Commit upstream/1.1.3 - idba

Imported Upstream version 1.1.3 Andreas Tille 7 years ago

20 changed file(s) with 3389 addition(s) and 1697 deletion(s). Raw diff Collapse all Expand all

+192

-137

Makefile.in less more

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1	1	# @configure_input@
2	2
3		# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
4		# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
5		# Foundation, Inc.
	3	# Copyright (C) 1994-2013 Free Software Foundation, Inc.
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6	5	# This Makefile.in is free software; the Free Software Foundation
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701	756	scan:

-77

~~README~~ less more

0		###############################################################################
1		Copyright (C) 2009 Yu Peng (ypeng@cs.hku.hk)
2
3		This program is free software; you can redistribute it and/or
4		modify it under the terms of the GNU General Public License
5		as published by the Free Software Foundation; either version 2
6		of the License, or (at your option) any later version.
7
8		This program is distributed in the hope that it will be useful,
9		but WITHOUT ANY WARRANTY; without even the implied warranty of
10		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11		GNU General Public License for more details.
12
13		You should have received a copy of the GNU General Public License
14		along with this program; if not, write to the Free Software
15		Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
16
17		Yu Peng (ypeng@cs.hku.hk)
18		Dept. of Computer Science,
19		The University of Hong Kong,
20		Pokfulam Road,
21		Hong Kong,
22		China
23		###############################################################################
24
25		Requirement
26
27		This software is suitable for all unix-like system with gcc installed.
28
29
30		Installation Guide
31
32		Exract the package, then use make to compile the source code.
33		$ ./configure
34		$ make
35
36
37		Introduction
38
39		IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads.
40		IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth
41		regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a
42		generic purpose assembler and epspacially good for single-cell and metagenomic sequencing data.
43		IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference
44		genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for
45		RNA-Seq data.
46
47		The basic IDBA is included for comparison, you should use more specific assemblers for your data.
48		If you are assembling genomic data without reference, please use IDBA-UD.
49		If you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.
50		If you are assembling transcriptome data, please use IDBA-Tran.
51
52
53		Comments
54
55		Note that IDBA assemblers are designed for short reads (around 100bp). If you want to assemble
56		paired-end reads with longer read length, please modify the constant kMaxShortSequence in
57		src/sequence/short_sequence.h to support longer read length.
58
59		Please find the manual by running the assembler without any parameters. For example:
60		$ bin/idba
61
62		IDBA series assemblers accept fasta format reads. Fastq format reads can be converted by
63		fq2fa program in the packcage.
64		$ bin/fq2fa read.fq read.fa
65
66		IDBA-UD IDBA-Hybrid and IDBA-Tran require paired-end reads stored in single FastA file and a pair of
67		reads is in consecutive two lines. If not, please use fq2fa to merge two
68		FastQ read files to single file.
69		$ bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa
70		or convert a FastQ read file to FastA file.
71		$ bin/fq2fa --paired --filter read.fq read.fa
72
73		The this tools assume the paired-end reads are in order (->, <-). If your data is in order (<-, ->),
74		please convert it by yourself.
75
76

+506

-328

aclocal.m4 less more

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2		# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
3		# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation,
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264	255	msvc7 \| msvc7msys \| msvisualcpp \| msvcmsys)
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482	480
483	481	_AM_IF_OPTION([no-define],,
484		[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
485		AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
	482	[AC_DEFINE_UNQUOTED([PACKAGE], ["$PACKAGE"], [Name of package])
	483	AC_DEFINE_UNQUOTED([VERSION], ["$VERSION"], [Version number of package])])dnl
486	484
487	485	# Some tools Automake needs.
488	486	AC_REQUIRE([AM_SANITY_CHECK])dnl
489	487	AC_REQUIRE([AC_ARG_PROGRAM])dnl
490		AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
491		AM_MISSING_PROG(AUTOCONF, autoconf)
492		AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
493		AM_MISSING_PROG(AUTOHEADER, autoheader)
494		AM_MISSING_PROG(MAKEINFO, makeinfo)
	488	AM_MISSING_PROG([ACLOCAL], [aclocal-${am__api_version}])
	489	AM_MISSING_PROG([AUTOCONF], [autoconf])
	490	AM_MISSING_PROG([AUTOMAKE], [automake-${am__api_version}])
	491	AM_MISSING_PROG([AUTOHEADER], [autoheader])
	492	AM_MISSING_PROG([MAKEINFO], [makeinfo])
495	493	AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
496	494	AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
497		AC_REQUIRE([AM_PROG_MKDIR_P])dnl
	495	AC_REQUIRE([AC_PROG_MKDIR_P])dnl
	496	# For better backward compatibility. To be removed once Automake 1.9.x
	497	# dies out for good. For more background, see:
	498	# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
	499	# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
	500	AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
498	501	# We need awk for the "check" target. The system "awk" is bad on
499	502	# some platforms.
500	503	AC_REQUIRE([AC_PROG_AWK])dnl

