform... " >&6; }
-if test "${am_cv_python_platform+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- am_cv_python_platform=`$PYTHON -c "import sys; print sys.platform"`
-fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_python_platform" >&5
-$as_echo "$am_cv_python_platform" >&6; }
- PYTHON_PLATFORM=$am_cv_python_platform
-
-
-
-
- { $as_echo "$as_me:$LINENO: checking for $am_display_PYTHON script directory" >&5
-$as_echo_n "checking for $am_display_PYTHON script directory... " >&6; }
-if test "${am_cv_python_pythondir+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX')" 2>/dev/null ||
- echo "$PYTHON_PREFIX/lib/python$PYTHON_VERSION/site-packages"`
-fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_python_pythondir" >&5
-$as_echo "$am_cv_python_pythondir" >&6; }
- pythondir=$am_cv_python_pythondir
-
-
-
- pkgpythondir=\${pythondir}/$PACKAGE
-
-
- { $as_echo "$as_me:$LINENO: checking for $am_display_PYTHON extension module directory" >&5
-$as_echo_n "checking for $am_display_PYTHON extension module directory... " >&6; }
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- $as_echo_n "(cached) " >&6
-else
- am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX')" 2>/dev/null ||
- echo "${PYTHON_EXEC_PREFIX}/lib/python${PYTHON_VERSION}/site-packages"`
-fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_python_pyexecdir" >&5
-$as_echo "$am_cv_python_pyexecdir" >&6; }
- pyexecdir=$am_cv_python_pyexecdir
-
-
-
- pkgpyexecdir=\${pyexecdir}/$PACKAGE
-
-
-
- fi
-
-
-
-
-
-# Check whether --with-boost was given.
-if test "${with_boost+set}" = set; then
- withval=$with_boost;
- if test "$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
-
-else
- want_boost="yes"
-fi
-
-
-
-
-# Check whether --with-boost-libdir was given.
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- withval=$with_boost_libdir;
- if test -d $withval
- then
- ac_boost_lib_path="$withval"
- else
- { { $as_echo "$as_me:$LINENO: error: --with-boost-libdir expected directory name" >&5
-$as_echo "$as_me: error: --with-boost-libdir expected directory name" >&2;}
- { (exit 1); exit 1; }; }
- fi
-
-else
- ac_boost_lib_path=""
-
-fi
-
-
-if test "x$want_boost" = "xyes"; then
- boost_lib_version_req=1.47.0
- 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"
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- { $as_echo "$as_me:$LINENO: checking for boostlib >= $boost_lib_version_req" >&5
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- succeeded=no
-
- if test "$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
-
- 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 $BOOST_LDFLAGS"
- export LDFLAGS
-
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
- #include <boost/version.hpp>
-
-int
-main ()
-{
-
- #if BOOST_VERSION >= $WANT_BOOST_VERSION
- // Everything is okay
- #else
- # error Boost version is too old
- #endif
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
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- *) ac_try_echo=$ac_try;;
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
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- } && test -s conftest.$ac_objext; then
-
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- succeeded=yes
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-
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- $as_echo "$as_me: failed program was:" >&5
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-
-
-
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-
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- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
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-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
-
- if test "x$succeeded" != "xyes"; then
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- if test "$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
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- 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
- { $as_echo "$as_me:$LINENO: We will use a staged boost library from $BOOST_ROOT" >&5
-$as_echo "$as_me: We will use a staged boost library from $BOOST_ROOT" >&6;}
- BOOST_CPPFLAGS="-I$BOOST_ROOT"
- BOOST_LDFLAGS="-L$BOOST_ROOT/stage/lib"
- fi
- fi
- fi
- fi
-
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
-
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
- #include <boost/version.hpp>
-
-int
-main ()
-{
-
- #if BOOST_VERSION >= $WANT_BOOST_VERSION
- // Everything is okay
- #else
- # error Boost version is too old
- #endif
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
-
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- succeeded=yes
- found_system=yes
-
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- fi
-
- if test "$succeeded" != "yes" ; then
- if test "$_version" = "0" ; then
- { { $as_echo "$as_me:$LINENO: error: We could not detect the boost libraries (version $boost_lib_version_req_shorten or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation." >&5
-$as_echo "$as_me: 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." >&2;}
- { (exit 1); exit 1; }; }
- else
- { $as_echo "$as_me:$LINENO: Your boost libraries seems to old (version $_version)." >&5
-$as_echo "$as_me: Your boost libraries seems to old (version $_version)." >&6;}
- fi
- else
-
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST /**/
-_ACEOF
-
- fi
-
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
-fi
-
-
-
-
-# Check whether --with-bam was given.
-if test "${with_bam+set}" = set; then
- withval=$with_bam;
- if test "$withval" = "no"; then
- want_bam="no"
- elif test "$withval" = "yes"; then
- want_bam="yes"
- ac_bam_path=""
- else
- want_bam="yes"
- ac_bam_path="$withval"
- fi
-
-else
- want_bam="yes"
-fi
-
-
-
-
-# Check whether --with-bam-libdir was given.
-if test "${with_bam_libdir+set}" = set; then
- withval=$with_bam_libdir;
- if test -d $withval
- then
- ac_bam_lib_path="$withval"
- else
- { { $as_echo "$as_me:$LINENO: error: --with-bam-libdir expected directory name" >&5
-$as_echo "$as_me: error: --with-bam-libdir expected directory name" >&2;}
- { (exit 1); exit 1; }; }
- fi
-
-else
- ac_bam_lib_path=""
-
-fi
-
-
-if test "x$want_bam" = "xyes"; then
-# bam_lib_version_req=ifelse([], ,1.20.0,)
-# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
-# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
-# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
-# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
-# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
-# bam_lib_version_req_sub_minor="0"
-# fi
-# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
- { $as_echo "$as_me:$LINENO: checking for bamlib" >&5
-$as_echo_n "checking for bamlib... " >&6; }
- succeeded=no
-
- if test "$ac_bam_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_path/lib"
- BAM_CPPFLAGS="-I$ac_bam_path/include"
- else
- for ac_bam_path_tmp in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path_tmp/include/bam" && test -r "$ac_bam_path_tmp/include/bam"; then
- BAM_LDFLAGS="-L$ac_bam_path_tmp/lib"
- BAM_CPPFLAGS="-I$ac_bam_path_tmp/include"
- break;
- fi
- done
- fi
-
- if test "$ac_bam_lib_path" != ""; then
- BAM_LDFLAGS="-L$ac_bam_lib_path"
- fi
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
- export LDFLAGS
-
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
- #include <bam/bam.h>
-
-int
-main ()
-{
-
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
-
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- succeeded=yes
- found_system=yes
-
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- if test "x$succeeded" != "xyes"; then
- _version=0
- if test "$ac_bam_path" != ""; then
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- fi
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
- done
- fi
- else
- for ac_bam_path in /usr /usr/local /opt /opt/local ; do
- if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
- for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
- _version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
- V_CHECK=`expr $_version_tmp \> $_version`
- if test "$V_CHECK" = "1" ; then
- _version=$_version_tmp
- best_path=$ac_bam_path
- fi
- done
- fi
- done
-
- VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
- BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
- if test "$ac_bam_lib_path" = ""
- then
- BAM_LDFLAGS="-L$best_path/lib"
- fi
-
- if test "x$BAM_ROOT" != "x"; then
- if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
- version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
- stage_version=`echo $version_dir | sed 's/bam_//' | 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_bam_lib_path" = "" ; then
- { $as_echo "$as_me:$LINENO: We will use a staged bam library from $BAM_ROOT" >&5
-$as_echo "$as_me: We will use a staged bam library from $BAM_ROOT" >&6;}
- BAM_CPPFLAGS="-I$BAM_ROOT"
- BAM_LDFLAGS="-L$BAM_ROOT/stage/lib"
- fi
- fi
- fi
- fi
-
- CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
- export CPPFLAGS
- LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
- export LDFLAGS
-
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
- #include <bam/version.hpp>
-
-int
-main ()
-{
-
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
-
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- succeeded=yes
- found_system=yes
-
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- fi
-
- if test "$succeeded" != "yes" ; then
- if test "$_version" = "0" ; then
- { { $as_echo "$as_me:$LINENO: error: We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation." >&5
-$as_echo "$as_me: error: We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation." >&2;}
- { (exit 1); exit 1; }; }
- else
- { $as_echo "$as_me:$LINENO: Your bam libraries seem too old (version $_version)." >&5
-$as_echo "$as_me: Your bam libraries seem too old (version $_version)." >&6;}
- fi
- else
- BAM_LIB="-lbam"
-
-
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BAM /**/
-_ACEOF
-
- fi
-
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
-fi
-
-
-# Make sure we can run config.sub.
-$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
- { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
-$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
- { (exit 1); exit 1; }; }
-
-{ $as_echo "$as_me:$LINENO: checking build system type" >&5
-$as_echo_n "checking build system type... " >&6; }
-if test "${ac_cv_build+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_build_alias=$build_alias
-test "x$ac_build_alias" = x &&
- ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
-test "x$ac_build_alias" = x &&
- { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
-$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
- { (exit 1); exit 1; }; }
-ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
- { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
-$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
- { (exit 1); exit 1; }; }
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5
-$as_echo "$ac_cv_build" >&6; }
-case $ac_cv_build in
-*-*-*) ;;
-*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
-$as_echo "$as_me: error: invalid value of canonical build" >&2;}
- { (exit 1); exit 1; }; };;
-esac
-build=$ac_cv_build
-ac_save_IFS=$IFS; IFS='-'
-set x $ac_cv_build
-shift
-build_cpu=$1
-build_vendor=$2
-shift; shift
-# Remember, the first character of IFS is used to create $*,
-# except with old shells:
-build_os=$*
-IFS=$ac_save_IFS
-case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
-
-
-
-
-
-# Check whether --with-boost-system was given.
-if test "${with_boost_system+set}" = set; then
- withval=$with_boost_system;
- if test "$withval" = "no"; then
- want_boost="no"
- elif test "$withval" = "yes"; then
- want_boost="yes"
- ax_boost_user_system_lib=""
- ax_booth_user_system_lib=""
- else
- want_boost="yes"
- echo "using $withval"
- ax_boost_user_system_lib="$withval"
- fi
-
-else
- want_boost="yes"
-
-fi
-
-
- if test "x$want_boost" = "xyes"; then
-
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
-
- { $as_echo "$as_me:$LINENO: checking whether the Boost::System library is available" >&5
-$as_echo_n "checking whether the Boost::System library is available... " >&6; }
-if test "${ax_cv_boost_system+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- CXXFLAGS_SAVE=$CXXFLAGS
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <boost/system/system_error.hpp>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_boost_system=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_boost_system=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS=$CXXFLAGS_SAVE
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_boost_system" >&5
-$as_echo "$ax_cv_boost_system" >&6; }
- if test "x$ax_cv_boost_system" = "xyes"; then
-
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST_SYSTEM /**/
-_ACEOF
-
- BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/[^\/]*//'`
-
- LDFLAGS_SAVE=$LDFLAGS
-
- if test "x$ax_boost_user_system_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-$as_echo_n "checking for exit in -l$ax_lib... " >&6; }
-if { as_var=$as_ac_Lib; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
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- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- eval "$as_ac_Lib=yes"
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- eval "$as_ac_Lib=no"
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-
-rm -rf conftest.dSYM
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-ac_res=`eval 'as_val=${'$as_ac_Lib'}
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-$as_echo "$ac_res" >&6; }
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-
- done
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- for libextension in `ls $BOOSTLIBDIR/boost_system*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_system.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-
-/* Override any GCC internal prototype to avoid an error.
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- builtin and then its argument prototype would still apply. */
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-{
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-$as_echo "$ac_try_echo") >&5
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-
- done
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-
- else
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-
- link_system="yes";
-
-
- fi
-
- if test "x$ax_boost_user_system_lib" = "x"; then
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-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-
-/* Override any GCC internal prototype to avoid an error.
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-{
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- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
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-_ACEOF
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-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
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- builtin and then its argument prototype would still apply. */
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-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
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- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
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-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
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- } && test -s conftest$ac_exeext && {
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- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- eval "$as_ac_Lib=no"
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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-LIBS=$ac_check_lib_save_LIBS
-fi
-ac_res=`eval 'as_val=${'$as_ac_Lib'}
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-fi
-
- done
- fi
-
- else
- BOOST_SYSTEM_LIB="$ax_boost_user_system_lib";
-
- link_system="yes";
-
-
- fi
- fi
-
- CPPFLAGS="$CPPFLAGS_SAVED"
- LDFLAGS="$LDFLAGS_SAVED"
- fi
-
-
-
-# Check whether --with-boost-serialization was given.
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- if test "$withval" = "no"; then
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- elif test "$withval" = "yes"; then
- want_boost="yes"
- ax_boost_user_serialization_lib=""
- ax_booth_user_serialization_lib=""
- else
- want_boost="yes"
- echo "using $withval"
- ax_boost_user_serialization_lib="$withval"
- fi
-
-else
- want_boost="yes"
-
-fi
-
-
- if test "x$want_boost" = "xyes"; then
-
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
- export CPPFLAGS
-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
- export LDFLAGS
-
- { $as_echo "$as_me:$LINENO: checking whether the Boost::Serialization library is available" >&5
-$as_echo_n "checking whether the Boost::Serialization library is available... " >&6; }
-if test "${ax_cv_boost_serialization+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
- CXXFLAGS_SAVE=$CXXFLAGS
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <boost/serialization/utility.hpp>
-int
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-{
-
- ;
- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
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-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
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- } && test -s conftest.$ac_objext; then
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-else
- $as_echo "$as_me: failed program was:" >&5
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- ax_cv_boost_serialization=no
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- CXXFLAGS=$CXXFLAGS_SAVE
- ac_ext=c
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-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_boost_serialization" >&5
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-
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST_SERIALIZATION /**/
-_ACEOF
-
- BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/[^\/]*//'`
-
- LDFLAGS_SAVE=$LDFLAGS
-
- if test "x$ax_boost_user_serialization_lib" = "x"; then
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- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
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- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
- ;
- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
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-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
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-
- eval "$as_ac_Lib=no"
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-rm -rf conftest.dSYM
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-LIBS=$ac_check_lib_save_LIBS
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-$as_echo "$ac_res" >&6; }
-as_val=`eval 'as_val=${'$as_ac_Lib'}
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-else
- link_serialization="no"
-fi
-
- done
- if test "x$link_serialization" != "xyes"; then
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- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-$as_echo_n "checking for exit in -l$ax_lib... " >&6; }
-if { as_var=$as_ac_Lib; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- eval "$as_ac_Lib=yes"
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- eval "$as_ac_Lib=no"
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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-LIBS=$ac_check_lib_save_LIBS
-fi
-ac_res=`eval 'as_val=${'$as_ac_Lib'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-as_val=`eval 'as_val=${'$as_ac_Lib'}
- $as_echo "$as_val"'`
- if test "x$as_val" = x""yes; then
- BOOST_SERIALIZATION_LIB="-l$ax_lib"; link_serialization="yes"; break
-else
- link_serialization="no"
-fi
-
- done
- fi
-
- else
- BOOST_SERIALIZATION_LIB="$ax_boost_user_serialization_lib";
-
- link_serialization="yes";
-
-
- fi
-
- if test "x$ax_boost_user_serialization_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_serialization*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_serialization*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_serialization.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
-$as_echo_n "checking for exit in -l$ax_lib... " >&6; }
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- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
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-{
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
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-
- done
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-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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- ac_check_lib_save_LIBS=$LIBS
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-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
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- builtin and then its argument prototype would still apply. */
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-extern "C"
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-{
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- done
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-
- else
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- link_serialization="yes";
-
-
- fi
- fi
-
- CPPFLAGS="$CPPFLAGS_SAVED"
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-
-
-
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- ax_booth_user_system_lib=""
- else
- want_boost="yes"
- echo "using $withval"
- ax_boost_user_thread_lib="$withval"
- fi
-
-else
- want_boost="yes"
-
-fi
-
-
- if test "x$want_boost" = "xyes"; then
-
-
- CPPFLAGS_SAVED="$CPPFLAGS"
- CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
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-
- LDFLAGS_SAVED="$LDFLAGS"
- LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
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-
- { $as_echo "$as_me:$LINENO: checking whether the Boost::Thread library is available" >&5
-$as_echo_n "checking whether the Boost::Thread library is available... " >&6; }
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- ac_ext=cpp
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-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
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- CXXFLAGS_SAVE=$CXXFLAGS
-
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- else
- CXXFLAGS="-pthread $CXXFLAGS"
- fi
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <boost/thread/thread.hpp>
-int
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-{
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- return 0;
- ;
- return 0;
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- } && test -s conftest.$ac_objext; then
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- $as_echo "$as_me: failed program was:" >&5
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-
- ax_cv_boost_thread=no
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- CXXFLAGS=$CXXFLAGS_SAVE
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-
-
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_boost_thread" >&5
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- BOOST_CPPFLAGS="-mthreads $BOOST_CPPFLAGS"
- else
- BOOST_CPPFLAGS="-pthread $BOOST_CPPFLAGS"
- fi
-
-
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BOOST_THREAD /**/
-_ACEOF
-
- BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/[^\/]*//'`
-
- LDFLAGS_SAVE=$LDFLAGS
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- LDFLAGS="-pthread $LDFLAGS"
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- esac
- if test "x$ax_boost_user_thread_lib" = "x"; then
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-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
- ;
- return 0;
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-_ACEOF
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-
- done
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-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
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- return 0;
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-_ACEOF
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-if { (ac_try="$ac_link"
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
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-
- eval "$as_ac_Lib=no"
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-LIBS=$ac_check_lib_save_LIBS
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- link_thread="no"
-fi
-
- done
- fi
-
- else
- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
-
- link_thread="yes";
-
-
- fi
- if test "x$link_thread" = "xno"; then
- { { $as_echo "$as_me:$LINENO: error: Could not link against $ax_lib !" >&5
-$as_echo "$as_me: error: Could not link against $ax_lib !" >&2;}
- { (exit 1); exit 1; }; }
- else
- case "x$build_os" in
- *bsd* )
- BOOST_LDFLAGS="-pthread $BOOST_LDFLAGS"
- break;
- ;;
- esac
-
- fi
-
- if test "x$ax_boost_user_system_lib" = "x"; then
- for libextension in `ls $BOOSTLIBDIR/libboost_system*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_system*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_system.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char exit ();
-int
-main ()
-{
-return exit ();
- ;
- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
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-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
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-
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-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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-LIBS=$ac_check_lib_save_LIBS
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- link_system="no"
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-
- done
- if test "x$link_system" != "xyes"; then
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- ax_lib=${libextension}
- as_ac_Lib=`$as_echo "ac_cv_lib_$ax_lib''_exit" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for exit in -l$ax_lib" >&5
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-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-l$ax_lib $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
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- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-( exit $ac_status )
-ac_cv_header_stdc=no
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
-fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
-$as_echo "$ac_cv_header_stdc" >&6; }
-if test $ac_cv_header_stdc = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define STDC_HEADERS 1
-_ACEOF
-
-fi
-
-# On IRIX 5.3, sys/types and inttypes.h are conflicting.
-
-
-
-
-
-
-
-
-
-for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
- inttypes.h stdint.h unistd.h
-do
-as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-
-#include <$ac_header>
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- eval "$as_ac_Header=yes"
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- eval "$as_ac_Header=no"
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-as_val=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- if test "x$as_val" = x""yes; then
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-
-done
-
-
-#
-# Handle user hints
-#
-{ $as_echo "$as_me:$LINENO: checking if zlib is wanted" >&5
-$as_echo_n "checking if zlib is wanted... " >&6; }
-
-# Check whether --with-zlib was given.
-if test "${with_zlib+set}" = set; then
- withval=$with_zlib; if test "$withval" != no ; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- if test -d "$withval"
- then
- ZLIB_HOME="$withval"
- else
- { $as_echo "$as_me:$LINENO: WARNING: Sorry, $withval does not exist, checking usual places" >&5
-$as_echo "$as_me: WARNING: Sorry, $withval does not exist, checking usual places" >&2;}
- fi
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-fi
-
-
-ZLIB_HOME=/usr/local
-if test ! -f "${ZLIB_HOME}/include/zlib.h"
-then
- ZLIB_HOME=/usr
-fi
-
-#
-# Locate zlib, if wanted
-#
-if test -n "${ZLIB_HOME}"
-then
- ZLIB_OLD_LDFLAGS=$LDFLAGS
- ZLIB_OLD_CPPFLAGS=$LDFLAGS
- LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
- CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
-
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- { $as_echo "$as_me:$LINENO: checking for inflateEnd in -lz" >&5
-$as_echo_n "checking for inflateEnd in -lz... " >&6; }
-if test "${ac_cv_lib_z_inflateEnd+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-lz $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char inflateEnd ();
-int
-main ()
-{
-return inflateEnd ();
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ac_cv_lib_z_inflateEnd=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_lib_z_inflateEnd=no
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_z_inflateEnd" >&5
-$as_echo "$ac_cv_lib_z_inflateEnd" >&6; }
-if test "x$ac_cv_lib_z_inflateEnd" = x""yes; then
- zlib_cv_libz=yes
-else
- zlib_cv_libz=no
-fi
-
- if test "${ac_cv_header_zlib_h+set}" = set; then
- { $as_echo "$as_me:$LINENO: checking for zlib.h" >&5
-$as_echo_n "checking for zlib.h... " >&6; }
-if test "${ac_cv_header_zlib_h+set}" = set; then
- $as_echo_n "(cached) " >&6
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
-$as_echo "$ac_cv_header_zlib_h" >&6; }
-else
- # Is the header compilable?
-{ $as_echo "$as_me:$LINENO: checking zlib.h usability" >&5
-$as_echo_n "checking zlib.h usability... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-#include <zlib.h>
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_header_compiler=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_compiler=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
-$as_echo "$ac_header_compiler" >&6; }
-
-# Is the header present?
-{ $as_echo "$as_me:$LINENO: checking zlib.h presence" >&5
-$as_echo_n "checking zlib.h presence... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <zlib.h>
-_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
- test ! -s conftest.err
- }; then
- ac_header_preproc=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_preproc=no
-fi
-
-rm -f conftest.err conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
-$as_echo "$ac_header_preproc" >&6; }
-
-# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
- yes:no: )
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&5
-$as_echo "$as_me: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: zlib.h: proceeding with the compiler's result" >&2;}
- ac_header_preproc=yes
- ;;
- no:yes:* )
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: present but cannot be compiled" >&5
-$as_echo "$as_me: WARNING: zlib.h: present but cannot be compiled" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: check for missing prerequisite headers?" >&5
-$as_echo "$as_me: WARNING: zlib.h: check for missing prerequisite headers?" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: see the Autoconf documentation" >&5
-$as_echo "$as_me: WARNING: zlib.h: see the Autoconf documentation" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: section \"Present But Cannot Be Compiled\"" >&5
-$as_echo "$as_me: WARNING: zlib.h: section \"Present But Cannot Be Compiled\"" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the preprocessor's result" >&5
-$as_echo "$as_me: WARNING: zlib.h: proceeding with the preprocessor's result" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: zlib.h: in the future, the compiler will take precedence" >&5
-$as_echo "$as_me: WARNING: zlib.h: in the future, the compiler will take precedence" >&2;}
- ( cat <<\_ASBOX
-## ------------------------------ ##
-## Report this to cole at cs.umd.edu ##
-## ------------------------------ ##
-_ASBOX
- ) | sed "s/^/$as_me: WARNING: /" >&2
- ;;
-esac
-{ $as_echo "$as_me:$LINENO: checking for zlib.h" >&5
-$as_echo_n "checking for zlib.h... " >&6; }
-if test "${ac_cv_header_zlib_h+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_cv_header_zlib_h=$ac_header_preproc
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
-$as_echo "$ac_cv_header_zlib_h" >&6; }
-
-fi
-if test "x$ac_cv_header_zlib_h" = x""yes; then
- zlib_cv_zlib_h=yes
-else
- zlib_cv_zlib_h=no
-fi
-
-
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- if test "$zlib_cv_libz" = "yes" -a "$zlib_cv_zlib_h" = "yes"
- then
- #
- # If both library and header were found, use them
- #
-
-{ $as_echo "$as_me:$LINENO: checking for inflateEnd in -lz" >&5
-$as_echo_n "checking for inflateEnd in -lz... " >&6; }
-if test "${ac_cv_lib_z_inflateEnd+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-lz $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char inflateEnd ();
-int
-main ()
-{
-return inflateEnd ();
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ac_cv_lib_z_inflateEnd=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_lib_z_inflateEnd=no
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_z_inflateEnd" >&5
-$as_echo "$ac_cv_lib_z_inflateEnd" >&6; }
-if test "x$ac_cv_lib_z_inflateEnd" = x""yes; then
- cat >>confdefs.h <<_ACEOF
-#define HAVE_LIBZ 1
-_ACEOF
-
- LIBS="-lz $LIBS"
-
-fi
-
- { $as_echo "$as_me:$LINENO: checking zlib in ${ZLIB_HOME}" >&5
-$as_echo_n "checking zlib in ${ZLIB_HOME}... " >&6; }
- { $as_echo "$as_me:$LINENO: result: ok" >&5
-$as_echo "ok" >&6; }
- ZLIB="-lz"
-
- else
- #
- # If either header or library was not found, revert and bomb
- #
- { $as_echo "$as_me:$LINENO: checking zlib in ${ZLIB_HOME}" >&5
-$as_echo_n "checking zlib in ${ZLIB_HOME}... " >&6; }
- LDFLAGS="$ZLIB_OLD_LDFLAGS"
- CPPFLAGS="$ZLIB_OLD_CPPFLAGS"
- { $as_echo "$as_me:$LINENO: result: failed" >&5
-$as_echo "failed" >&6; }
- { { $as_echo "$as_me:$LINENO: error: either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib" >&5
-$as_echo "$as_me: error: either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib" >&2;}
- { (exit 1); exit 1; }; }
- fi
-fi
-
-
-
-
-# Check whether --with-eigen was given.
-if test "${with_eigen+set}" = set; then
- withval=$with_eigen;
-if test "$withval" = "no"; then
-want_eigen="no"
-elif test "$withval" = "yes"; then
-want_eigen="yes"
-ac_eigen_path=""
-else
-want_eigen="yes"
-ac_eigen_path="$withval"
-fi
-
-else
- want_eigen="yes"
-fi
-
-
-if test "x$want_eigen" = "xyes"; then
-{ $as_echo "$as_me:$LINENO: checking for eigenlib" >&5
-$as_echo_n "checking for eigenlib... " >&6; }
-succeeded=no
-
-if test "$ac_eigen_path" != ""; then
-EIGEN_CPPFLAGS="-I$ac_eigen_path/include"
-else
-for ac_eigen_path_tmp in /usr /usr/local /opt /opt/local ; do
-if test -d "$ac_eigen_path_tmp/include/eigen" && test -r "$ac_eigen_path_tmp/include/eigen"; then
-EIGEN_CPPFLAGS="-I$ac_eigen_path_tmp/include"
-break;
-fi
-done
-fi
-
-CPPFLAGS_SAVED="$CPPFLAGS"
-CPPFLAGS="$CPPFLAGS $EIGEN_CPPFLAGS"
-export EIGEN_CPPFLAGS
-
-ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-#include <Eigen/Dense>
-
-int
-main ()
-{
-
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
-
-{ $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-succeeded=yes
-found_system=yes
-
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-CPPFLAGS="$CPPFLAGS $EIGEN_CPPFLAGS"
-export CPPFLAGS
-LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"
-export LDFLAGS
-export EIGEN_CPPFLAGS
-
-if test "$succeeded" == "yes" ; then
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_EIGEN /**/
-_ACEOF
-
-fi
-
-CPPFLAGS="$CPPFLAGS_SAVED"
-LDFLAGS="$LDFLAGS_SAVED"
-fi
-
-
-# Checks for header files.
-
-
-
-for ac_header in stdlib.h string.h unistd.h
-do
-as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
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-{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
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- /* Catch a bug in an HP-UX C compiler. See
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-{
-
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-{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdbool_h" >&5
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-
-
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-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type__Bool" >&5
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-
-
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-
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-
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-
-{ $as_echo "$as_me:$LINENO: checking for inline" >&5
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-{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5
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-
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-{ $as_echo "$as_me:$LINENO: checking for pid_t" >&5
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-$ac_includes_default
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- return 0;
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-_ACEOF
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-
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-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_pid_t" >&5
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-_ACEOF
-
-fi
-
-{ $as_echo "$as_me:$LINENO: checking for size_t" >&5
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_type_size_t=yes
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
-$as_echo "$ac_cv_type_size_t" >&6; }
-if test "x$ac_cv_type_size_t" = x""yes; then
- :
-else
-
-cat >>confdefs.h <<_ACEOF
-#define size_t unsigned int
-_ACEOF
-
-fi
-
-{ $as_echo "$as_me:$LINENO: checking for ptrdiff_t" >&5
-$as_echo_n "checking for ptrdiff_t... " >&6; }
-if test "${ac_cv_type_ptrdiff_t+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_cv_type_ptrdiff_t=no
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof (ptrdiff_t))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof ((ptrdiff_t)))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_type_ptrdiff_t=yes
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_ptrdiff_t" >&5
-$as_echo "$ac_cv_type_ptrdiff_t" >&6; }
-if test "x$ac_cv_type_ptrdiff_t" = x""yes; then
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_PTRDIFF_T 1
-_ACEOF
-
-
-fi
-
-
-
-# Checks for library functions.
-#AC_FUNC_FORK
-#AC_CHECK_FUNCS([floor memmove pow regcomp sqrt strchr strcspn strspn strstr])
-
-# check the platform
-{ $as_echo "$as_me:$LINENO: checking host system type" >&5
-$as_echo_n "checking host system type... " >&6; }
-if test "${ac_cv_host+set}" = set; then
- $as_echo_n "(cached) " >&6
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- if test "x$host_alias" = x; then
- ac_cv_host=$ac_cv_build
-else
- ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
- { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
-$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
- { (exit 1); exit 1; }; }
-fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5
-$as_echo "$ac_cv_host" >&6; }
-case $ac_cv_host in
-*-*-*) ;;
-*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
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- { (exit 1); exit 1; }; };;
-esac
-host=$ac_cv_host
-ac_save_IFS=$IFS; IFS='-'
-set x $ac_cv_host
-shift
-host_cpu=$1
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-# Remember, the first character of IFS is used to create $*,
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-host_os=$*
-IFS=$ac_save_IFS
-case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
-
-
-
-# set CFLAGS and CXXFLAGS
-user_CFLAGS=${CFLAGS}
-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
-ext_CFLAGS=""
-debug_CFLAGS=""
-#echo "${host_cpu}-${host_os}"
-case "${host_cpu}-${host_os}" in
- i*86-*linux*)
- ext_CFLAGS="-march=i686";;
- i*86-darwin*)
- CFLAGS="-m64"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
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-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
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- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
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-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
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- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ext_CFLAGS="-arch x86_64"
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext;;
- *)
- { $as_echo "$as_me:$LINENO: checking if gcc accepts -m64" >&5
-$as_echo_n "checking if gcc accepts -m64... " >&6; }
- CFLAGS="-m64"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ext_CFLAGS="-m64"; { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext;;
-esac
-
-# Check whether --enable-vectorize was given.
-if test "${enable_vectorize+set}" = set; then
- enableval=$enable_vectorize; ext_CFLAGS="${ext_CFLAGS} -ftree-vectorize -msse3 -ffast-math -ftree-vectorizer-verbose=99"
-fi
-
-
-# Check whether --enable-intel64 was given.
-if test "${enable_intel64+set}" = set; then
- enableval=$enable_intel64; ext_CFLAGS="${ext_CFLAGS} -march=nocona"
-fi
-
-
-# Check whether --enable-debug was given.
-if test "${enable_debug+set}" = set; then
- enableval=$enable_debug;
-else
- enable_debug=no
-fi
-
-
-
-# Check whether --enable-optim was given.
-if test "${enable_optim+set}" = set; then
- enableval=$enable_optim; if test "x$enable_optim" = xyes; then enable_optim=3; fi
-else
- enable_optim=3
-fi
-
-
-if test "x$enable_optim" != xno; then
- ext_CFLAGS="$ext_CFLAGS -O$enable_optim"
-fi
-
-
-if test "x$enable_debug" = xyes; then
- debug_CFLAGS="-DDEBUG"
-else
- debug_CFLAGS="-DNDEBUG"
-fi
-
-
-# Check whether --enable-profiling was given.
-if test "${enable_profiling+set}" = set; then
- enableval=$enable_profiling; ext_LDFLAGS="-lprofiler -ltcmalloc"
-fi
-
-
-CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
-CXXFLAGS="$CFLAGS"
-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
-user_LDFLAGS="$LDFLAGS"
-LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
-
-# Checks for structures/functions that can be used to determine system memory
-{ $as_echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5
-$as_echo_n "checking for struct sysinfo.totalram... " >&6; }
-if test "${ac_cv_member_struct_sysinfo_totalram+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <sys/sysinfo.h>
-
-int
-main ()
-{
-static struct sysinfo ac_aggr;
-if (ac_aggr.totalram)
-return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_member_struct_sysinfo_totalram=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <sys/sysinfo.h>
-
-int
-main ()
-{
-static struct sysinfo ac_aggr;
-if (sizeof ac_aggr.totalram)
-return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_member_struct_sysinfo_totalram=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_member_struct_sysinfo_totalram=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_member_struct_sysinfo_totalram" >&5
-$as_echo "$ac_cv_member_struct_sysinfo_totalram" >&6; }
-if test "x$ac_cv_member_struct_sysinfo_totalram" = x""yes; then
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_STRUCT_SYSINFO_TOTALRAM 1
-_ACEOF
-
-
-fi
-
-{ $as_echo "$as_me:$LINENO: checking whether sysctl is declared" >&5
-$as_echo_n "checking whether sysctl is declared... " >&6; }
-if test "${ac_cv_have_decl_sysctl+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <sys/sysctl.h>
-
-int
-main ()
-{
-#ifndef sysctl
- (void) sysctl;
-#endif
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_have_decl_sysctl=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_have_decl_sysctl=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_have_decl_sysctl" >&5
-$as_echo "$ac_cv_have_decl_sysctl" >&6; }
-if test "x$ac_cv_have_decl_sysctl" = x""yes; then
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_SYSCTL 1
-_ACEOF
-
-
-else
- cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_SYSCTL 0
-_ACEOF
-
-
-fi
-{ $as_echo "$as_me:$LINENO: checking whether CTL_HW is declared" >&5
-$as_echo_n "checking whether CTL_HW is declared... " >&6; }
-if test "${ac_cv_have_decl_CTL_HW+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <sys/sysctl.h>
-
-int
-main ()
-{
-#ifndef CTL_HW
- (void) CTL_HW;
-#endif
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_have_decl_CTL_HW=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_have_decl_CTL_HW=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_have_decl_CTL_HW" >&5
-$as_echo "$ac_cv_have_decl_CTL_HW" >&6; }
-if test "x$ac_cv_have_decl_CTL_HW" = x""yes; then
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_CTL_HW 1
-_ACEOF
-
-
-else
- cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_CTL_HW 0
-_ACEOF
-
-
-fi
-{ $as_echo "$as_me:$LINENO: checking whether HW_PHYSMEM is declared" >&5
-$as_echo_n "checking whether HW_PHYSMEM is declared... " >&6; }
-if test "${ac_cv_have_decl_HW_PHYSMEM+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <sys/sysctl.h>
-
-int
-main ()
-{
-#ifndef HW_PHYSMEM
- (void) HW_PHYSMEM;
-#endif
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_have_decl_HW_PHYSMEM=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_have_decl_HW_PHYSMEM=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_have_decl_HW_PHYSMEM" >&5
-$as_echo "$ac_cv_have_decl_HW_PHYSMEM" >&6; }
-if test "x$ac_cv_have_decl_HW_PHYSMEM" = x""yes; then
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_HW_PHYSMEM 1
-_ACEOF
-
-
-else
- cat >>confdefs.h <<_ACEOF
-#define HAVE_DECL_HW_PHYSMEM 0
-_ACEOF
-
-
-fi
-
-
-
-# test to see if srcdir already configured
-if test "`cd $srcdir && pwd`" != "`pwd`" &&
- test -f $srcdir/config.status; then
- { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
-$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
- { (exit 1); exit 1; }; }
-fi
-
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- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
-$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
- { (exit 1); exit 1; }; }; }
- # echo "creating $dirpart/$file"
- echo '# dummy' > "$dirpart/$file"
- done
-done
- ;;
-
- esac
-done # for ac_tag
-
-
-{ (exit 0); exit 0; }
-_ACEOF
-chmod +x $CONFIG_STATUS
-ac_clean_files=$ac_clean_files_save
-
-test $ac_write_fail = 0 ||
- { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5
-$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;}
- { (exit 1); exit 1; }; }
-
-
-# configure is writing to config.log, and then calls config.status.
-# config.status does its own redirection, appending to config.log.
-# Unfortunately, on DOS this fails, as config.log is still kept open
-# by configure, so config.status won't be able to write to it; its
-# output is simply discarded. So we exec the FD to /dev/null,
-# effectively closing config.log, so it can be properly (re)opened and
-# appended to by config.status. When coming back to configure, we
-# need to make the FD available again.
-if test "$no_create" != yes; then
- ac_cs_success=:
- ac_config_status_args=
- test "$silent" = yes &&
- ac_config_status_args="$ac_config_status_args --quiet"
- exec 5>/dev/null
- $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
- exec 5>>config.log
- # Use ||, not &&, to avoid exiting from the if with $? = 1, which
- # would make configure fail if this is the last instruction.
- $ac_cs_success || { (exit 1); exit 1; }
-fi
-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
- { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
-fi
-
-# dump some configuration confirmations
-echo \
-"
--- ${PACKAGE_STRING} Configuration Results --
- C++ compiler: ${CXX} ${CXXFLAGS} ${LDFLAGS}"
-
-if test x"${GCC}" = x"yes" ; then
- gcc_version=`${CC} --version | head -n 1`
- echo " GCC version: ${gcc_version}"
-else
- gcc_version=''
-fi
-
-echo \
-" Host System type: ${host}
- Install prefix: ${prefix}
- Install eprefix: ${exec_prefix}
-
- See config.h for further configuration information.
- Email <${PACKAGE_BUGREPORT}> with questions and bug reports.
-"
-
-if test x"${PYTHON}" = x":" || ! test -x "${PYTHON}"; then
- echo "WARNING! python was not found and is required to run some utility scripts"
- echo " We recommend installing python and pointing configure to the installed location"
-fi
-
diff --git a/make_bin.sh b/make_bin.sh
index fa2a730..32c2e6e 100755
--- a/make_bin.sh
+++ b/make_bin.sh
@@ -10,10 +10,12 @@ echo "packing up $1.tar.gz, using boost in $2, linking against $3 and using BAM
mkdir $1
#make clean
make distclean
-if [[ $(uname) = "Darwin" ]]; then
+if [[ $(uname) = "Darwin" ]]
+then
export CFLAGS="-mmacosx-version-min=10.7 -stdlib=libc++"
export LDFLAGS="-stdlib=libc++"
-elif [[ $(uname -m) = "x86_64" ]]; then
+elif [ $(uname -m) = "x86_64"]
+then
echo "Linking statically on x86_64 (only for gcc 4.5+).."
export LDFLAGS="-static-libgcc -static-libstdc++"
else
diff --git a/src/LICENSE b/src/LICENSE
new file mode 100644
index 0000000..bca5e08
--- /dev/null
+++ b/src/LICENSE
@@ -0,0 +1,18 @@
+
+==================================================================
+ LICENSE
+==================================================================
+
+FSA is licensed under the GNU GPL.
+MAD is licensed under the GNU GPL.
+
+Please see the file COPYING for the text of version 3 of the
+GNU General Public License.
+
+The bundled Java Media Framework 2.1.1e API,
+located in display/JMF-2.1.1e/
+is covered by the
+JavaTM Media Framework (JMF) 2.1.x Binary Code License Agreement.
+
+Please see the file display/JMF-2.1.1e/readme.html for a
+copy of the JavaTM Media Framework (JMF) 2.1.x Binary Code License Agreement.
diff --git a/src/Makefile.in b/src/Makefile.in
deleted file mode 100644
index b20c0fb..0000000
--- a/src/Makefile.in
+++ /dev/null
@@ -1,1624 +0,0 @@
-# Makefile.in generated by automake 1.9.6 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005 Free Software Foundation, Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
- at SET_MAKE@
-
-#include $(top_srcdir)/build-aux/cufflinks.mk
-
-
-
-
-srcdir = @srcdir@
-top_srcdir = @top_srcdir@
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-top_builddir = ..
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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-install_sh_DATA = $(install_sh) -c -m 644
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-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
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- cuffdiff$(EXEEXT) gtf_to_sam$(EXEEXT) compress_gtf$(EXEEXT) \
- gffread$(EXEEXT) cuffquant$(EXEEXT) cuffnorm$(EXEEXT)
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-DIST_COMMON = $(dist_bin_SCRIPTS) $(noinst_HEADERS) \
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- pout.$(OBJEXT) preplot.$(OBJEXT) random.$(OBJEXT) \
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- simul.$(OBJEXT) solve.$(OBJEXT) startlf.$(OBJEXT) \
- strings.$(OBJEXT) vari.$(OBJEXT) wdiag.$(OBJEXT) \
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- $(am__DEPENDENCIES_1)
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-am__depfiles_maybe = depfiles
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-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
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-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
- -o $@
-SOURCES = $(libcufflinks_a_SOURCES) $(libgc_a_SOURCES) \
- $(compress_gtf_SOURCES) $(cuffcompare_SOURCES) \
- $(cuffdiff_SOURCES) $(cufflinks_SOURCES) $(cuffnorm_SOURCES) \
- $(cuffquant_SOURCES) $(gffread_SOURCES) $(gtf_to_sam_SOURCES)
-DIST_SOURCES = $(libcufflinks_a_SOURCES) $(libgc_a_SOURCES) \
- $(compress_gtf_SOURCES) $(cuffcompare_SOURCES) \
- $(cuffdiff_SOURCES) $(cufflinks_SOURCES) $(cuffnorm_SOURCES) \
- $(cuffquant_SOURCES) $(gffread_SOURCES) $(gtf_to_sam_SOURCES)
-HEADERS = $(noinst_HEADERS)
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMDEP_FALSE = @AMDEP_FALSE@
-AMDEP_TRUE = @AMDEP_TRUE@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-BAM_CPPFLAGS = @BAM_CPPFLAGS@
-BAM_LDFLAGS = @BAM_LDFLAGS@
-BAM_LIB = @BAM_LIB@
-BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
-BOOST_LDFLAGS = @BOOST_LDFLAGS@
-BOOST_SERIALIZATION_LIB = @BOOST_SERIALIZATION_LIB@
-BOOST_SYSTEM_LIB = @BOOST_SYSTEM_LIB@
-BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
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-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EIGEN_CPPFLAGS = @EIGEN_CPPFLAGS@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-OBJEXT = @OBJEXT@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
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-PYTHON = @PYTHON@
-PYTHON_EXEC_PREFIX = @PYTHON_EXEC_PREFIX@
-PYTHON_PLATFORM = @PYTHON_PLATFORM@
-PYTHON_PREFIX = @PYTHON_PREFIX@
-PYTHON_VERSION = @PYTHON_VERSION@
-RANLIB = @RANLIB@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-ZLIB = @ZLIB@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
-am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
-am__fastdepCXX_FALSE = @am__fastdepCXX_FALSE@
-am__fastdepCXX_TRUE = @am__fastdepCXX_TRUE@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
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-build = @build@
-build_alias = @build_alias@
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-build_os = @build_os@
-build_vendor = @build_vendor@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
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-pkgpythondir = @pkgpythondir@
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-program_transform_name = @program_transform_name@
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-AM_CPPFLAGS = -I$(top_srcdir)/src
-EXTRA_DIST = \
- $(top_srcdir)/AUTHORS $(top_srcdir)/make_bin.sh
-
-AM_CXXFLAGS =
-# cuffcluster
-# gtf_reads
-noinst_HEADERS = \
- update_check.h \
- biascorrection.h \
- codons.h \
- clustering.h \
- differential.h \
- GArgs.h \
- GBase.h \
- gdna.h \
- GFaSeqGet.h \
- GFastaIndex.h \
- gff.h \
- GHash.hh \
- GVec.hh \
- GList.hh \
- GStr.h \
- assemble.h \
- bundles.h \
- filters.h \
- hits.h \
- tokenize.h \
- scaffolds.h \
- abundances.h \
- genes.h \
- transitive_closure.h \
- transitive_reduction.h \
- gff_utils.h \
- gtf_tracking.h \
- progressbar.h \
- bundles.h \
- scaffold_graph.h \
- matching_merge.h \
- graph_optimize.h \
- jensen_shannon.h \
- sampling.h \
- lemon/maps.h \
- lemon/bin_heap.h \
- lemon/fib_heap.h \
- lemon/bipartite_matching.h \
- lemon/topology.h \
- lemon/bucket_heap.h \
- lemon/smart_graph.h \
- lemon/list_graph.h \
- lemon/error.h \
- lemon/graph_utils.h \
- lemon/bfs.h \
- lemon/dfs.h \
- lemon/math.h \
- lemon/tolerance.h \
- lemon/graph_adaptor.h \
- lemon/concept_check.h \
- lemon/bits/default_map.h \
- lemon/bits/array_map.h \
- lemon/bits/vector_map.h \
- lemon/bits/debug_map.h \
- lemon/bits/map_extender.h \
- lemon/bits/base_extender.h \
- lemon/bits/graph_adaptor_extender.h \
- lemon/bits/graph_extender.h \
- lemon/bits/invalid.h \
- lemon/bits/path_dump.h \
- lemon/bits/traits.h \
- lemon/bits/utility.h \
- lemon/bits/alteration_notifier.h \
- lemon/bits/variant.h \
- lemon/concepts/graph.h \
- lemon/concepts/bpugraph.h \
- lemon/concepts/graph_components.h \
- lemon/concepts/ugraph.h \
- lemon/concepts/heap.h \
- lemon/concepts/maps.h \
- lemon/concepts/path.h \
- lemon/concepts/matrix_maps.h \
- locfit/design.h \
- locfit/lfcons.h \
- locfit/lfstruc.h \
- locfit/local.h \
- locfit/imatlb.h \
- locfit/lffuns.h \
- locfit/lfwin.h \
- locfit/mutil.h \
- locfit/vari.hpp \
- replicates.h \
- multireads.h \
- rounding.h \
- negative_binomial_distribution.h \
- tracking.h \
- common.h
-
-noinst_LIBRARIES = libcufflinks.a libgc.a
-libcufflinks_a_SOURCES = \
- clustering.cpp \
- differential.cpp \
- common.cpp \
- assemble.cpp \
- tokenize.cpp \
- abundances.cpp \
- scaffolds.cpp \
- hits.cpp \
- genes.cpp \
- bundles.cpp \
- filters.cpp \
- scaffold_graph.cpp \
- matching_merge.cpp \
- graph_optimize.cpp \
- biascorrection.cpp \
- sampling.cpp \
- locfit/adap.c \
- locfit/ar_funs.c \
- locfit/arith.c \
- locfit/band.c \
- locfit/c_args.c \
- locfit/c_plot.c \
- locfit/cmd.c \
- locfit/dens_haz.c \
- locfit/dens_int.c \
- locfit/dens_odi.c \
- locfit/density.c \
- locfit/dist.c \
- locfit/ev_atree.c \
- locfit/ev_interp.c \
- locfit/ev_kdtre.c \
- locfit/ev_main.c \
- locfit/ev_trian.c \
- locfit/family.c \
- locfit/fitted.c \
- locfit/frend.c \
- locfit/help.c \
- locfit/lf_dercor.c \
- locfit/lf_fitfun.c \
- locfit/lf_robust.c \
- locfit/lf_vari.c \
- locfit/lfd.c \
- locfit/lfstr.c \
- locfit/linalg.c \
- locfit/locfit.c \
- locfit/m_chol.c \
- locfit/m_eigen.c \
- locfit/m_jacob.c \
- locfit/m_max.c \
- locfit/makecmd.c \
- locfit/math.c \
- locfit/minmax.c \
- locfit/nbhd.c \
- locfit/pcomp.c \
- locfit/pout.c \
- locfit/preplot.c \
- locfit/random.c \
- locfit/readfile.c \
- locfit/scb.c \
- locfit/scb_cons.c \
- locfit/simul.c \
- locfit/solve.c \
- locfit/startlf.c \
- locfit/strings.c \
- locfit/vari.cpp \
- locfit/wdiag.c \
- locfit/weight.c \
- replicates.cpp \
- multireads.cpp \
- jensen_shannon.cpp \
- tracking.cpp
-
-libgc_a_SOURCES = \
- codons.cpp \
- GArgs.cpp \
- GBase.cpp \
- gdna.cpp \
- GStr.cpp \
- GFaSeqGet.cpp \
- GFastaIndex.cpp \
- gff.cpp \
- gff_utils.cpp \
- gtf_tracking.cpp
-
-
-#-- scripts to be installed in $prefix/bin
-dist_bin_SCRIPTS = \
- cuffmerge
-
-CLEANFILES = $(bin_SCRIPTS)
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- if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
- fi; \
- cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
- else \
- test -f $(distdir)/$$file \
- || cp -p $$d/$$file $(distdir)/$$file \
- || exit 1; \
- fi; \
- done
-check-am: all-am
-check: check-am
-all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) $(HEADERS)
-installdirs:
- for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"; do \
- test -z "$$dir" || $(mkdir_p) "$$dir"; \
- done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
- @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
- `test -z '$(STRIP)' || \
- echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
- -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
- -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-
-maintainer-clean-generic:
- @echo "This command is intended for maintainers to use"
- @echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
- mostlyclean-am
-
-distclean: distclean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic \
- distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-exec-am: install-binPROGRAMS install-dist_binSCRIPTS
-
-install-info: install-info-am
-
-install-man:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
- uninstall-info-am
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstLIBRARIES ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am \
- install-dist_binSCRIPTS install-exec install-exec-am \
- install-info install-info-am install-man install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
- uninstall-info-am
-
-
-#gtf_reads_SOURCES = gtf_reads.cpp
-#gtf_reads_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
-#gtf_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS)
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/src/biascorrection.cpp b/src/biascorrection.cpp
index e44a0ae..4a76abc 100644
--- a/src/biascorrection.cpp
+++ b/src/biascorrection.cpp
@@ -107,7 +107,7 @@ void learn_bias(BundleFactory& bundle_factory, BiasLearner& bl, bool progress_ba
{
HitBundle* bundle_ptr = new HitBundle();
- if (!bundle_factory.next_bundle(*bundle_ptr))
+ if (!bundle_factory.next_bundle(*bundle_ptr, false))
{
delete bundle_ptr;
break;
diff --git a/src/bundles.cpp b/src/bundles.cpp
index c9e42d1..b3af130 100644
--- a/src/bundles.cpp
+++ b/src/bundles.cpp
@@ -1147,7 +1147,7 @@ bool BundleFactory::_expand_by_hits(HitBundle& bundle)
return (bundle.right() > initial_right);
}
-bool BundleFactory::next_bundle(HitBundle& bundle)
+bool BundleFactory::next_bundle(HitBundle& bundle, bool cache_bundle)
{
#if ENABLE_THREADS
boost::mutex::scoped_lock lock(_factory_lock);
@@ -1661,7 +1661,7 @@ void inspect_map(boost::shared_ptr<BundleFactory> bundle_factory,
{
HitBundle* bundle_ptr = new HitBundle();
- bool valid_bundle = bundle_factory->next_bundle(*bundle_ptr);
+ bool valid_bundle = bundle_factory->next_bundle(*bundle_ptr, false);
HitBundle& bundle = *bundle_ptr;
if (use_compat_mass) //only count hits that are compatible with ref transcripts
@@ -1993,7 +1993,8 @@ void inspect_map(boost::shared_ptr<BundleFactory> bundle_factory,
rg_props->frag_len_dist(fld);
rg_props->normalized_map_mass(norm_map_mass);
rg_props->total_map_mass(map_mass);
-
+ rg_props->median_transcript_coverage(bundle_factory->median_transcript_coverage());
+
if (show_stats)
{
fprintf(stderr, "> Map Properties:\n");
@@ -2036,12 +2037,12 @@ void inspect_map(boost::shared_ptr<BundleFactory> bundle_factory,
//////////////////////
-bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle& bundle)
+bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle& bundle, bool cache_bundle)
{
#if ENABLE_THREADS
boost::mutex::scoped_lock lock(_factory_lock);
#endif
- bool got_bundle = BundleFactory::next_bundle(bundle);
+ bool got_bundle = BundleFactory::next_bundle(bundle, cache_bundle);
if (got_bundle)
{
RefSequenceTable& rt = ref_table();
@@ -2049,7 +2050,7 @@ bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle& bundle)
char bundle_label_buf[2048];
sprintf(bundle_label_buf, "%s:%d-%d", rt.get_name(bundle.ref_id()), bundle.left(), bundle.right());
- boost::shared_ptr<const AbundanceGroup> ab = _hit_fac->next_locus(bundle.id());
+ boost::shared_ptr<const AbundanceGroup> ab = _hit_fac->next_locus(bundle.id(), cache_bundle);
if (ab)
{
double compatible_mass = _hit_fac->get_compat_mass(bundle_label_buf);
@@ -2059,10 +2060,34 @@ bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle& bundle)
bundle.add_raw_mass(total_mass);
bundle.compatible_mass(compatible_mass);
+ // calculate the depth of coverage for each transcript and store it in the factory
+ // in case we need it later for library size normalization
+ size_t max_FPKM_idx = 0;
+ double max_FPKM = -1;
+ for (size_t i = 0; i < ab->abundances().size(); ++i)
+ {
+ if (max_FPKM < ab->abundances()[i]->FPKM())
+ {
+ max_FPKM = ab->abundances()[i]->FPKM();
+ max_FPKM_idx = i;
+ }
+ }
+
+ if (max_FPKM_idx < ab->abundances().size())
+ {
+ double num_frags = ab->abundances()[max_FPKM_idx]->num_fragments();
+ double length = ab->abundances()[max_FPKM_idx]->effective_length();
+ if (num_frags >= 1 && length != 0)
+ {
+ double coverage = num_frags / length;
+ transcript_coverages.push_back(coverage);
+ }
+ }
+
//fprintf (stderr, "Reconstituting bundle %s (%d) with mass %lf\n", bundle_label_buf, bundle.id(), compatible_mass);
if (bundle.ref_scaffolds().size() != ab->abundances().size())
{
- fprintf (stderr, "Error in file %s: reconstituted expression bundle %s (%d transcripts) does not match GTF (%d transcripts):\n", read_group_properties()->file_path().c_str(), bundle_label_buf, ab->abundances().size(), bundle.ref_scaffolds().size());
+ fprintf (stderr, "Error in file %s: reconstituted expression bundle %s (%lu transcripts) does not match GTF (%d transcripts):\n", read_group_properties()->file_path().c_str(), bundle_label_buf, ab->abundances().size(), bundle.ref_scaffolds().size());
fprintf(stderr, "Reconstituted:\n");
for (size_t i = 0; i < ab->abundances().size(); ++i)
{
diff --git a/src/bundles.h b/src/bundles.h
index c1b5d64..e7caf06 100644
--- a/src/bundles.h
+++ b/src/bundles.h
@@ -227,7 +227,7 @@ public:
return _curr_bundle < num_bundles();
}
- virtual bool next_bundle(HitBundle& bundle_out);
+ virtual bool next_bundle(HitBundle& bundle_out, bool cache_bundle);
bool next_bundle_hit_driven(HitBundle& bundle_out);
bool next_bundle_ref_driven(HitBundle& bundle_out);
bool next_bundle_ref_guided(HitBundle& bundle_out);
@@ -239,7 +239,7 @@ public:
int num_bundles() const { return _num_bundles; }
void num_bundles(int n) { _num_bundles = n; }
- void reset()
+ virtual void reset()
{
#if ENABLE_THREADS
boost::mutex::scoped_lock lock(_factory_lock);
@@ -327,6 +327,8 @@ public:
bool spans_bad_intron(const ReadHit& read);
+ virtual double median_transcript_coverage() { return -1; }
+
private:
bool _expand_by_hits(HitBundle& bundle);
@@ -379,17 +381,34 @@ public:
}
- bool next_bundle(HitBundle& bundle_out);
+ bool next_bundle(HitBundle& bundle_out, bool cache_bundle);
boost::shared_ptr<const AbundanceGroup> get_abundance_for_locus(int locus_id);
void clear_abundance_for_locus(int locus_id);
+ void reset() { BundleFactory::reset(); transcript_coverages.clear(); }
+
+ double median_transcript_coverage() {
+
+ if (transcript_coverages.size() > 0)
+ {
+ size_t median_idx = transcript_coverages.size() * 0.5;
+ return transcript_coverages[median_idx];
+ }
+ else
+ {
+ return 0.0;
+ }
+ }
+
private:
boost::shared_ptr<PrecomputedExpressionHitFactory> _hit_fac;
#if ENABLE_THREADS
boost::mutex _factory_lock;
#endif
+
+ vector<double> transcript_coverages;
};
void identify_bad_splices(const HitBundle& bundle,
diff --git a/src/common.h b/src/common.h
index 08757dd..acdde28 100644
--- a/src/common.h
+++ b/src/common.h
@@ -9,8 +9,14 @@
*
*/
+#include <boost/version.hpp>
+
#ifdef HAVE_CONFIG_H
#include <config.h>
+#else
+#define PACKAGE_VERSION "INTERNAL"
+#define SVN_REVISION "XXX"
+#define BOOST_VERSION 104700
#endif
#include <stdint.h>
@@ -592,6 +598,9 @@ public:
int replicate_num() const { return _replicate_num; }
void replicate_num(int rn) { _replicate_num = rn; }
+ void median_transcript_coverage(double coverage) { _median_coverage = coverage; }
+ double median_transcript_coverage() const { return _median_coverage; }
+
void ref_gtf(const std::string& file_path, const boost::crc_32_type& gtf_crc )
{
_checked_params.ref_gtf_file_path = file_path;
@@ -688,6 +697,7 @@ private:
std::string _condition_name;
std::string _file_path;
int _replicate_num;
+ double _median_coverage;
CheckedParameters _checked_params;
};
diff --git a/src/compress_gtf.cpp b/src/compress_gtf.cpp
index 7660e33..a617a6a 100644
--- a/src/compress_gtf.cpp
+++ b/src/compress_gtf.cpp
@@ -7,12 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#endif
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
diff --git a/src/cuffcluster.cpp b/src/cuffcluster.cpp
new file mode 100644
index 0000000..0df9632
--- /dev/null
+++ b/src/cuffcluster.cpp
@@ -0,0 +1,942 @@
+/*
+ * sorting_hat.cpp
+ * cufflinks
+ *
+ * Created by Cole Trapnell on 8/30/10.
+ * Copyright 2010 Cole Trapnell. All rights reserved.
+ *
+ */
+
+#include <stdlib.h>
+#include <getopt.h>
+#include <string>
+
+#include <boost/numeric/ublas/matrix.hpp>
+#include <boost/numeric/ublas/matrix_proxy.hpp>
+#include <boost/numeric/ublas/vector.hpp>
+#include <boost/numeric/ublas/vector_proxy.hpp>
+#include <boost/numeric/ublas/io.hpp>
+#include <boost/random/linear_congruential.hpp>
+#include <boost/random/uniform_real.hpp>
+#include <boost/random/variate_generator.hpp>
+
+
+#include "common.h"
+#include "tokenize.h"
+
+#include "differential.h"
+
+using namespace std;
+using namespace boost;
+
+bool compute_row_matrix = false;
+bool log_transform_fpkm = false;
+bool output_row_density = false;
+
+int k_clusters = 0;
+int max_iterations = 1000;
+
+string row_matrix_out_filename = "";
+string row_density_out_filename = "";
+
+#if ENABLE_THREADS
+const char *short_options = "o:p:d:P:k:I:l";
+#else
+const char *short_options = "o:d:P:k:I:l";
+#endif
+
+static struct option long_options[] = {
+ {"output-dir", required_argument, 0, 'o'},
+ {"row-matrix", required_argument, 0, 'd'},
+ {"row-densities", required_argument, 0, 'P'},
+ {"log-fpkm", no_argument, 0, 'l'},
+ {"k-means", required_argument, 0, 'k'},
+ {"max-iterations", required_argument, 0, 'I'},
+#if ENABLE_THREADS
+ {"num-threads", required_argument, 0, 'p'},
+#endif
+ {0, 0, 0, 0} // terminator
+};
+
+void print_usage()
+{
+ fprintf(stderr, "sorting_hat v%s (%s)\n", PACKAGE_VERSION, SVN_REVISION);
+ fprintf(stderr, "-----------------------------\n");
+
+ //NOTE: SPACES ONLY, bozo
+ fprintf(stderr, "Usage: cuffdiff [options] <input.fpkm_tracking> <output.shout>\n");
+ fprintf(stderr, "Options:\n\n");
+ fprintf(stderr, "-o/--output-dir write all output files to this directory [ default: ./ ]\n");
+ fprintf(stderr, "-d/--row-matrix compute row distance matrix [ default: off ]\n");
+ fprintf(stderr, "-l/--log-fpkm JS on log(fpkm+1) instead of [ default: off ]\n");
+#if ENABLE_THREADS
+ fprintf(stderr, "-p/--num-threads number of threads used during assembly [ default: 1 ]\n");
+#endif
+}
+
+int parse_options(int argc, char** argv)
+{
+ int option_index = 0;
+ int next_option;
+ do {
+ next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
+ switch (next_option) {
+ case -1: /* Done with options. */
+ break;
+
+ case 'd':
+ {
+ compute_row_matrix = true;
+ row_matrix_out_filename = optarg;
+ break;
+ }
+
+ case 'P':
+ {
+ output_row_density = true;
+ row_density_out_filename = optarg;
+ break;
+ }
+
+ case 'l':
+ {
+ log_transform_fpkm = true;
+ break;
+ }
+
+ case 'k':
+ {
+ k_clusters = (int)parseInt(1, "-k/--k-means arg must be at least 1", print_usage);
+ break;
+ }
+
+ case 'I':
+ {
+ max_iterations = (int)parseInt(1, "-I/--max-iterations arg must be at least 1", print_usage);
+ break;
+ }
+
+ case 'o':
+ {
+ output_dir = optarg;
+ break;
+ }
+
+ default:
+ print_usage();
+ return 1;
+ }
+ } while(next_option != -1);
+
+ allow_junk_filtering = false;
+
+ return 0;
+}
+
+
+struct ExprRecord
+{
+ ExprRecord() :
+ total_FPKM(0.0),
+ total_FPKM_conf_hi(0.0),
+ total_FPKM_conf_lo(0.0),
+ max_FPKM(0.0),
+ total_log_FPKM(std::numeric_limits<double>::infinity()),
+ total_log_FPKM_conf_hi(std::numeric_limits<double>::infinity()),
+ total_log_FPKM_conf_lo(std::numeric_limits<double>::infinity()),
+ max_log_FPKM(std::numeric_limits<double>::infinity()),
+ cluster_id(-1) {}
+
+ string tracking_id;
+ string class_code;
+ string nearest_ref_id;
+ string gene_id;
+ string gene_short_name;
+ string tss_id;
+ string locus;
+
+ string length;
+ string coverage;
+ string status;
+
+ vector<double> FPKMs;
+ vector<double> FPKM_conf_los;
+ vector<double> FPKM_conf_his;
+
+ vector<double> log_FPKMs;
+ vector<double> log_FPKM_conf_los;
+ vector<double> log_FPKM_conf_his;
+
+ double total_FPKM;
+ double total_FPKM_conf_hi;
+ double total_FPKM_conf_lo;
+ double max_FPKM;
+
+ double total_log_FPKM;
+ double total_log_FPKM_conf_hi;
+ double total_log_FPKM_conf_lo;
+ double max_log_FPKM;
+
+ ublas::vector<double> cond_density;
+ vector<double> cond_specificities;
+
+ int cluster_id;
+};
+
+struct ClusterStats
+{
+ ClusterStats(int dim)
+ {
+ mean = ublas::zero_vector<double>(dim);
+ variance = 0.0;
+ }
+
+ ublas::vector<double> mean;
+ double variance;
+ vector<size_t> members;
+};
+
+struct SortByVariance
+{
+ bool operator()(const ClusterStats& lhs, const ClusterStats& rhs)
+ {
+ if (lhs.variance != rhs.variance)
+ return lhs.variance < rhs.variance;
+ else if (lhs.members.size() != rhs.members.size())
+ return lhs.members.size() < rhs.members.size();
+ return false;
+ }
+};
+
+
+void assign_to_nearest_cluster(vector<ExprRecord>& expr_records, vector<ClusterStats>& clusters)
+{
+
+ int num_clusters = clusters.size();
+ int num_conditions = expr_records.front().cond_density.size();
+
+ BOOST_FOREACH(ClusterStats& c, clusters)
+ {
+ c.members.clear();
+ }
+
+ // E step - assign each record to nearest cluster
+ for (size_t r = 0; r < expr_records.size(); ++r)
+ {
+ ExprRecord& rec = expr_records[r];
+
+ // Skip unexpressed records;
+ if (log_transform_fpkm)
+ {
+ if (rec.total_log_FPKM == 0 ||
+ rec.total_log_FPKM == std::numeric_limits<double>::infinity())
+ {
+ continue;
+ }
+ }
+ else
+ {
+ if (rec.total_FPKM == 0)
+ {
+ continue;
+ }
+ }
+
+ double min_dist = std::numeric_limits<double>::max();
+ size_t closest_mean = 0;
+ vector<ublas::vector<double> > kappas;
+
+ kappas.push_back(rec.cond_density);
+ //cerr << rec.cond_density << endl;
+ kappas.push_back(ublas::zero_vector<double>());
+
+ for (size_t m = 0; m < clusters.size(); ++m)
+ {
+ kappas[1] = clusters[m].mean;
+ double js = jensen_shannon_distance(kappas);
+ if (js < min_dist)
+ {
+ closest_mean = m;
+ min_dist = js;
+ }
+ }
+
+ clusters[closest_mean].members.push_back(r);
+ }
+
+ // M step - calculate new means
+
+ vector<ublas::vector<double> > tmp_means(num_clusters,
+ ublas::zero_vector<double>(num_conditions));
+ // Calculate mean
+
+ for (size_t c = 0; c < clusters.size(); ++c)
+ {
+ ClusterStats& cluster = clusters[c];
+ BOOST_FOREACH(int m, cluster.members)
+ {
+ tmp_means[c] += expr_records[m].cond_density;
+ }
+ }
+
+ for (size_t c = 0; c < clusters.size(); ++c)
+ {
+ if (clusters[c].members.size() > 0)
+ {
+ clusters[c].mean = tmp_means[c] / clusters[c].members.size();
+ }
+ }
+
+ // And now the variance
+ for (size_t c = 0; c < clusters.size(); ++c)
+ {
+ ClusterStats& cluster = clusters[c];
+ if (cluster.members.empty())
+ continue;
+
+ vector<ublas::vector<double> > kappas;
+ kappas.push_back(cluster.mean);
+ kappas.push_back(ublas::zero_vector<double>());
+ BOOST_FOREACH (int m, cluster.members)
+ {
+ kappas[1] = expr_records[m].cond_density;
+ double js = jensen_shannon_distance(kappas);
+ cluster.variance += (js * js);
+ }
+
+ cluster.variance /= cluster.members.size();
+ }
+}
+
+void get_assignments(const vector<ClusterStats>& clusters,
+ vector<int>& assignments)
+{
+ BOOST_FOREACH (int& i, assignments)
+ {
+ i = -1;
+ }
+
+ for (size_t c = 0; c < clusters.size(); ++c)
+ {
+ for (size_t r = 0; r < clusters[c].members.size(); ++r)
+ {
+ assignments[clusters[c].members[r]] = c;
+ }
+ }
+}
+
+
+void split_cluster(const vector<ExprRecord>& expr_records,
+ ClusterStats& to_split,
+ vector<ClusterStats>& new_clusters)
+{
+
+ fprintf (stderr, "Splitting cluster...\n");
+
+ int num_conditions = expr_records.front().cond_density.size();
+
+ vector<ublas::vector<double> > kappas;
+ kappas.push_back(to_split.mean);
+
+ vector<double> dist_from_mean;
+
+ for (size_t m = 0; m < to_split.members.size(); ++m)
+ {
+ kappas.push_back(expr_records[to_split.members[m]].cond_density);
+ double js = jensen_shannon_distance(kappas);
+ dist_from_mean.push_back(js);
+ }
+
+ // pick the point farthest from the mean and the point closest.
+
+ double largest_dist = -1.0;
+ size_t farthest_point = 0;
+
+ double smallest_dist = std::numeric_limits<double>::max();
+ size_t closest_point = 0;
+
+ for (size_t i = 0; i < dist_from_mean.size(); ++i)
+ {
+ if (largest_dist > dist_from_mean[i])
+ {
+ largest_dist = dist_from_mean[i];
+ farthest_point = i;
+ }
+
+ if (smallest_dist < dist_from_mean[i])
+ {
+ smallest_dist = dist_from_mean[i];
+ closest_point = i;
+ }
+ }
+
+ vector<ublas::vector<double> > a_kappas;
+ a_kappas.push_back(expr_records[to_split.members[closest_point]].cond_density);
+ a_kappas.push_back(ublas::zero_vector<double>());
+
+ vector<ublas::vector<double> > b_kappas;
+ b_kappas.push_back(expr_records[to_split.members[farthest_point]].cond_density);
+ b_kappas.push_back(ublas::zero_vector<double>());
+
+ ClusterStats a_cluster(num_conditions);
+ ClusterStats b_cluster(num_conditions);
+
+ a_cluster.mean = ublas::zero_vector<double>(num_conditions);
+ b_cluster.mean = ublas::zero_vector<double>(num_conditions);
+
+ for (size_t m = 0; m < to_split.members.size(); ++m)
+ {
+ a_kappas[1] = expr_records[to_split.members[m]].cond_density;
+ double a_js = jensen_shannon_distance(a_kappas);
+
+ b_kappas[1] = expr_records[to_split.members[m]].cond_density;
+ double b_js = jensen_shannon_distance(b_kappas);
+
+ if (a_js < b_js)
+ {
+ a_cluster.members.push_back(to_split.members[m]);
+ a_cluster.mean += expr_records[to_split.members[m]].cond_density;
+ }
+ else
+ {
+ b_cluster.members.push_back(to_split.members[m]);
+ b_cluster.mean += expr_records[to_split.members[m]].cond_density;
+ }
+ }
+
+ a_cluster.mean /= a_cluster.members.size();
+ b_cluster.mean /= b_cluster.members.size();
+
+ // Calculate the variances of the split clusters.
+ a_kappas[0] = a_cluster.mean;
+ b_kappas[0] = b_cluster.mean;
+
+ for (size_t m = 0; m < a_cluster.members.size(); ++m)
+ {
+ a_kappas[1] = expr_records[a_cluster.members[m]].cond_density;
+ double js = jensen_shannon_distance(a_kappas);
+ a_cluster.variance += (js * js);
+ }
+
+ a_cluster.variance /= a_cluster.members.size();
+
+ for (size_t m = 0; m < b_cluster.members.size(); ++m)
+ {
+ b_kappas[1] = expr_records[b_cluster.members[m]].cond_density;
+ double js = jensen_shannon_distance(b_kappas);
+ b_cluster.variance += (js * js);
+ }
+
+ b_cluster.variance /= b_cluster.members.size();
+
+ new_clusters.push_back(a_cluster);
+ new_clusters.push_back(b_cluster);
+}
+
+void kmeans(vector<ExprRecord>& expr_records, int num_clusters, int num_iterations)
+{
+ // generate k random means
+ size_t num_conditions = 0;
+ for (size_t i = 1; i < expr_records.size(); ++i)
+ {
+ if (expr_records[i - 1].FPKMs.size() != expr_records[i].FPKMs.size())
+ {
+ fprintf(stderr, "Error: not all records have the same number of conditions!\n");
+ exit(1);
+ }
+ num_conditions = expr_records[i].FPKMs.size();
+ }
+
+ // This is a typedef for a random number generator.
+ typedef boost::minstd_rand base_generator_type;
+ base_generator_type generator(time(NULL));
+
+ boost::uniform_real<> uni_dist(0,1);
+ boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
+
+ // each mean gets an accumulation vector and a counter. For now,
+ // let's just keep ClusterStats thin and do all this outside the class.
+ vector<ClusterStats> clusters(num_clusters, ClusterStats(num_conditions));
+
+ for (size_t i = 0; i < clusters.size(); ++i)
+ {
+ ClusterStats& c = clusters[i];
+ ublas::vector<double>& mean_i = c.mean;
+
+ for (size_t j = 0; j < mean_i.size(); ++j)
+ {
+ mean_i(j) = uni();
+ }
+ double total = accumulate(mean_i.begin(), mean_i.end(), 0.0);
+ mean_i /= total;
+ //cerr << mean_i << endl;
+ }
+
+ vector<int> assignments(expr_records.size());
+ vector<int> prev_assignments;
+
+ size_t iter = 0;
+ for (;iter < num_iterations; ++iter)
+ {
+ if (iter % 5 == 0)
+ {
+ fprintf(stderr, "Iteration # %d\n", iter);
+ }
+
+ assign_to_nearest_cluster(expr_records, clusters);
+ get_assignments(clusters, assignments);
+
+ sort(clusters.begin(), clusters.end(), SortByVariance());
+
+ vector<ClusterStats> empty_clusters;
+ vector<ClusterStats> full_clusters;
+
+ // Look for empty clusters, and if found split others (in order of
+ // largest variance)
+ for(size_t p = 0; p < clusters.size(); ++p)
+ {
+ const ClusterStats& P = clusters[p];
+ if (P.members.size() == 0) // found empty cluster
+ {
+ empty_clusters.push_back(P);
+ }
+ else
+ {
+ full_clusters.push_back(P);
+ }
+ }
+
+ if (!empty_clusters.empty())
+ {
+ vector<ClusterStats> new_clusters;
+ for (size_t c = 0; c < empty_clusters.size(); ++c)
+ {
+ //size_t full = 0;
+ // split this cluster.
+ ClusterStats to_split = full_clusters.back();
+ full_clusters.pop_back();
+ split_cluster(expr_records, to_split, new_clusters);
+ //get_assignments(clusters, assignments);
+ //prev_assignments = assignments;
+ }
+
+ full_clusters.insert(full_clusters.end(), new_clusters.begin(), new_clusters.end());
+ clusters = full_clusters;
+ get_assignments(clusters, assignments);
+ prev_assignments = assignments;
+ }
+
+ else
+ {
+ if (assignments == prev_assignments)
+ {
+ break;
+ }
+ else
+ {
+ prev_assignments = assignments;
+ }
+
+ }
+ }
+
+ for (size_t a = 0; a < assignments.size(); ++a)
+ {
+ expr_records[a].cluster_id = assignments[a];
+ }
+
+ if (iter == num_iterations)
+ {
+ fprintf(stderr, "Warning: clustering did not converge after %d iterations\n", iter);
+ }
+}
+
+void driver(FILE* fpkm_file, FILE* spec_out, FILE* row_matrix_out, FILE* row_density_out)
+{
+ char buf[10 * 1024];
+
+ vector<string> sample_names;
+
+ int line_num = 1;
+
+ while(fgets(buf, sizeof(buf), fpkm_file))
+ {
+ if (buf[0])
+ {
+ // Chomp the newline
+ char* nl = strrchr(buf, '\n');
+ if (nl) *nl = 0;
+
+ vector<string> tokens;
+ tokenize(buf, "\t", tokens);
+
+ if (tokens.size() < 16)
+ {
+ fprintf(stderr, "Error: FPKM tracking files must have at least 12 columns\n");
+ exit(1);
+ }
+
+ if ((tokens.size() - 10) % 3 != 0)
+ {
+ fprintf(stderr, "Error: FPKM tracking files must have FPKM, FPKM_lo, and FPKM_hi columns for each sample\n");
+ exit(1);
+ }
+
+ static const size_t first_sample_idx = 10;
+
+ for (size_t i = first_sample_idx; i < tokens.size(); i += 3)
+ {
+ string FPKM_label = tokens[i];
+ string::size_type name_end = FPKM_label.rfind("_FPKM");
+ if (name_end == string::npos)
+ {
+ fprintf(stderr, "Error: Malformed FPKM column header %s. Should end in \"_FPKM\".\n", FPKM_label.c_str());
+ exit(1);
+ }
+ string name = FPKM_label.substr(0, name_end);
+ sample_names.push_back(name);
+ }
+
+ break;
+ }
+
+ line_num++;
+ }
+
+ fprintf(spec_out, "tracking_id\tclass_code\tnearest_ref\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage\tstatus\ttotal_FPKM\ttotal_FPKM_lo\ttotal_FPKM_hi\tmax_FPKM\tcluster_id");
+
+ for (size_t i = 0; i < sample_names.size(); ++i)
+ {
+ fprintf(spec_out, "\t%s", sample_names[i].c_str());
+ }
+ fprintf(spec_out, "\n");
+
+ vector<ExprRecord> expr_records;
+
+ while(fgets(buf, sizeof(buf), fpkm_file))
+ {
+ // Chomp the newline
+ char* nl = strrchr(buf, '\n');
+ if (nl) *nl = 0;
+
+ vector<string> tokens;
+ tokenize(buf, "\t", tokens);
+
+ if (((tokens.size() - 10) / 3) != sample_names.size())
+ {
+ fprintf(stderr, "Error: Line %d has %lu columns, should have %lu\n", line_num, tokens.size(), (sample_names.size() * 3) + 6);
+ exit(1);
+ }
+
+ ExprRecord rec;
+
+ rec.tracking_id = tokens[0];
+ rec.class_code = tokens[1];
+ rec.nearest_ref_id = tokens[2];
+ rec.gene_id = tokens[3];
+ rec.gene_short_name = tokens[4];
+ rec.tss_id = tokens[5];
+ rec.locus = tokens[6];
+
+ rec.length = tokens[7];
+ rec.coverage = tokens[8];
+ rec.status = tokens[9];
+
+ static const size_t first_sample_idx = 10;
+
+ size_t num_samples = sample_names.size();
+ ublas::vector<double> u1 = ublas::unit_vector<double>(sample_names.size(), 0);
+ ublas::vector<double> u2 = ublas::unit_vector<double>(sample_names.size(), 1);
+
+ vector<ublas::vector<double> > norm_kappas;
+ norm_kappas.push_back(u1);
+ norm_kappas.push_back(u2);
+
+ double norm_js = jensen_shannon_distance(norm_kappas);
+ double max_FPKM = -1;
+ double max_log_FPKM = -1;
+
+ for (size_t i = first_sample_idx; i < tokens.size() - 2; i += 3)
+ {
+ string FPKM_string = tokens[i];
+ double fpkm = atof(FPKM_string.c_str());
+
+ string FPKM_conf_lo_string = tokens[i+1];
+ double fpkm_conf_lo = atof(FPKM_conf_lo_string.c_str());
+
+ string FPKM_conf_hi_string = tokens[i+2];
+ double fpkm_conf_hi = atof(FPKM_conf_hi_string.c_str());
+
+ double log_fpkm = log10(fpkm + 1.0);
+ double log_fpkm_conf_lo = log10(fpkm_conf_lo + 1.0);
+ double log_fpkm_conf_hi = log10(fpkm_conf_hi + 1.0);
+
+ if (isnan(fpkm) || isnan(fpkm_conf_lo) || isnan(fpkm_conf_hi))
+ {
+ fprintf (stderr, "Warning: gene %s (%s) on line %d has FPKM = NaN\n",
+ rec.tracking_id.c_str(), rec.gene_short_name.c_str(), line_num);
+ fpkm = 0.0;
+ fpkm_conf_lo = 0;
+ fpkm_conf_hi = 0;
+
+ log_fpkm = std::numeric_limits<double>::infinity();
+ log_fpkm_conf_lo = std::numeric_limits<double>::infinity();
+ log_fpkm_conf_hi = std::numeric_limits<double>::infinity();
+ }
+ else
+ {
+ if (log_fpkm > max_log_FPKM)
+ {
+ max_log_FPKM = log_fpkm;
+ }
+
+ if (fpkm > max_FPKM)
+ {
+ max_FPKM = fpkm;
+ }
+ }
+
+ rec.FPKMs.push_back(fpkm);
+ rec.FPKM_conf_los.push_back(fpkm_conf_lo);
+ rec.FPKM_conf_his.push_back(fpkm_conf_hi);
+
+ rec.log_FPKMs.push_back(log_fpkm);
+ rec.log_FPKM_conf_los.push_back(log_fpkm_conf_lo);
+ rec.log_FPKM_conf_his.push_back(log_fpkm_conf_hi);
+ }
+
+ rec.total_FPKM = accumulate(rec.FPKMs.begin(), rec.FPKMs.end(), 0.0);
+ rec.total_FPKM_conf_lo = accumulate(rec.FPKM_conf_los.begin(), rec.FPKM_conf_los.end(), 0.0);
+ rec.total_FPKM_conf_hi = accumulate(rec.FPKM_conf_his.begin(), rec.FPKM_conf_his.end(), 0.0);
+ rec.max_FPKM = max_FPKM;
+
+ rec.total_log_FPKM = accumulate(rec.log_FPKMs.begin(), rec.log_FPKMs.end(), 0.0);
+ rec.total_log_FPKM_conf_lo = accumulate(rec.log_FPKM_conf_los.begin(), rec.log_FPKM_conf_los.end(), 0.0);
+ rec.total_log_FPKM_conf_hi = accumulate(rec.log_FPKM_conf_his.begin(), rec.log_FPKM_conf_his.end(), 0.0);
+ rec.max_log_FPKM = max_log_FPKM;
+
+ assert (!isnan(rec.total_FPKM) && !isinf(rec.total_FPKM));
+
+ rec.cond_density = ublas::vector<double>(sample_names.size());
+ rec.cond_specificities = vector<double>(sample_names.size(), std::numeric_limits<double>::max());
+
+
+ if (rec.total_FPKM == 0.0 || (log_transform_fpkm && (rec.total_log_FPKM == 0.0 || rec.total_log_FPKM == std::numeric_limits<double>::infinity())))
+ {
+ rec.cond_density = ublas::zero_vector<double>(sample_names.size());
+ }
+ else
+ {
+ for (size_t i = 0; i < rec.cond_density.size(); ++i)
+ {
+ if (log_transform_fpkm)
+ {
+
+ rec.cond_density(i) = rec.log_FPKMs[i] / rec.total_log_FPKM;
+ }
+ else
+ {
+ rec.cond_density(i) = rec.FPKMs[i] / rec.total_FPKM;
+ }
+
+
+ }
+
+ //fpkm_dists.push_back(FPKM_dist);
+
+ //cerr << tracking_id << FPKM_dist<< endl;
+
+ const size_t N = sample_names.size();
+
+ assert (N >= 2);
+
+ vector<ublas::vector<double> > kappas;
+ kappas.push_back(rec.cond_density);
+ kappas.push_back(ublas::zero_vector<double>(sample_names.size()));
+
+ for (size_t i = 0; i < sample_names.size(); ++i)
+ {
+ ublas::vector<double> specific_vec = ublas::unit_vector<double>(N, i);
+ kappas[1] = specific_vec;
+
+ double js = jensen_shannon_distance(kappas);
+ js /= norm_js;
+
+ rec.cond_specificities[i] = 1.0 - js;
+ }
+ }
+
+ expr_records.push_back(rec);
+
+ line_num++;
+ }
+
+ if (k_clusters > 0)
+ {
+ kmeans(expr_records, k_clusters, max_iterations);
+ }
+
+
+ for (size_t i = 0; i < expr_records.size(); ++i)
+ {
+ const ExprRecord& rec = expr_records[i];
+
+ char cluster_str[256];
+
+ if (k_clusters == 0)
+ {
+ sprintf(cluster_str, "-");
+ }
+ else
+ {
+ sprintf(cluster_str, "%d", rec.cluster_id);
+ }
+
+ fprintf(spec_out,
+ "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%g\t%g\t%g\t%lg\t%s",
+ rec.tracking_id.c_str(),
+ rec.class_code.c_str(),
+ rec.nearest_ref_id.c_str(),
+ rec.gene_id.c_str(),
+ rec.gene_short_name.c_str(),
+ rec.tss_id.c_str(),
+ rec.locus.c_str(),
+ rec.length.c_str(),
+ rec.coverage.c_str(),
+ rec.status.c_str(),
+ rec.total_FPKM,
+ rec.total_FPKM_conf_lo,
+ rec.total_FPKM_conf_hi,
+ rec.max_FPKM,
+ cluster_str);
+
+ for (size_t i = 0; i < rec.cond_density.size(); ++i)
+ {
+ fprintf(spec_out, "\t%g", rec.cond_specificities[i]);
+ }
+
+ fprintf(spec_out, "\n");
+ }
+
+// if (row_matrix_out)
+// {
+// for (size_t i = 0; i < fpkm_dists.size(); ++i)
+// {
+// const ublas::vector<double>& i_vec = fpkm_dists[i];
+// vector<ublas::vector<double> > kappas;
+// kappas.push_back(i_vec);
+// kappas.push_back(ublas::zero_vector<double>(i_vec.size()));
+// if (i % 100 == 0)
+// {
+// fprintf(stderr, "%lu of %lu (%g percent)\n", i, fpkm_dists.size(), (double)i/(double)fpkm_dists.size());
+// }
+//
+// for(size_t j = 0; j < fpkm_dists.size(); ++j)
+// {
+// const ublas::vector<double>& j_vec = fpkm_dists[j];
+// kappas[1] = j_vec;
+// double i_j_js = jensen_shannon_distance(kappas);
+// if (j == fpkm_dists.size() - 1)
+// {
+// fprintf(row_matrix_out, "%g\n", i_j_js);
+// }
+// else
+// {
+// fprintf(row_matrix_out, "%g\t", i_j_js);
+// }
+//
+// }
+// }
+// }
+//
+ if (row_density_out)
+ {
+ for (size_t i = 0; i < expr_records.size(); ++i)
+ {
+ const ExprRecord& rec = expr_records[i];
+ const ublas::vector<double>& i_vec = rec.cond_density;
+ fprintf(row_density_out, "%s\t", rec.tracking_id.c_str());
+ for (size_t j = 0; j < i_vec.size(); ++j)
+ {
+ if (j == i_vec.size() - 1)
+ {
+ fprintf(row_density_out, "%g\n", i_vec(j));
+ }
+ else
+ {
+ fprintf(row_density_out, "%g\t", i_vec(j));
+ }
+ }
+ }
+ }
+}
+
+int main(int argc, char** argv)
+{
+ int parse_ret = parse_options(argc,argv);
+ if (parse_ret)
+ return parse_ret;
+
+ if(optind >= argc)
+ {
+ print_usage();
+ return 1;
+ }
+
+ string fpkm_filename = argv[optind++];
+
+ if(optind >= argc)
+ {
+ print_usage();
+ return 1;
+ }
+
+ string spec_out_filename = argv[optind++];
+
+
+ FILE* fpkm_file = fopen(fpkm_filename.c_str(), "r");
+ if (!fpkm_file)
+ {
+ fprintf(stderr, "Error: cannot open FPKM tracking file %s for reading\n",
+ fpkm_filename.c_str());
+ exit(1);
+ }
+
+ FILE* spec_out_file = fopen(spec_out_filename.c_str(), "w");
+ if (!spec_out_file)
+ {
+ fprintf(stderr, "Error: cannot open output file %s for writing\n",
+ spec_out_filename.c_str());
+ exit(1);
+ }
+
+ FILE* row_matrix_out = NULL;
+ if (compute_row_matrix)
+ {
+ row_matrix_out = fopen(row_matrix_out_filename.c_str(), "w");
+ if (!row_matrix_out)
+ {
+ fprintf(stderr, "Error: cannot open output file %s for writing\n",
+ row_matrix_out_filename.c_str());
+ exit(1);
+ }
+ }
+
+ FILE* row_density_out = NULL;
+ if (output_row_density)
+ {
+ row_density_out = fopen(row_density_out_filename.c_str(), "w");
+ if (!row_density_out)
+ {
+ fprintf(stderr, "Error: cannot open output file %s for writing\n",
+ row_density_out_filename.c_str());
+ exit(1);
+ }
+ }
+
+ driver(fpkm_file, spec_out_file, row_matrix_out, row_density_out);
+
+ return 0;
+}
+
+
diff --git a/src/cuffcompare.cpp b/src/cuffcompare.cpp
index 0cdfc9a..019b3f5 100644
--- a/src/cuffcompare.cpp
+++ b/src/cuffcompare.cpp
@@ -1,10 +1,3 @@
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#define SVN_REVISION "SVN"
-#endif
-
#include "GArgs.h"
#include <ctype.h>
#include <errno.h>
diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp
index 04c8d6d..4ca3be4 100644
--- a/src/cuffdiff.cpp
+++ b/src/cuffdiff.cpp
@@ -7,14 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#define SVN_REVISION "XXX"
-#endif
-
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
@@ -1013,7 +1005,7 @@ bool quantitate_next_locus(const RefSequenceTable& rt,
locus_thread_pool_lock.unlock();
boost::shared_ptr<HitBundle> pBundle = boost::shared_ptr<HitBundle>(new HitBundle());
- bool non_empty = bundle_factories[i]->next_bundle(*pBundle);
+ bool non_empty = bundle_factories[i]->next_bundle(*pBundle, true);
if (pBundle->compatible_mass() > 0)
{
@@ -1847,7 +1839,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
Tracking tracking;
- test_launcher = boost::shared_ptr<TestLauncher>(new TestLauncher(bundle_factories.size(), contrasts, NULL, &tracking, &p_bar));
+ test_launcher = boost::shared_ptr<TestLauncher>(new TestLauncher(bundle_factories.size(), contrasts, NULL, &tracking, &p_bar, true));
if (model_mle_error || corr_bias || corr_multi) // Only run initial estimation if correcting bias or multi-reads
{
diff --git a/src/cuffdiff_to_gct.py b/src/cuffdiff_to_gct.py
new file mode 100755
index 0000000..c0d6e1e
--- /dev/null
+++ b/src/cuffdiff_to_gct.py
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+# encoding: utf-8
+"""
+cuffdiff_to_gct.py
+
+Created by Cole Trapnell on 2010-08-30.
+Copyright (c) 2010 Cole Trapnell. All rights reserved.
+"""
+
+import sys
+import getopt
+import math
+
+help_message = '''
+This script transforms a Cuffdiff FPKM tracking file to an IGV-compatible GCT expression file
+
+Usage:
+ cuffdiff_to_gct.py <input.fpkm_tracking> <output.gct>
+'''
+
+
+class Usage(Exception):
+ def __init__(self, msg):
+ self.msg = msg
+
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "ho:v", ["help", "output="])
+ except getopt.error, msg:
+ raise Usage(msg)
+
+ # option processing
+ for option, value in opts:
+ if option == "-v":
+ verbose = True
+ if option in ("-h", "--help"):
+ raise Usage(help_message)
+ if option in ("-o", "--output"):
+ output = value
+
+ if len(args) < 2:
+ raise Usage(help_message)
+
+ fpkm_tracking = open(args[0])
+ gct_out = open(args[1], "w")
+
+ num_descriptor_cols = 6
+ sample_names = []
+ while True:
+ h = fpkm_tracking.readline()
+ h = h.strip()
+ if h != "":
+ h_cols = h.split("\t")
+ if len(h_cols) < 12:
+ print >> sys.stderr, "Error: malformed header"
+ sys.exit(1)
+ num_samples = (len(h_cols) - num_descriptor_cols) / 3
+ for i in range(0, num_samples):
+ FPKM_label = h_cols[num_descriptor_cols + (3 * i)]
+ name_end = FPKM_label.rfind("_FPKM")
+ name = FPKM_label[:name_end]
+ sample_names.append(name)
+ break
+
+ #print sample_names
+ expr_records = []
+ for line in fpkm_tracking.readlines():
+ line = line.strip()
+ if line == "":
+ continue
+ cols = line.split("\t")
+ if len(cols) != 6 + (3 * num_samples):
+ print >> sys.stderr, "Error: malformed record"
+ sys.exit(1)
+ expr_strs = []
+ for i in range(0, num_samples):
+ FPKM_string = cols[num_descriptor_cols + (3 * i)]
+ FPKM = float(FPKM_string)
+ if math.isnan(FPKM) or math.isinf(FPKM):
+ FPKM = 0.0
+ FPKM = str(FPKM)
+ expr_strs.append(FPKM)
+ rec = []
+ rec.append(cols[0])
+ desc = "na|@%s|" % cols[5]
+ rec.append(desc)
+ rec.extend(expr_strs)
+ expr_records.append(rec)
+
+ print >> gct_out, "#1.2"
+ print >> gct_out, "%d\t%d" % (len(expr_records), num_samples)
+ print >> gct_out, "NAME\tDescription\t%s" % ("\t".join(sample_names))
+ for rec in expr_records:
+ print >> gct_out, "%s" % "\t".join(rec)
+
+
+ except Usage, err:
+ print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >> sys.stderr, "\t for help use --help"
+ return 2
+
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/cufflinks.cpp b/src/cufflinks.cpp
index e8df03a..8f375db 100644
--- a/src/cufflinks.cpp
+++ b/src/cufflinks.cpp
@@ -7,12 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#endif
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
@@ -1477,7 +1471,7 @@ bool assemble_hits(BundleFactory& bundle_factory, boost::shared_ptr<BiasLearner>
{
HitBundle* bundle_ptr = new HitBundle();
- if (!bundle_factory.next_bundle(*bundle_ptr))
+ if (!bundle_factory.next_bundle(*bundle_ptr, true))
{
delete bundle_ptr;
break;
diff --git a/src/cuffnorm.cpp b/src/cuffnorm.cpp
index e27393e..a4383e2 100644
--- a/src/cuffnorm.cpp
+++ b/src/cuffnorm.cpp
@@ -7,14 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#define SVN_REVISION "XXX"
-#endif
-
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
@@ -317,403 +309,6 @@ int parse_options(int argc, char** argv)
return 0;
}
-void print_FPKM_tracking(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage");
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (first_itr != tracking.end())
- {
- const FPKMTracking& track = first_itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- fprintf(fout, "\t%s_FPKM\t%s_conf_lo\t%s_conf_hi\t%s_status", sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str());
- }
- }
- fprintf(fout, "\n");
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- AbundanceStatus status = NUMERIC_OK;
- BOOST_FOREACH (const FPKMContext& c, fpkms)
- {
- if (c.status == NUMERIC_FAIL)
- status = NUMERIC_FAIL;
- }
-
- string all_gene_ids = cat_strings(track.gene_ids);
- if (all_gene_ids == "")
- all_gene_ids = "-";
-
- string all_gene_names = cat_strings(track.gene_names);
- if (all_gene_names == "")
- all_gene_names = "-";
-
- string all_tss_ids = cat_strings(track.tss_ids);
- if (all_tss_ids == "")
- all_tss_ids = "-";
-
- char length_buff[33] = "-";
- if (track.length)
- sprintf(length_buff, "%d", track.length);
-
- fprintf(fout, "%s\t%c\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
- description.c_str(),
- track.classcode ? track.classcode : '-',
- track.ref_match.c_str(),
- all_gene_ids.c_str(),
- all_gene_names.c_str(),
- all_tss_ids.c_str(),
- track.locus_tag.c_str(),
- length_buff,
- "-");
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- double fpkm = fpkms[i].FPKM;
- //double std_dev = sqrt(fpkms[i].FPKM_variance);
- double fpkm_conf_hi = fpkms[i].FPKM_conf_hi;
- double fpkm_conf_lo = fpkms[i].FPKM_conf_lo;
- const char* status_str = "OK";
-
- if (fpkms[i].status == NUMERIC_OK)
- {
- status_str = "OK";
- }
- else if (fpkms[i].status == NUMERIC_FAIL)
- {
- status_str = "FAIL";
- }
- else if (fpkms[i].status == NUMERIC_LOW_DATA)
- {
- status_str = "LOWDATA";
- }
- else if (fpkms[i].status == NUMERIC_HI_DATA)
- {
- status_str = "HIDATA";
- }
- else
- {
- assert(false);
- }
-
- fprintf(fout, "\t%lg\t%lg\t%lg\t%s", fpkm, fpkm_conf_lo, fpkm_conf_hi, status_str);
- }
-
- fprintf(fout, "\n");
- }
-}
-
-void print_count_tracking(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id");
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (first_itr != tracking.end())
- {
- const FPKMTracking& track = first_itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- fprintf(fout, "\t%s_count\t%s_count_variance\t%s_count_uncertainty_var\t%s_count_dispersion_var\t%s_status", sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str());
- }
- }
- fprintf(fout, "\n");
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- AbundanceStatus status = NUMERIC_OK;
- BOOST_FOREACH (const FPKMContext& c, fpkms)
- {
- if (c.status == NUMERIC_FAIL)
- status = NUMERIC_FAIL;
- }
-
- fprintf(fout, "%s",
- description.c_str());
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- const char* status_str = "OK";
-
- if (fpkms[i].status == NUMERIC_OK)
- {
- status_str = "OK";
- }
- else if (fpkms[i].status == NUMERIC_FAIL)
- {
- status_str = "FAIL";
- }
- else if (fpkms[i].status == NUMERIC_LOW_DATA)
- {
- status_str = "LOWDATA";
- }
- else if (fpkms[i].status == NUMERIC_HI_DATA)
- {
- status_str = "HIDATA";
- }
- else
- {
- assert(false);
- }
-
- double external_counts = fpkms[i].count_mean;
- double external_count_var = fpkms[i].count_var;
- double uncertainty_var = fpkms[i].count_uncertainty_var;
- double dispersion_var = fpkms[i].count_dispersion_var;
- fprintf(fout, "\t%lg\t%lg\t%lg\t%lg\t%s", external_counts, external_count_var, uncertainty_var, dispersion_var, status_str);
- }
-
- fprintf(fout, "\n");
- }
-}
-
-void print_FPKM_simple_table(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id");
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (first_itr != tracking.end())
- {
- const FPKMTracking& track = first_itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
- int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
- fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
- }
- }
- }
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- fprintf(fout, "\n%s", description.c_str());
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (itr != tracking.end())
- {
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- double FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
- fprintf(fout, "\t%lg", FPKM);
- }
- }
- }
- }
-}
-
-void print_count_simple_table(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id");
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (first_itr != tracking.end())
- {
- const FPKMTracking& track = first_itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
- int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
- fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
- }
- }
- }
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- fprintf(fout, "\n%s", description.c_str());
- FPKMTrackingTable::const_iterator first_itr = tracking.begin();
- if (itr != tracking.end())
- {
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- double count = fpkms[i].tracking_info_per_rep[j].count;
- fprintf(fout, "\t%lg", count);
- }
- }
- }
- }
-}
-
-
-
-void print_read_group_tracking(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id\tcondition\treplicate\traw_frags\tinternal_scaled_frags\texternal_scaled_frags\tFPKM\teffective_length\tstatus");
-
- fprintf(fout, "\n");
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- double FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
- double internal_count = fpkms[i].tracking_info_per_rep[j].count;
- double external_count = internal_count / fpkms[i].tracking_info_per_rep[j].rg_props->external_scale_factor();
- double raw_count = internal_count * fpkms[i].tracking_info_per_rep[j].rg_props->internal_scale_factor();
- const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
- AbundanceStatus status = fpkms[i].tracking_info_per_rep[j].status;
-
- int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
-
- const char* status_str = "OK";
-
- if (status == NUMERIC_OK)
- {
- status_str = "OK";
- }
- else if (status == NUMERIC_FAIL)
- {
- status_str = "FAIL";
- }
- else if (status == NUMERIC_LOW_DATA)
- {
- status_str = "LOWDATA";
- }
- else if (status == NUMERIC_HI_DATA)
- {
- status_str = "HIDATA";
- }
- else
- {
- assert(false);
- }
-
- fprintf(fout, "%s\t%s\t%d\t%lg\t%lg\t%lg\t%lg\t%s\t%s\n",
- description.c_str(),
- condition_name.c_str(),
- rep_num,
- raw_count,
- internal_count,
- external_count,
- FPKM,
- "-",
- status_str);
- }
- }
- }
-}
-
-void print_read_group_cuffdiff_info(FILE* fout,
- const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups)
-{
- fprintf(fout, "file\tcondition\treplicate_num\ttotal_mass\tnorm_mass\tinternal_scale\texternal_scale\n");
- for (size_t i = 0; i < all_read_groups.size(); ++i)
- {
- boost::shared_ptr<ReadGroupProperties const> rg_props = all_read_groups[i];
- fprintf(fout, "%s\t%s\t%d\t%Lg\t%Lg\t%lg\t%lg\n",
- rg_props->file_path().c_str(),
- rg_props->condition_name().c_str(),
- rg_props->replicate_num(),
- rg_props->total_map_mass(),
- rg_props->normalized_map_mass(),
- rg_props->internal_scale_factor(),
- rg_props->external_scale_factor());
-
- }
-}
-
-void print_read_group_simple_table_info(FILE* fout,
- const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups)
-{
- //fprintf(fout, "file\tcondition\treplicate_num\ttotal_mass\tnorm_mass\tinternal_scale\texternal_scale\n");
- fprintf(fout, "sample_id\tfile\ttotal_mass\tinternal_scale\texternal_scale\n");
- for (size_t i = 0; i < all_read_groups.size(); ++i)
- {
- boost::shared_ptr<ReadGroupProperties const> rg_props = all_read_groups[i];
- fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\n",
- rg_props->condition_name().c_str(),
- rg_props->replicate_num(),
- rg_props->file_path().c_str(),
- rg_props->total_map_mass(),
- rg_props->internal_scale_factor(),
- rg_props->external_scale_factor());
-
- }
-}
-
-void print_feature_attr_simple_table(FILE* fout,
- const FPKMTrackingTable& tracking)
-{
- fprintf(fout,"tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength");
-
- fprintf(fout, "\n");
- for (FPKMTrackingTable::const_iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- const string& description = itr->first;
- const string& locus_tag = itr->second.locus_tag;
- const string& ref_match = itr->second.ref_match;
- int length = itr->second.length;
- char length_buff[33] = "-";
- if (length)
- sprintf(length_buff, "%d", length);
- const set<string>& gene_names = itr->second.gene_names;
- const set<string>& gene_ids = itr->second.gene_ids;
- const set<string>& tss_ids = itr->second.tss_ids;
- char class_code = itr->second.classcode ? itr->second.classcode : '-';
- string all_gene_names = cat_strings(gene_names);
- if (all_gene_names == "")
- all_gene_names = "-";
- string all_gene_ids = cat_strings(gene_ids);
- if (all_gene_ids == "")
- all_gene_ids = "-";
- string all_tss_ids = cat_strings(tss_ids);
- if (all_tss_ids == "")
- all_tss_ids = "-";
- fprintf(fout, "%s\t%c\t%s\t%s\t%s\t%s\t%s\t%s\n",
- description.c_str(),
- class_code,
- ref_match.c_str(),
- all_gene_ids.c_str(),
- all_gene_names.c_str(),
- all_tss_ids.c_str(),
- locus_tag.c_str(),
- length_buff);
- }
-}
-
-void print_run_info(FILE* fout)
-{
- fprintf(fout, "param\tvalue\n");
- fprintf(fout, "cmd_line\t%s\n", cmd_str.c_str());
- fprintf(fout, "version\t%s\n", PACKAGE_VERSION);
- fprintf(fout, "SVN_revision\t%s\n",SVN_REVISION);
- fprintf(fout, "boost_version\t%d\n", BOOST_VERSION);
-}
-
#if ENABLE_THREADS
boost::mutex inspect_lock;
#endif
@@ -741,7 +336,7 @@ void inspect_map_worker(ReplicatedBundleFactory& fac,
#endif
}
-boost::shared_ptr<TestLauncher> test_launcher;
+boost::shared_ptr<TrackingDataWriter> tracking_data_writer;
bool quantitate_next_locus(const RefSequenceTable& rt,
vector<boost::shared_ptr<ReplicatedBundleFactory> >& bundle_factories,
@@ -770,7 +365,7 @@ bool quantitate_next_locus(const RefSequenceTable& rt,
locus_thread_pool_lock.unlock();
boost::shared_ptr<HitBundle> pBundle = boost::shared_ptr<HitBundle>(new HitBundle());
- bool non_empty = bundle_factories[i]->next_bundle(*pBundle);
+ bool non_empty = bundle_factories[i]->next_bundle(*pBundle, true);
if (pBundle->compatible_mass() > 0)
{
@@ -953,183 +548,6 @@ void print_variability_models(FILE* var_model_out, const vector<boost::shared_pt
}
-void write_output_cuffdiff_format(const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups,
- const Tracking& tracking,
- Outfiles& outfiles)
-{
- // FPKM tracking
-
- FILE* fiso_fpkm_tracking = outfiles.isoform_fpkm_tracking_out;
- fprintf(stderr, "Writing isoform-level FPKM tracking\n");
- print_FPKM_tracking(fiso_fpkm_tracking,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_fpkm_tracking = outfiles.tss_group_fpkm_tracking_out;
- fprintf(stderr, "Writing TSS group-level FPKM tracking\n");
- print_FPKM_tracking(ftss_fpkm_tracking,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_fpkm_tracking = outfiles.gene_fpkm_tracking_out;
- fprintf(stderr, "Writing gene-level FPKM tracking\n");
- print_FPKM_tracking(fgene_fpkm_tracking,tracking.gene_fpkm_tracking);
-
- FILE* fcds_fpkm_tracking = outfiles.cds_fpkm_tracking_out;
- fprintf(stderr, "Writing CDS-level FPKM tracking\n");
- print_FPKM_tracking(fcds_fpkm_tracking,tracking.cds_fpkm_tracking);
-
- // Count tracking
-
- FILE* fiso_count_tracking = outfiles.isoform_count_tracking_out;
- fprintf(stderr, "Writing isoform-level count tracking\n");
- print_count_tracking(fiso_count_tracking,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_count_tracking = outfiles.tss_group_count_tracking_out;
- fprintf(stderr, "Writing TSS group-level count tracking\n");
- print_count_tracking(ftss_count_tracking,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_count_tracking = outfiles.gene_count_tracking_out;
- fprintf(stderr, "Writing gene-level count tracking\n");
- print_count_tracking(fgene_count_tracking,tracking.gene_fpkm_tracking);
-
- FILE* fcds_count_tracking = outfiles.cds_count_tracking_out;
- fprintf(stderr, "Writing CDS-level count tracking\n");
- print_count_tracking(fcds_count_tracking,tracking.cds_fpkm_tracking);
-
- // Read group tracking
-
- FILE* fiso_rep_tracking = outfiles.isoform_rep_tracking_out;
- fprintf(stderr, "Writing isoform-level read group tracking\n");
- print_read_group_tracking(fiso_rep_tracking,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_rep_tracking = outfiles.tss_group_rep_tracking_out;
- fprintf(stderr, "Writing TSS group-level read group tracking\n");
- print_read_group_tracking(ftss_rep_tracking,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_rep_tracking = outfiles.gene_rep_tracking_out;
- fprintf(stderr, "Writing gene-level read group tracking\n");
- print_read_group_tracking(fgene_rep_tracking,tracking.gene_fpkm_tracking);
-
- FILE* fcds_rep_tracking = outfiles.cds_rep_tracking_out;
- fprintf(stderr, "Writing CDS-level read group tracking\n");
- print_read_group_tracking(fcds_rep_tracking,tracking.cds_fpkm_tracking);
-
- FILE* fread_group_info = outfiles.read_group_info_out;
- fprintf(stderr, "Writing read group info\n");
- print_read_group_cuffdiff_info(fread_group_info,all_read_groups);
-
- FILE* frun_info = outfiles.run_info_out;
- fprintf(stderr, "Writing run info\n");
- print_run_info(frun_info);
-
-}
-
-void write_output_simple_table_format(const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups,
- const Tracking& tracking,
- Outfiles& outfiles)
-{
- // FPKM tracking
-
- FILE* fiso_fpkm_tracking = outfiles.isoform_fpkm_tracking_out;
- fprintf(stderr, "Writing isoform-level FPKM tracking\n");
- print_FPKM_simple_table(fiso_fpkm_tracking,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_fpkm_tracking = outfiles.tss_group_fpkm_tracking_out;
- fprintf(stderr, "Writing TSS group-level FPKM tracking\n");
- print_FPKM_simple_table(ftss_fpkm_tracking,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_fpkm_tracking = outfiles.gene_fpkm_tracking_out;
- fprintf(stderr, "Writing gene-level FPKM tracking\n");
- print_FPKM_simple_table(fgene_fpkm_tracking,tracking.gene_fpkm_tracking);
-
- FILE* fcds_fpkm_tracking = outfiles.cds_fpkm_tracking_out;
- fprintf(stderr, "Writing CDS-level FPKM tracking\n");
- print_FPKM_simple_table(fcds_fpkm_tracking,tracking.cds_fpkm_tracking);
-
- // Count tracking
-
- FILE* fiso_count_tracking = outfiles.isoform_count_tracking_out;
- fprintf(stderr, "Writing isoform-level count tracking\n");
- print_count_simple_table(fiso_count_tracking,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_count_tracking = outfiles.tss_group_count_tracking_out;
- fprintf(stderr, "Writing TSS group-level count tracking\n");
- print_count_simple_table(ftss_count_tracking,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_count_tracking = outfiles.gene_count_tracking_out;
- fprintf(stderr, "Writing gene-level count tracking\n");
- print_count_simple_table(fgene_count_tracking,tracking.gene_fpkm_tracking);
-
- FILE* fcds_count_tracking = outfiles.cds_count_tracking_out;
- fprintf(stderr, "Writing CDS-level count tracking\n");
- print_count_simple_table(fcds_count_tracking,tracking.cds_fpkm_tracking);
-
- FILE* fiso_attr = outfiles.isoform_attr_out;
- fprintf(stderr, "Writing isoform-level attributes\n");
- print_feature_attr_simple_table(fiso_attr,tracking.isoform_fpkm_tracking);
-
- FILE* ftss_attr = outfiles.tss_group_attr_out;
- fprintf(stderr, "Writing TSS group-level attributes\n");
- print_feature_attr_simple_table(ftss_attr,tracking.tss_group_fpkm_tracking);
-
- FILE* fgene_attr = outfiles.gene_attr_out;
- fprintf(stderr, "Writing gene-level attributes\n");
- print_feature_attr_simple_table(fgene_attr,tracking.gene_fpkm_tracking);
-
- FILE* fcds_attr = outfiles.cds_attr_out;
- fprintf(stderr, "Writing CDS-level attributes\n");
- print_feature_attr_simple_table(fcds_attr,tracking.cds_fpkm_tracking);
-
- FILE* fread_group_info = outfiles.read_group_info_out;
- fprintf(stderr, "Writing read group info\n");
- print_read_group_simple_table_info(fread_group_info,all_read_groups);
-
- FILE* frun_info = outfiles.run_info_out;
- fprintf(stderr, "Writing run info\n");
- print_run_info(frun_info);
-
-}
-
-void write_output(const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups,
- const Tracking& tracking,
- Outfiles& outfiles)
-{
- if (output_format == CUFFDIFF_OUTPUT_FMT)
- {
- write_output_cuffdiff_format(all_read_groups, tracking, outfiles);
- }
- else if (output_format == SIMPLE_TABLE_OUTPUT_FMT)
- {
- write_output_simple_table_format(all_read_groups, tracking, outfiles);
- }
- else{
- fprintf(stderr, "Error: unrecognized output format!\n");
- exit(1);
- }
-}
-
-void adjust_fpkms_by_median_coverage(const vector<vector<double > >& median_coverage,
- FPKMTrackingTable& tracking)
-{
- for (FPKMTrackingTable::iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
- {
- if (itr != tracking.end())
- {
- FPKMTracking& track = itr->second;
- vector<FPKMContext>& fpkms = track.fpkm_series;
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- double& FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
- FPKM /= median_coverage[i][j];
- FPKM *= fpkms[i].tracking_info_per_rep[j].rg_props->normalized_map_mass();
- FPKM /= 1000000000;
- }
- }
- }
- }
-}
-
void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_standards_file, vector<string>& sam_hit_filename_lists, Outfiles& outfiles)
{
@@ -1315,48 +733,15 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
Tracking tracking;
- test_launcher = boost::shared_ptr<TestLauncher>(new TestLauncher(bundle_factories.size(), contrasts, NULL, &tracking, &p_bar));
-
- // Allow the multiread tables to do their thing...
- BOOST_FOREACH (boost::shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
- {
- rg_props->multi_read_table()->valid_mass(true);
- }
-
- test_launcher->clear_tracking_data();
-
- Tests tests;
-
- int N = (int)sam_hit_filename_lists.size();
-
- tests.isoform_de_tests = vector<vector<SampleDiffs> >(N);
- tests.tss_group_de_tests = vector<vector<SampleDiffs> >(N);
- tests.gene_de_tests = vector<vector<SampleDiffs> >(N);
- tests.cds_de_tests = vector<vector<SampleDiffs> >(N);
- tests.diff_splicing_tests = vector<vector<SampleDiffs> >(N);
- tests.diff_promoter_tests = vector<vector<SampleDiffs> >(N);
- tests.diff_cds_tests = vector<vector<SampleDiffs> >(N);
-
- for (int i = 1; i < N; ++i)
- {
- tests.isoform_de_tests[i] = vector<SampleDiffs>(i);
- tests.tss_group_de_tests[i] = vector<SampleDiffs>(i);
- tests.gene_de_tests[i] = vector<SampleDiffs>(i);
- tests.cds_de_tests[i] = vector<SampleDiffs>(i);
- tests.diff_splicing_tests[i] = vector<SampleDiffs>(i);
- tests.diff_promoter_tests[i] = vector<SampleDiffs>(i);
- tests.diff_cds_tests[i] = vector<SampleDiffs>(i);
- }
-
final_est_run = true;
p_bar = ProgressBar("Normalizing expression levels for locus", num_bundles);
- test_launcher = boost::shared_ptr<TestLauncher>(new TestLauncher(bundle_factories.size(), contrasts, &tests, &tracking, &p_bar));
-
+ tracking_data_writer = boost::shared_ptr<TrackingDataWriter>(new TrackingDataWriter(bundle_factories.size(), &outfiles, &tracking, all_read_groups, sample_labels, &p_bar));
+
while (true)
{
//boost::shared_ptr<vector<boost::shared_ptr<SampleAbundances> > > abundances(new vector<boost::shared_ptr<SampleAbundances> >());
- quantitate_next_locus(rt, bundle_factories, test_launcher);
+ quantitate_next_locus(rt, bundle_factories, tracking_data_writer);
bool more_loci_remain = false;
BOOST_FOREACH (boost::shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
{
@@ -1391,82 +776,6 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
p_bar.complete();
- // If we're using estimated absolute quantification, fly through the FPKMs and adjust them
- if (lib_norm_method == ESTIMATED_ABSOLUTE)
- {
- vector<vector<vector<double > > > coverages;
- vector<vector<double> > median_coverages;
-
- FPKMTrackingTable::const_iterator first_itr = tracking.isoform_fpkm_tracking.begin();
- if (first_itr != tracking.isoform_fpkm_tracking.end())
- {
- size_t num_conditions = first_itr->second.fpkm_series.size();
- coverages = vector<vector<vector<double > > > (num_conditions);
- median_coverages = vector<vector<double > >(num_conditions);
-
- for (size_t i = 0; i < num_conditions; ++i)
- {
- const vector<FPKMContext>& fpkms = first_itr->second.fpkm_series;
- size_t num_reps = fpkms[i].tracking_info_per_rep.size();
- coverages[i] = vector<vector<double> >(num_reps);
- median_coverages[i] = vector<double>(num_reps);
- }
-
- for (FPKMTrackingTable::const_iterator itr = tracking.isoform_fpkm_tracking.begin();
- itr != tracking.isoform_fpkm_tracking.end(); ++itr)
- {
- const FPKMTracking& track = itr->second;
- const vector<FPKMContext>& fpkms = track.fpkm_series;
-
- for (size_t i = 0; i < fpkms.size(); ++i)
- {
- for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
- ++j)
- {
- //double FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
- double count = fpkms[i].tracking_info_per_rep[j].count;
- double coverage = count/track.length; // FIXME: this should be effective length, not length.
- if (count >= 1)
- {
- coverages[i][j].push_back(coverage);
- }
- }
- }
- }
-
- for (size_t i = 0; i < coverages.size(); ++i)
- {
- for (size_t j = 0; j < coverages[i].size(); ++j)
- {
- vector<double>& cvgs = coverages[i][j];
- sort(cvgs.begin(), cvgs.end());
- if (cvgs.empty() == false)
- {
- int median_cvgs_idx = cvgs.size() * 0.5;
- double median_coverage = coverages[i][j][median_cvgs_idx];
- median_coverages[i][j] = median_coverage;
- }
- else
- {
- assert(false);
- median_coverages[i][j] = 1;
- }
- }
- }
- }
-
-
- adjust_fpkms_by_median_coverage(median_coverages, tracking.isoform_fpkm_tracking);
-
- adjust_fpkms_by_median_coverage(median_coverages, tracking.tss_group_fpkm_tracking);
-
- adjust_fpkms_by_median_coverage(median_coverages, tracking.gene_fpkm_tracking);
-
- adjust_fpkms_by_median_coverage(median_coverages, tracking.cds_fpkm_tracking);
- }
-
-
- write_output(all_read_groups, tracking, outfiles);
}
void open_outfiles_for_writing_cuffdiff_format(Outfiles& outfiles)
diff --git a/src/cuffquant.cpp b/src/cuffquant.cpp
index f13a395..2634e98 100644
--- a/src/cuffquant.cpp
+++ b/src/cuffquant.cpp
@@ -7,14 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#define SVN_REVISION "XXX"
-#endif
-
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
@@ -855,7 +847,7 @@ void sample_worker(const RefSequenceTable& rt,
#endif
boost::shared_ptr<HitBundle> bundle(new HitBundle);
- bool non_empty = sample_factory.next_bundle(*bundle);
+ bool non_empty = sample_factory.next_bundle(*bundle, true);
char bundle_label_buf[2048];
sprintf(bundle_label_buf,
diff --git a/src/differential.cpp b/src/differential.cpp
index d6eae35..5f84c8a 100644
--- a/src/differential.cpp
+++ b/src/differential.cpp
@@ -141,8 +141,6 @@ void TestLauncher::perform_testing(vector<boost::shared_ptr<SampleAbundances> >
test_differential(abundances.front()->locus_tag, abundances, _contrasts, *_tests, *_tracking);
}
-// Note: this routine should be called under lock - it doesn't
-// acquire the lock itself.
void TestLauncher::record_tracking_data(vector<boost::shared_ptr<SampleAbundances> >& abundances)
{
assert (abundances.size() == _orig_workers);
@@ -206,7 +204,7 @@ void TestLauncher::record_tracking_data(vector<boost::shared_ptr<SampleAbundance
}
-void TestLauncher::test_finished_loci()
+vector<vector<boost::shared_ptr<SampleAbundances> > > TestLauncher::test_finished_loci()
{
#if ENABLE_THREADS
_launcher_lock.lock();
@@ -219,28 +217,14 @@ void TestLauncher::test_finished_loci()
{
if (all_samples_reported_in(itr->second))
{
- // In some abundance runs, we don't actually want to perform testing
- // (eg initial quantification before bias correction).
- // _tests and _tracking will be NULL in these cases.
- if (_tests != NULL && _tracking != NULL)
- {
- if (_p_bar)
- {
- verbose_msg("Estimating expression in locus [%s]\n", itr->second.front()->locus_tag.c_str());
- _p_bar->update(itr->second.front()->locus_tag.c_str(), 1);
- }
- record_tracking_data(itr->second);
- samples_for_testing.push_back(itr->second);
- }
- else
+ if (_p_bar)
{
- if (_p_bar)
- {
- //verbose_msg("Testing for differential expression and regulation in locus [%s]\n", abundances.front()->locus_tag.c_str());
- _p_bar->update(itr->second.front()->locus_tag.c_str(), 1);
- }
- record_tracking_data(itr->second);
+ //verbose_msg("Estimating expression in locus [%s]\n", itr->second.front()->locus_tag.c_str());
+ _p_bar->update(itr->second.front()->locus_tag.c_str(), 1);
}
+ record_tracking_data(itr->second);
+ if (!_track_only)
+ samples_for_testing.push_back(itr->second);
// Removes the samples that have already been tested and transferred to the tracking tables,
itr = _samples.erase(itr);
@@ -255,112 +239,12 @@ void TestLauncher::test_finished_loci()
#if ENABLE_THREADS
_launcher_lock.unlock();
#endif
-
- for (size_t i = 0; i < samples_for_testing.size(); ++i)
- {
- vector<boost::shared_ptr<SampleAbundances> > samples_i = samples_for_testing[i];
- perform_testing(samples_i);
- }
-}
-
-long double wrapped_lgamma(double gamma_k)
-{
- long double lgamma_k = 1;
- try
- {
- lgamma_k = boost::math::lgamma<long double>(gamma_k);
- }
- catch (boost::exception_detail::error_info_injector<std::overflow_error>& e)
- {
- lgamma_k = numeric_limits<long double>::max();
- }
- catch (boost::exception_detail::error_info_injector<std::underflow_error>& e)
- {
- lgamma_k = numeric_limits<long double>::max();
- }
- catch (boost::exception_detail::error_info_injector<std::domain_error>& e)
- {
- lgamma_k = numeric_limits<long double>::max();
- }
- return lgamma_k;
-}
-
-struct TruncNormalMoments
-{
- double m1;
- double m2;
- double m3;
-};
-
-void calculate_sample_moments(const vector<double>& samples, TruncNormalMoments& moments)
-{
- double m1 = accumulate(samples.begin(), samples.end(), 0.0);
- if (samples.size())
- m1 /= samples.size();
-
- double m2 = 0.0;
- for (size_t i = 0; i < samples.size(); ++i)
- {
- m2 += samples[i]*samples[i];
- }
- if (samples.size())
- m2 /= samples.size();
-
- double m3 = 0.0;
- for (size_t i = 0; i < samples.size(); ++i)
- {
- m3 += samples[i]*samples[i]*samples[i];
- }
- if (samples.size())
- m3 /= samples.size();
-
- moments.m1 = m1;
- moments.m2 = m2;
- moments.m3 = m3;
-}
-
-// Estimate the location and scale parameters for the normal distribution
-// that's truncated at zero.
-void estimate_trunc_normal_params(const TruncNormalMoments& m, double& location, double& scale)
-{
- double denom = 2.0*m.m1*m.m1 - m.m2;
- if (denom > 0)
- {
- location = (2.0*m.m1*m.m2 - m.m3)/denom;
- scale = (m.m1*m.m3 - m.m2*m.m2)/denom;
- }
- else
- {
- location = 0;
- scale = 0;
- }
-
-}
-
-long double trunc_normal_log_likelihood(const vector<double>& samples, double mean, double variance)
-{
- boost::math::normal norm; //standard normal
-
- if (mean < 0 || variance <= 0.0)
- return 0;
-
- double denom_sigma = 1.0/sqrt(variance);
-
- long double log_likelihood = 0.0;
- for (size_t i = 0; i < samples.size(); ++i)
- {
- long double sL = 0.0;
- sL = denom_sigma * pdf(norm, (samples[i] - mean) * denom_sigma);
- double sL_denom = (1.0 - cdf(norm, (0.0 - mean) * denom_sigma));
- if (sL_denom != 0)
- sL /= sL_denom;
- else
- sL = 0.0;
-
- sL = logl(sL);
- log_likelihood += sL;
- }
- return log_likelihood;
+ return samples_for_testing;
+// for (size_t i = 0; i < samples_for_testing.size(); ++i)
+// {
+// vector<boost::shared_ptr<SampleAbundances> > samples_i = samples_for_testing[i];
+// perform_testing(samples_i);
+// }
}
//// Sampling-based test:
@@ -1017,7 +901,8 @@ void sample_worker(bool non_empty,
// the testing functor, which will check to see if all the workers
// are done, and if so, perform the cross sample testing.
launcher->abundance_avail(locus_tag, abundance, factory_id);
- launcher->test_finished_loci();
+ vector<vector<boost::shared_ptr<SampleAbundances> > > to_be_tested = launcher->test_finished_loci();
+ launcher->perform_testing(to_be_tested);
//launcher();
#endif
return;
@@ -1099,8 +984,11 @@ void sample_worker(bool non_empty,
}
launcher->abundance_avail(locus_tag, abundance, factory_id);
- launcher->test_finished_loci();
+ vector<vector<boost::shared_ptr<SampleAbundances> > > to_be_tested = launcher->test_finished_loci();
+ for (size_t i = 0; i < to_be_tested.size(); ++i)
+ launcher->perform_testing(to_be_tested[i]);
+
#if !ENABLE_THREADS
// If Cuffdiff was built without threads, we need to manually invoke
// the testing functor, which will check to see if all the workers
@@ -1703,3 +1591,22 @@ void validate_cross_sample_parameters(const vector<boost::shared_ptr<ReadGroupPr
print_checked_params_table(all_read_groups);
}
+void TrackingDataWriter::perform_testing(vector<boost::shared_ptr<SampleAbundances> > abundances)
+{
+#if ENABLE_THREADS
+ test_storage_lock.lock();
+#endif
+ if (headers_written == false)
+ {
+ write_header_output();
+ headers_written = true;
+ }
+
+ write_output(abundances);
+ //test_differential(abundances.front()->locus_tag, abundances, _contrasts, *_tests, *_tracking);
+#if ENABLE_THREADS
+ test_storage_lock.unlock();
+#endif
+
+}
+
diff --git a/src/differential.h b/src/differential.h
index fbd5193..ef80094 100644
--- a/src/differential.h
+++ b/src/differential.h
@@ -137,6 +137,10 @@ struct Tests
extern boost::mutex _launcher_lock;
#endif
+#if ENABLE_THREADS
+extern boost::mutex test_storage_lock;
+#endif
+
struct TestLauncher
{
private:
@@ -147,13 +151,15 @@ public:
const vector<pair<size_t, size_t> >& contrasts,
Tests* tests,
Tracking* tracking,
- ProgressBar* p_bar)
+ ProgressBar* p_bar,
+ bool track_only = false)
:
_orig_workers(num_samples),
_contrasts(contrasts),
_tests(tests),
_tracking(tracking),
- _p_bar(p_bar)
+ _p_bar(p_bar),
+ _track_only(track_only)
{
}
@@ -163,8 +169,8 @@ public:
void abundance_avail(const string& locus_id,
boost::shared_ptr<SampleAbundances> ab,
size_t factory_id);
- void test_finished_loci();
- void perform_testing(vector<boost::shared_ptr<SampleAbundances> > abundances);
+ virtual vector<vector<boost::shared_ptr<SampleAbundances> > > test_finished_loci();
+ virtual void perform_testing(vector<boost::shared_ptr<SampleAbundances> > abundances);
void record_tracking_data(vector<boost::shared_ptr<SampleAbundances> >& abundances);
bool all_samples_reported_in(vector<boost::shared_ptr<SampleAbundances> >& abundances);
bool all_samples_reported_in(const string& locus_id);
@@ -183,9 +189,724 @@ private:
Tests* _tests;
Tracking* _tracking;
ProgressBar* _p_bar;
+ bool _track_only;
+
+};
+
+// This routine doesn't actually do any tests. Use this when you just want to
+// Flush tracking data once all samples have reported in.
+class TrackingDataWriter : public TestLauncher
+{
+
+public:
+ TrackingDataWriter(int num_samples,
+ Outfiles* outfiles,
+ Tracking* tracking,
+ const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups,
+ vector<string> sls,
+ ProgressBar* p_bar)
+ : TestLauncher(num_samples, vector<pair<size_t, size_t> >(), NULL, tracking, p_bar),
+ _tracking(tracking),
+ _outfiles(outfiles),
+ _all_read_groups(all_read_groups),
+ sample_labels(sls),
+ headers_written(false)
+ {
+
+ }
+
+ void perform_testing(vector<boost::shared_ptr<SampleAbundances> > abundances);
+
+private:
+ Tracking* _tracking;
+ Outfiles* _outfiles;
+ const vector<boost::shared_ptr<ReadGroupProperties> >& _all_read_groups;
+ bool headers_written; // this flag records whether we've written out the file headers yet.
+ vector<string> sample_labels;
+
+ void print_FPKM_tracking_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength\tcoverage");
+ FPKMTrackingTable::const_iterator first_itr = tracking.begin();
+ if (first_itr != tracking.end())
+ {
+ const FPKMTracking& track = first_itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ fprintf(fout, "\t%s_FPKM\t%s_conf_lo\t%s_conf_hi\t%s_status", sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str());
+ }
+ }
+ fprintf(fout, "\n");
+ }
+
+ void print_count_tracking_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id");
+ FPKMTrackingTable::const_iterator first_itr = tracking.begin();
+ if (first_itr != tracking.end())
+ {
+ const FPKMTracking& track = first_itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ fprintf(fout, "\t%s_count\t%s_count_variance\t%s_count_uncertainty_var\t%s_count_dispersion_var\t%s_status", sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str(), sample_labels[i].c_str());
+ }
+ }
+ fprintf(fout, "\n");
+ }
+
+ void print_FPKM_simple_table_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id");
+ FPKMTrackingTable::const_iterator first_itr = tracking.begin();
+ if (first_itr != tracking.end())
+ {
+ const FPKMTracking& track = first_itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+ ++j)
+ {
+ const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
+ int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
+ fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
+ }
+ }
+ }
+ }
+
+ void print_count_simple_table_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id");
+ FPKMTrackingTable::const_iterator first_itr = tracking.begin();
+ if (first_itr != tracking.end())
+ {
+ const FPKMTracking& track = first_itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+ ++j)
+ {
+ const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
+ int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
+ fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
+ }
+ }
+ }
+ }
+
+ void print_FPKM_tracking(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ const FPKMTracking& track = itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ AbundanceStatus status = NUMERIC_OK;
+ BOOST_FOREACH (const FPKMContext& c, fpkms)
+ {
+ if (c.status == NUMERIC_FAIL)
+ status = NUMERIC_FAIL;
+ }
+
+ string all_gene_ids = cat_strings(track.gene_ids);
+ if (all_gene_ids == "")
+ all_gene_ids = "-";
+
+ string all_gene_names = cat_strings(track.gene_names);
+ if (all_gene_names == "")
+ all_gene_names = "-";
+
+ string all_tss_ids = cat_strings(track.tss_ids);
+ if (all_tss_ids == "")
+ all_tss_ids = "-";
+
+ char length_buff[33] = "-";
+ if (track.length)
+ sprintf(length_buff, "%d", track.length);
+
+ fprintf(fout, "%s\t%c\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
+ description.c_str(),
+ track.classcode ? track.classcode : '-',
+ track.ref_match.c_str(),
+ all_gene_ids.c_str(),
+ all_gene_names.c_str(),
+ all_tss_ids.c_str(),
+ track.locus_tag.c_str(),
+ length_buff,
+ "-");
+
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ double fpkm = fpkms[i].FPKM;
+ //double std_dev = sqrt(fpkms[i].FPKM_variance);
+ double fpkm_conf_hi = fpkms[i].FPKM_conf_hi;
+ double fpkm_conf_lo = fpkms[i].FPKM_conf_lo;
+ const char* status_str = "OK";
+
+ if (fpkms[i].status == NUMERIC_OK)
+ {
+ status_str = "OK";
+ }
+ else if (fpkms[i].status == NUMERIC_FAIL)
+ {
+ status_str = "FAIL";
+ }
+ else if (fpkms[i].status == NUMERIC_LOW_DATA)
+ {
+ status_str = "LOWDATA";
+ }
+ else if (fpkms[i].status == NUMERIC_HI_DATA)
+ {
+ status_str = "HIDATA";
+ }
+ else
+ {
+ assert(false);
+ }
+
+ fprintf(fout, "\t%lg\t%lg\t%lg\t%s", fpkm, fpkm_conf_lo, fpkm_conf_hi, status_str);
+ }
+
+ fprintf(fout, "\n");
+ }
+ }
+
+ void print_count_tracking(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ const FPKMTracking& track = itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ AbundanceStatus status = NUMERIC_OK;
+ BOOST_FOREACH (const FPKMContext& c, fpkms)
+ {
+ if (c.status == NUMERIC_FAIL)
+ status = NUMERIC_FAIL;
+ }
+
+ fprintf(fout, "%s",
+ description.c_str());
+
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ const char* status_str = "OK";
+
+ if (fpkms[i].status == NUMERIC_OK)
+ {
+ status_str = "OK";
+ }
+ else if (fpkms[i].status == NUMERIC_FAIL)
+ {
+ status_str = "FAIL";
+ }
+ else if (fpkms[i].status == NUMERIC_LOW_DATA)
+ {
+ status_str = "LOWDATA";
+ }
+ else if (fpkms[i].status == NUMERIC_HI_DATA)
+ {
+ status_str = "HIDATA";
+ }
+ else
+ {
+ assert(false);
+ }
+
+ double external_counts = fpkms[i].count_mean;
+ double external_count_var = fpkms[i].count_var;
+ double uncertainty_var = fpkms[i].count_uncertainty_var;
+ double dispersion_var = fpkms[i].count_dispersion_var;
+ fprintf(fout, "\t%lg\t%lg\t%lg\t%lg\t%s", external_counts, external_count_var, uncertainty_var, dispersion_var, status_str);
+ }
+
+ fprintf(fout, "\n");
+ }
+ }
+
+ void print_FPKM_simple_table(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ fprintf(fout, "\n%s", description.c_str());
+
+ const FPKMTracking& track = itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+ ++j)
+ {
+ double FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
+ fprintf(fout, "\t%lg", FPKM);
+ }
+ }
+ }
+ }
+
+ void print_count_simple_table(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ fprintf(fout, "\n%s", description.c_str());
+
+ const FPKMTracking& track = itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+ ++j)
+ {
+ double count = fpkms[i].tracking_info_per_rep[j].count;
+ fprintf(fout, "\t%lg", count);
+ }
+ }
+ }
+ }
+
+ void remove_abundance_from_tracking_table(const string& target_desc,
+ FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ tracking.erase(itr);
+ }
+ }
+
+ void print_read_group_tracking_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id\tcondition\treplicate\traw_frags\tinternal_scaled_frags\texternal_scaled_frags\tFPKM\teffective_length\tstatus");
+ fprintf(fout, "\n");
+ }
+
+ void print_read_group_tracking(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ const FPKMTracking& track = itr->second;
+ const vector<FPKMContext>& fpkms = track.fpkm_series;
+
+ for (size_t i = 0; i < fpkms.size(); ++i)
+ {
+ for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+ ++j)
+ {
+ double FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
+ double internal_count = fpkms[i].tracking_info_per_rep[j].count;
+ double external_count = internal_count / fpkms[i].tracking_info_per_rep[j].rg_props->external_scale_factor();
+ double raw_count = internal_count * fpkms[i].tracking_info_per_rep[j].rg_props->internal_scale_factor();
+ const string& condition_name = fpkms[i].tracking_info_per_rep[j].rg_props->condition_name();
+ AbundanceStatus status = fpkms[i].tracking_info_per_rep[j].status;
+
+ int rep_num = fpkms[i].tracking_info_per_rep[j].rg_props->replicate_num();
+
+ const char* status_str = "OK";
+
+ if (status == NUMERIC_OK)
+ {
+ status_str = "OK";
+ }
+ else if (status == NUMERIC_FAIL)
+ {
+ status_str = "FAIL";
+ }
+ else if (status == NUMERIC_LOW_DATA)
+ {
+ status_str = "LOWDATA";
+ }
+ else if (status == NUMERIC_HI_DATA)
+ {
+ status_str = "HIDATA";
+ }
+ else
+ {
+ assert(false);
+ }
+
+ fprintf(fout, "%s\t%s\t%d\t%lg\t%lg\t%lg\t%lg\t%s\t%s\n",
+ description.c_str(),
+ condition_name.c_str(),
+ rep_num,
+ raw_count,
+ internal_count,
+ external_count,
+ FPKM,
+ "-",
+ status_str);
+ }
+ }
+ }
+ }
+
+ void print_read_group_cuffdiff_info(FILE* fout,
+ const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups)
+ {
+ fprintf(fout, "file\tcondition\treplicate_num\ttotal_mass\tnorm_mass\tinternal_scale\texternal_scale\n");
+ for (size_t i = 0; i < all_read_groups.size(); ++i)
+ {
+ boost::shared_ptr<ReadGroupProperties const> rg_props = all_read_groups[i];
+ fprintf(fout, "%s\t%s\t%d\t%Lg\t%Lg\t%lg\t%lg\n",
+ rg_props->file_path().c_str(),
+ rg_props->condition_name().c_str(),
+ rg_props->replicate_num(),
+ rg_props->total_map_mass(),
+ rg_props->normalized_map_mass(),
+ rg_props->internal_scale_factor(),
+ rg_props->external_scale_factor());
+
+ }
+ }
+ void print_read_group_simple_table_info(FILE* fout,
+ const vector<boost::shared_ptr<ReadGroupProperties> >& all_read_groups)
+ {
+ //fprintf(fout, "file\tcondition\treplicate_num\ttotal_mass\tnorm_mass\tinternal_scale\texternal_scale\n");
+ fprintf(fout, "sample_id\tfile\ttotal_mass\tinternal_scale\texternal_scale\tmedian_transcript_frags\n");
+ for (size_t i = 0; i < all_read_groups.size(); ++i)
+ {
+ boost::shared_ptr<ReadGroupProperties const> rg_props = all_read_groups[i];
+ fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n",
+ rg_props->condition_name().c_str(),
+ rg_props->replicate_num(),
+ rg_props->file_path().c_str(),
+ rg_props->total_map_mass(),
+ rg_props->internal_scale_factor(),
+ rg_props->external_scale_factor(),
+ rg_props->median_transcript_coverage());
+
+ }
+ }
+
+ void print_feature_attr_simple_table_header(FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ fprintf(fout,"tracking_id\tclass_code\tnearest_ref_id\tgene_id\tgene_short_name\ttss_id\tlocus\tlength");
+ fprintf(fout, "\n");
+ }
+
+
+ void print_feature_attr_simple_table(const string& target_desc,
+ FILE* fout,
+ const FPKMTrackingTable& tracking)
+ {
+ FPKMTrackingTable::const_iterator itr = tracking.find(target_desc);
+ if (itr != tracking.end())
+ {
+ const string& description = itr->first;
+ const string& locus_tag = itr->second.locus_tag;
+ const string& ref_match = itr->second.ref_match;
+ int length = itr->second.length;
+ char length_buff[33] = "-";
+ if (length)
+ sprintf(length_buff, "%d", length);
+ const set<string>& gene_names = itr->second.gene_names;
+ const set<string>& gene_ids = itr->second.gene_ids;
+ const set<string>& tss_ids = itr->second.tss_ids;
+ char class_code = itr->second.classcode ? itr->second.classcode : '-';
+ string all_gene_names = cat_strings(gene_names);
+ if (all_gene_names == "")
+ all_gene_names = "-";
+ string all_gene_ids = cat_strings(gene_ids);
+ if (all_gene_ids == "")
+ all_gene_ids = "-";
+ string all_tss_ids = cat_strings(tss_ids);
+ if (all_tss_ids == "")
+ all_tss_ids = "-";
+ fprintf(fout, "%s\t%c\t%s\t%s\t%s\t%s\t%s\t%s\n",
+ description.c_str(),
+ class_code,
+ ref_match.c_str(),
+ all_gene_ids.c_str(),
+ all_gene_names.c_str(),
+ all_tss_ids.c_str(),
+ locus_tag.c_str(),
+ length_buff);
+ }
+ }
+
+ void print_run_info(FILE* fout)
+ {
+ fprintf(fout, "param\tvalue\n");
+ fprintf(fout, "cmd_line\t%s\n", cmd_str.c_str());
+ fprintf(fout, "version\t%s\n", PACKAGE_VERSION);
+ fprintf(fout, "SVN_revision\t%s\n",SVN_REVISION);
+ fprintf(fout, "boost_version\t%d\n", BOOST_VERSION);
+ }
+
+ void write_header_output_cuffdiff_format()
+ {
+ // FPKM tracking
+
+ FILE* fiso_fpkm_tracking = _outfiles->isoform_fpkm_tracking_out;
+ //fprintf(stderr, "Writing isoform-level FPKM tracking\n");
+ print_FPKM_tracking_header(fiso_fpkm_tracking,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_fpkm_tracking = _outfiles->tss_group_fpkm_tracking_out;
+ //fprintf(stderr, "Writing TSS group-level FPKM tracking\n");
+ print_FPKM_tracking_header(ftss_fpkm_tracking,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_fpkm_tracking = _outfiles->gene_fpkm_tracking_out;
+ //fprintf(stderr, "Writing gene-level FPKM tracking\n");
+ print_FPKM_tracking_header(fgene_fpkm_tracking,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_fpkm_tracking = _outfiles->cds_fpkm_tracking_out;
+ //fprintf(stderr, "Writing CDS-level FPKM tracking\n");
+ print_FPKM_tracking_header(fcds_fpkm_tracking,_tracking->cds_fpkm_tracking);
+
+ // Count tracking
+
+ FILE* fiso_count_tracking = _outfiles->isoform_count_tracking_out;
+ //fprintf(stderr, "Writing isoform-level count tracking\n");
+ print_count_tracking_header(fiso_count_tracking,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_count_tracking = _outfiles->tss_group_count_tracking_out;
+ //fprintf(stderr, "Writing TSS group-level count tracking\n");
+ print_count_tracking_header(ftss_count_tracking,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_count_tracking = _outfiles->gene_count_tracking_out;
+ //fprintf(stderr, "Writing gene-level count tracking\n");
+ print_count_tracking_header(fgene_count_tracking,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_count_tracking = _outfiles->cds_count_tracking_out;
+ //fprintf(stderr, "Writing CDS-level count tracking\n");
+ print_count_tracking_header(fcds_count_tracking,_tracking->cds_fpkm_tracking);
+
+ // Read group tracking
+
+ FILE* fiso_rep_tracking = _outfiles->isoform_rep_tracking_out;
+ //fprintf(stderr, "Writing isoform-level read group tracking\n");
+ print_read_group_tracking_header(fiso_rep_tracking,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_rep_tracking = _outfiles->tss_group_rep_tracking_out;
+ //fprintf(stderr, "Writing TSS group-level read group tracking\n");
+ print_read_group_tracking_header(ftss_rep_tracking,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_rep_tracking = _outfiles->gene_rep_tracking_out;
+ //fprintf(stderr, "Writing gene-level read group tracking\n");
+ print_read_group_tracking_header(fgene_rep_tracking,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_rep_tracking = _outfiles->cds_rep_tracking_out;
+ //fprintf(stderr, "Writing CDS-level read group tracking\n");
+ print_read_group_tracking_header(fcds_rep_tracking,_tracking->cds_fpkm_tracking);
+
+ FILE* fread_group_info = _outfiles->read_group_info_out;
+ //fprintf(stderr, "Writing read group info\n");
+ print_read_group_cuffdiff_info(fread_group_info,_all_read_groups);
+
+ FILE* frun_info = _outfiles->run_info_out;
+ //fprintf(stderr, "Writing run info\n");
+ print_run_info(frun_info);
+
+ }
+
+ void write_header_output_simple_table_format()
+ {
+ // FPKM tracking
+
+ FILE* fiso_fpkm_tracking = _outfiles->isoform_fpkm_tracking_out;
+ //fprintf(stderr, "Writing isoform-level FPKM tracking\n");
+ print_FPKM_simple_table_header(fiso_fpkm_tracking,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_fpkm_tracking = _outfiles->tss_group_fpkm_tracking_out;
+ //fprintf(stderr, "Writing TSS group-level FPKM tracking\n");
+ print_FPKM_simple_table_header(ftss_fpkm_tracking,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_fpkm_tracking = _outfiles->gene_fpkm_tracking_out;
+ //fprintf(stderr, "Writing gene-level FPKM tracking\n");
+ print_FPKM_simple_table_header(fgene_fpkm_tracking,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_fpkm_tracking = _outfiles->cds_fpkm_tracking_out;
+ //fprintf(stderr, "Writing CDS-level FPKM tracking\n");
+ print_FPKM_simple_table_header(fcds_fpkm_tracking,_tracking->cds_fpkm_tracking);
+
+ // Count tracking
+
+ FILE* fiso_count_tracking = _outfiles->isoform_count_tracking_out;
+ //fprintf(stderr, "Writing isoform-level count tracking\n");
+ print_count_simple_table_header(fiso_count_tracking,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_count_tracking = _outfiles->tss_group_count_tracking_out;
+ //fprintf(stderr, "Writing TSS group-level count tracking\n");
+ print_count_simple_table_header(ftss_count_tracking,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_count_tracking = _outfiles->gene_count_tracking_out;
+ //fprintf(stderr, "Writing gene-level count tracking\n");
+ print_count_simple_table_header(fgene_count_tracking,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_count_tracking = _outfiles->cds_count_tracking_out;
+ //fprintf(stderr, "Writing CDS-level count tracking\n");
+ print_count_simple_table_header(fcds_count_tracking,_tracking->cds_fpkm_tracking);
+
+ // We can also take care of all this metadata about samples and genes
+ FILE* fiso_attr = _outfiles->isoform_attr_out;
+ //fprintf(stderr, "Writing isoform-level attributes\n");
+ print_feature_attr_simple_table_header(fiso_attr,_tracking->isoform_fpkm_tracking);
+
+ FILE* ftss_attr = _outfiles->tss_group_attr_out;
+ //fprintf(stderr, "Writing TSS group-level attributes\n");
+ print_feature_attr_simple_table_header(ftss_attr,_tracking->tss_group_fpkm_tracking);
+
+ FILE* fgene_attr = _outfiles->gene_attr_out;
+ //fprintf(stderr, "Writing gene-level attributes\n");
+ print_feature_attr_simple_table_header(fgene_attr,_tracking->gene_fpkm_tracking);
+
+ FILE* fcds_attr = _outfiles->cds_attr_out;
+ //fprintf(stderr, "Writing CDS-level attributes\n");
+ print_feature_attr_simple_table_header(fcds_attr,_tracking->cds_fpkm_tracking);
+
+ FILE* fread_group_info = _outfiles->read_group_info_out;
+ //fprintf(stderr, "Writing read group info\n");
+ print_read_group_simple_table_info(fread_group_info,_all_read_groups);
+
+ FILE* frun_info = _outfiles->run_info_out;
+ //fprintf(stderr, "Writing run info\n");
+ print_run_info(frun_info);
+
+ }
+
+ void write_output(const vector<boost::shared_ptr<SampleAbundances> >& abundances)
+ {
+ if (output_format == CUFFDIFF_OUTPUT_FMT)
+ {
+ write_cuffdiff_output(abundances);
+ }
+ else if (output_format == SIMPLE_TABLE_OUTPUT_FMT)
+ {
+ write_simple_table_output(abundances);
+ }
+ else{
+ fprintf(stderr, "Error: unrecognized output format!\n");
+ exit(1);
+ }
+ }
+
+ void write_header_output()
+ {
+ if (output_format == CUFFDIFF_OUTPUT_FMT)
+ {
+ write_header_output_cuffdiff_format();
+ }
+ else if (output_format == SIMPLE_TABLE_OUTPUT_FMT)
+ {
+ write_header_output_simple_table_format();
+ }
+ else{
+ fprintf(stderr, "Error: unrecognized output format!\n");
+ exit(1);
+ }
+ }
+
+ void write_cuffdiff_output(const vector<boost::shared_ptr<SampleAbundances> >& abundances)
+ {
+ const AbundanceGroup& ab_group = abundances.front()->transcripts;
+ //fprintf(stderr, "[%d] count = %lg\n",i, ab_group.num_fragments());
+ BOOST_FOREACH (boost::shared_ptr<Abundance> ab, ab_group.abundances())
+ {
+ print_FPKM_tracking(ab->description(), _outfiles->isoform_fpkm_tracking_out, _tracking->isoform_fpkm_tracking);
+ print_count_tracking(ab->description(), _outfiles->isoform_count_tracking_out, _tracking->isoform_fpkm_tracking);
+ print_read_group_tracking(ab->description(), _outfiles->isoform_rep_tracking_out, _tracking->isoform_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab->description(), _tracking->isoform_fpkm_tracking);
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->cds)
+ {
+ print_FPKM_tracking(ab.description(), _outfiles->cds_fpkm_tracking_out, _tracking->cds_fpkm_tracking);
+ print_count_tracking(ab.description(), _outfiles->cds_count_tracking_out, _tracking->cds_fpkm_tracking);
+ print_read_group_tracking(ab.description(), _outfiles->cds_rep_tracking_out, _tracking->cds_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->cds_fpkm_tracking);
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->primary_transcripts)
+ {
+ print_FPKM_tracking(ab.description(), _outfiles->tss_group_fpkm_tracking_out, _tracking->tss_group_fpkm_tracking);
+ print_count_tracking(ab.description(), _outfiles->tss_group_count_tracking_out, _tracking->tss_group_fpkm_tracking);
+ print_read_group_tracking(ab.description(), _outfiles->tss_group_rep_tracking_out, _tracking->tss_group_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->tss_group_fpkm_tracking);
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->genes)
+ {
+ print_FPKM_tracking(ab.description(), _outfiles->gene_fpkm_tracking_out, _tracking->gene_fpkm_tracking);
+ print_count_tracking(ab.description(), _outfiles->gene_count_tracking_out, _tracking->gene_fpkm_tracking);
+ print_read_group_tracking(ab.description(), _outfiles->gene_rep_tracking_out, _tracking->gene_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->gene_fpkm_tracking);
+ }
+ }
+
+
+ void write_simple_table_output(const vector<boost::shared_ptr<SampleAbundances> >& abundances)
+ {
+ const AbundanceGroup& ab_group = abundances.front()->transcripts;
+ //fprintf(stderr, "[%d] count = %lg\n",i, ab_group.num_fragments());
+ BOOST_FOREACH (boost::shared_ptr<Abundance> ab, ab_group.abundances())
+ {
+ print_FPKM_simple_table(ab->description(), _outfiles->isoform_fpkm_tracking_out, _tracking->isoform_fpkm_tracking);
+ print_count_simple_table(ab->description(), _outfiles->isoform_count_tracking_out, _tracking->isoform_fpkm_tracking);
+ print_feature_attr_simple_table(ab->description(), _outfiles->isoform_attr_out, _tracking->isoform_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab->description(), _tracking->isoform_fpkm_tracking);
+
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->cds)
+ {
+ print_FPKM_simple_table(ab.description(), _outfiles->cds_fpkm_tracking_out, _tracking->cds_fpkm_tracking);
+ print_count_simple_table(ab.description(), _outfiles->cds_count_tracking_out, _tracking->cds_fpkm_tracking);
+ print_feature_attr_simple_table(ab.description(), _outfiles->cds_attr_out, _tracking->cds_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->cds_fpkm_tracking);
+
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->primary_transcripts)
+ {
+ print_FPKM_simple_table(ab.description(), _outfiles->tss_group_fpkm_tracking_out, _tracking->tss_group_fpkm_tracking);
+ print_count_simple_table(ab.description(), _outfiles->tss_group_count_tracking_out, _tracking->tss_group_fpkm_tracking);
+ print_feature_attr_simple_table(ab.description(), _outfiles->tss_group_attr_out, _tracking->tss_group_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->tss_group_fpkm_tracking);
+ }
+
+ BOOST_FOREACH (AbundanceGroup& ab, abundances.front()->genes)
+ {
+ print_FPKM_simple_table(ab.description(), _outfiles->gene_fpkm_tracking_out, _tracking->gene_fpkm_tracking);
+ print_count_simple_table(ab.description(), _outfiles->gene_count_tracking_out, _tracking->gene_fpkm_tracking);
+ print_feature_attr_simple_table(ab.description(), _outfiles->gene_attr_out, _tracking->gene_fpkm_tracking);
+ remove_abundance_from_tracking_table(ab.description(), _tracking->gene_fpkm_tracking);
+ }
+ }
};
+
extern double min_read_count;
void sample_worker(bool non_empty,
diff --git a/src/gtf_reads.cpp b/src/gtf_reads.cpp
new file mode 100644
index 0000000..5b9b131
--- /dev/null
+++ b/src/gtf_reads.cpp
@@ -0,0 +1,187 @@
+/*
+ * reads_of_interest.cpp
+ * cufflinks
+ *
+ * Created by Cole Trapnell on 11/29/09.
+ * Copyright 2009 Cole Trapnell. All rights reserved.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <getopt.h>
+#include <string>
+#include <numeric>
+#include <cfloat>
+#include <iostream>
+
+#include "common.h"
+#include "hits.h"
+#include "bundles.h"
+#include "abundances.h"
+
+#if ENABLE_THREADS
+const char *short_options = "";
+#else
+const char *short_options = "";
+#endif
+
+static struct option long_options[] = {
+{0, 0, 0, 0} // terminator
+};
+
+void print_usage()
+{
+ //NOTE: SPACES ONLY, bozo
+ fprintf(stderr, "Usage: cuffdiff <transcripts.gtf> <sample_hits.sam>\n");
+}
+
+int parse_options(int argc, char** argv)
+{
+ int option_index = 0;
+ int next_option;
+ do {
+ next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
+ switch (next_option) {
+ case -1: /* Done with options. */
+ break;
+
+ default:
+ print_usage();
+ return 1;
+ }
+ } while(next_option != -1);
+
+ return 0;
+}
+
+void driver(FILE* ref_gtf, FILE* sam_hit_file)
+{
+ ReadTable it;
+ RefSequenceTable rt(true, false);
+
+ vector<Scaffold> ref_mRNAs;
+
+ SAMHitFactory hs(it, rt);
+
+ boost::shared_ptr<HitFactory> hit_factory;
+
+ try
+ {
+ hit_factory = boost::shared_ptr<BAMHitFactory>(new BAMHitFactory(hit_file_name, it, rt));
+ }
+ catch (std::runtime_error& e)
+ {
+ fprintf(stderr, "File %s doesn't appear to be a valid BAM file, trying SAM...\n",
+ hit_file_name.c_str());
+
+ try
+ {
+ hit_factory = boost::shared_ptr<SAMHitFactory>(new SAMHitFactory(hit_file_name, it, rt));
+ }
+ catch (std::runtime_error& e)
+ {
+ fprintf(stderr, "Error: cannot open alignment file %s for reading\n",
+ hit_file_name.c_str());
+ exit(1);
+ }
+ }
+ BundleFactory& bundle_factory = *(new BundleFactory(hit_factory, bundle_mode));
+
+ boost::crc_32_type ref_gtf_crc_result;
+ vector<boost::shared_ptr<Scaffold> > ref_mRNAs;
+ if (ref_gtf)
+ {
+ ::load_ref_rnas(ref_gtf, bundle_factory.ref_table(), ref_mRNAs, ref_gtf_crc_result, false, false);
+ bundle_factory.set_ref_rnas(ref_mRNAs);
+ }
+ rt.print_rec_ordering();
+ vector<boost::shared_ptr<Scaffold> > mask_rnas;
+ boost::crc_32_type mask_gtf_crc_result;
+ if (mask_gtf)
+ {
+ ::load_ref_rnas(mask_gtf, bundle_factory.ref_table(), mask_rnas, mask_gtf_crc_result, false, false);
+ bundle_factory.set_mask_rnas(mask_rnas);
+ }
+
+ long num_fragments = 0;
+ long num_reads = 0;
+
+ const vector<MateHit>& hits = bundle.hits();
+ for (size_t i = 0; i < bundle.hits().size(); ++i)
+ {
+ bool compatible = false;
+ for (vector<Scaffold>::iterator ri = ref_mrnas.begin();
+ ri != ref_mrnas.end();
+ ++ri)
+ {
+ if (Scaffold::overlap_in_genome(*ri, hits[i], 0) &&
+ Scaffold::compatible(*ri,hits[i]))
+ {
+ compatible = true;
+ break;
+ }
+ }
+ if (!compatible)
+ continue;
+
+ if (hits[i].left_alignment() || hits[i].right_alignment())
+ num_fragments++;
+ if (hits[i].left_alignment())
+ {
+ printf("%s\n", hits[i].left_alignment()->hitfile_rec().c_str());
+ num_reads++;
+ }
+ if (hits[i].right_alignment())
+ {
+ printf("%s\n", hits[i].right_alignment()->hitfile_rec().c_str());
+ num_reads++;
+ }
+ }
+
+ fprintf(stderr, "Extracted %ld fragments, %ld reads\n", num_fragments, num_reads);
+}
+
+int main(int argc, char** argv)
+{
+ int parse_ret = parse_options(argc,argv);
+ if (parse_ret)
+ return parse_ret;
+
+ if(optind >= argc)
+ {
+ print_usage();
+ return 1;
+ }
+
+ string ref_gtf_filename = argv[optind++];
+
+ string sam_hits_file_name = argv[optind++];
+ // Open the approppriate files
+ FILE* sam_hits_file = fopen(sam_hits_file_name.c_str(), "r");
+ if (sam_hits_file == NULL)
+ {
+ fprintf(stderr, "Error: cannot open SAM file %s for reading\n",
+ sam_hits_file_name.c_str());
+ exit(1);
+ }
+
+ FILE* ref_gtf = NULL;
+ if (ref_gtf_filename != "")
+ {
+ ref_gtf = fopen(ref_gtf_filename.c_str(), "r");
+ if (!ref_gtf)
+ {
+ fprintf(stderr, "Error: cannot open GTF file %s for reading\n",
+ ref_gtf_filename.c_str());
+ exit(1);
+ }
+ }
+
+ driver(ref_gtf, sam_hits_file);
+
+ return 0;
+}
diff --git a/src/gtf_to_sam.cpp b/src/gtf_to_sam.cpp
index 38b8311..ba259e9 100644
--- a/src/gtf_to_sam.cpp
+++ b/src/gtf_to_sam.cpp
@@ -7,12 +7,6 @@
*
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#else
-#define PACKAGE_VERSION "INTERNAL"
-#endif
-
#include <stdlib.h>
#include <getopt.h>
#include <string>
diff --git a/src/hits.cpp b/src/hits.cpp
index 5387363..4cac1f1 100644
--- a/src/hits.cpp
+++ b/src/hits.cpp
@@ -1231,7 +1231,7 @@ void PrecomputedExpressionHitFactory::clear_abundance_for_locus(int locus_id)
_curr_ab_groups.erase(itr);
}
-boost::shared_ptr<const AbundanceGroup> PrecomputedExpressionHitFactory::next_locus(int locus_id)
+boost::shared_ptr<const AbundanceGroup> PrecomputedExpressionHitFactory::next_locus(int locus_id, bool cache_locus)
{
#if ENABLE_THREADS
boost::mutex::scoped_lock lock(_factory_lock);
@@ -1264,10 +1264,12 @@ boost::shared_ptr<const AbundanceGroup> PrecomputedExpressionHitFactory::next_lo
}
else // we don't want to lose this one...
{
- _curr_ab_groups[_last_locus_id] = ab;
+ if (cache_locus)
+ _curr_ab_groups[_last_locus_id] = ab;
}
}
- _curr_ab_groups[locus_id] = sought_group;
+ if (cache_locus)
+ _curr_ab_groups[locus_id] = sought_group;
return sought_group;
}
diff --git a/src/hits.h b/src/hits.h
index f5d2a23..4072389 100644
--- a/src/hits.h
+++ b/src/hits.h
@@ -883,7 +883,7 @@ public:
bool inspect_header();
- boost::shared_ptr<const AbundanceGroup> next_locus(int locus_id);
+ boost::shared_ptr<const AbundanceGroup> next_locus(int locus_id, bool cache_locus);
boost::shared_ptr<const AbundanceGroup> get_abundance_for_locus(int locus_id);
void clear_abundance_for_locus(int locus_id);
diff --git a/src/replicates.cpp b/src/replicates.cpp
index 544f322..9bcb03c 100644
--- a/src/replicates.cpp
+++ b/src/replicates.cpp
@@ -389,6 +389,57 @@ void calc_classic_fpkm_scaling_factors(const vector<LocusCountList>& sample_comp
}
}
+void calc_estimated_absolute_scaling_factors(vector<boost::shared_ptr<ReadGroupProperties> > & all_read_groups,
+ vector<double>& scale_factors)
+{
+ assert (scale_factors.size() == all_read_groups.size());
+ for (size_t i = 0; i < scale_factors.size(); ++i)
+ {
+ double med_cov = all_read_groups[i]->median_transcript_coverage();
+ if (med_cov == 0)
+ {
+ scale_factors[i] = 0.0;
+ }
+ else if (med_cov == -1)
+ {
+ fprintf(stderr, "Error: estimated-absolute requires pre-calculated CXB files\n");
+ exit(1);
+ }
+
+ scale_factors[i] = med_cov * 1000000000 / (all_read_groups[i]->normalized_map_mass()) ;
+ }
+
+//
+// void adjust_fpkms_by_median_coverage(const vector<vector<double > >& median_coverage,
+// FPKMTrackingTable& tracking)
+// {
+// for (FPKMTrackingTable::iterator itr = tracking.begin(); itr != tracking.end(); ++itr)
+// {
+// if (itr != tracking.end())
+// {
+// FPKMTracking& track = itr->second;
+// vector<FPKMContext>& fpkms = track.fpkm_series;
+//
+// for (size_t i = 0; i < fpkms.size(); ++i)
+// {
+// for (size_t j = 0; j != fpkms[i].tracking_info_per_rep.size();
+// ++j)
+// {
+// double& FPKM = fpkms[i].tracking_info_per_rep[j].fpkm;
+// FPKM /= median_coverage[i][j];
+// FPKM *= fpkms[i].tracking_info_per_rep[j].rg_props->normalized_map_mass();
+// FPKM /= 1000000000;
+// }
+// }
+// }
+// }
+// }
+//
+//
+}
+
+
+
void calc_quartile_scaling_factors(const vector<LocusCountList>& sample_compatible_count_table,
vector<double>& scale_factors)
{
@@ -1042,7 +1093,7 @@ void normalize_counts(vector<boost::shared_ptr<ReadGroupProperties> > & all_read
}
else if (lib_norm_method == ESTIMATED_ABSOLUTE)
{
- calc_classic_fpkm_scaling_factors(norm_table, scale_factors);
+ calc_estimated_absolute_scaling_factors(all_read_groups, scale_factors);
}
else
{
diff --git a/src/replicates.h b/src/replicates.h
index 7e02947..02165cf 100644
--- a/src/replicates.h
+++ b/src/replicates.h
@@ -176,7 +176,7 @@ public:
return false;
}
- bool next_bundle(HitBundle& bundle_out)
+ bool next_bundle(HitBundle& bundle_out, bool cache_bundle)
{
#if ENABLE_THREADS
boost::mutex::scoped_lock lock(_rep_factory_lock);
@@ -187,7 +187,7 @@ public:
BOOST_FOREACH (boost::shared_ptr<BundleFactory> fac, _factories)
{
bundles.push_back(new HitBundle());
- if (fac->next_bundle(*(bundles.back())))
+ if (fac->next_bundle(*(bundles.back()), cache_bundle))
{
non_empty_bundle = true;
}
diff --git a/version.m4 b/version.m4
new file mode 100644
index 0000000..b0a55a9
--- /dev/null
+++ b/version.m4
@@ -0,0 +1 @@
+m4_define([VERSION_NUMBER], [0.0.0])
--
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