505	508	[_AM_PROG_TAR([v7])])])
506	509	_AM_IF_OPTION([no-dependencies],,
507	510	[AC_PROVIDE_IFELSE([AC_PROG_CC],
508		[_AM_DEPENDENCIES(CC)],
509		[define([AC_PROG_CC],
510		defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
	511	[_AM_DEPENDENCIES([CC])],
	512	[m4_define([AC_PROG_CC],
	513	m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
511	514	AC_PROVIDE_IFELSE([AC_PROG_CXX],
512		[_AM_DEPENDENCIES(CXX)],
513		[define([AC_PROG_CXX],
514		defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
	515	[_AM_DEPENDENCIES([CXX])],
	516	[m4_define([AC_PROG_CXX],
	517	m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
515	518	AC_PROVIDE_IFELSE([AC_PROG_OBJC],
516		[_AM_DEPENDENCIES(OBJC)],
517		[define([AC_PROG_OBJC],
518		defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
519		])
520		_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
521		dnl The `parallel-tests' driver may need to know about EXEEXT, so add the
522		dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro
523		dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
	519	[_AM_DEPENDENCIES([OBJC])],
	520	[m4_define([AC_PROG_OBJC],
	521	m4_defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
	522	AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
	523	[_AM_DEPENDENCIES([OBJCXX])],
	524	[m4_define([AC_PROG_OBJCXX],
	525	m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
	526	])
	527	AC_REQUIRE([AM_SILENT_RULES])dnl
	528	dnl The testsuite driver may need to know about EXEEXT, so add the
	529	dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This
	530	dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
524	531	AC_CONFIG_COMMANDS_PRE(dnl
525	532	[m4_provide_if([_AM_COMPILER_EXEEXT],
526	533	[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
527		])
528
529		dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
	534
	535	# POSIX will say in a future version that running "rm -f" with no argument
	536	# is OK; and we want to be able to make that assumption in our Makefile
	537	# recipes. So use an aggressive probe to check that the usage we want is
	538	# actually supported "in the wild" to an acceptable degree.
	539	# See automake bug#10828.
	540	# To make any issue more visible, cause the running configure to be aborted
	541	# by default if the 'rm' program in use doesn't match our expectations; the
	542	# user can still override this though.
	543	if rm -f && rm -fr && rm -rf; then : OK; else
	544	cat >&2 <<'END'
	545	Oops!
	546
	547	Your 'rm' program seems unable to run without file operands specified
	548	on the command line, even when the '-f' option is present. This is contrary
	549	to the behaviour of most rm programs out there, and not conforming with
	550	the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
	551
	552	Please tell bug-automake@gnu.org about your system, including the value
	553	of your $PATH and any error possibly output before this message. This
	554	can help us improve future automake versions.
	555
	556	END
	557	if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
	558	echo 'Configuration will proceed anyway, since you have set the' >&2
	559	echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
	560	echo >&2
	561	else
	562	cat >&2 <<'END'
	563	Aborting the configuration process, to ensure you take notice of the issue.
	564
	565	You can download and install GNU coreutils to get an 'rm' implementation
	566	that behaves properly: <http://www.gnu.org/software/coreutils/>.
	567
	568	If you want to complete the configuration process using your problematic
	569	'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
	570	to "yes", and re-run configure.
	571
	572	END
	573	AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
	574	fi
	575	fi])
	576
	577	dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
530	578	dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
531	579	dnl mangled by Autoconf and run in a shell conditional statement.
532	580	m4_define([_AC_COMPILER_EXEEXT],
533	581	m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
534
535	582
536	583	# When config.status generates a header, we must update the stamp-h file.
537	584	# This file resides in the same directory as the config header

554	601	done
555	602	echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
556	603
557		# Copyright (C) 2001, 2003, 2005, 2008, 2011 Free Software Foundation,
558		# Inc.
559		#
560		# This file is free software; the Free Software Foundation
561		# gives unlimited permission to copy and/or distribute it,
562		# with or without modifications, as long as this notice is preserved.
563
564		# serial 1
	604	# Copyright (C) 2001-2013 Free Software Foundation, Inc.
	605	#
	606	# This file is free software; the Free Software Foundation
	607	# gives unlimited permission to copy and/or distribute it,
	608	# with or without modifications, as long as this notice is preserved.
565	609
566	610	# AM_PROG_INSTALL_SH
567	611	# ------------------

576	620	install_sh="\${SHELL} $am_aux_dir/install-sh"
577	621	esac
578	622	fi
579		AC_SUBST(install_sh)])
580
581		# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
582		#
583		# This file is free software; the Free Software Foundation
584		# gives unlimited permission to copy and/or distribute it,
585		# with or without modifications, as long as this notice is preserved.
586
587		# serial 2
	623	AC_SUBST([install_sh])])
	624
	625	# Copyright (C) 2003-2013 Free Software Foundation, Inc.
	626	#
	627	# This file is free software; the Free Software Foundation
	628	# gives unlimited permission to copy and/or distribute it,
	629	# with or without modifications, as long as this notice is preserved.
588	630
589	631	# Check whether the underlying file-system supports filenames
590	632	# with a leading dot. For instance MS-DOS doesn't.

601	643
602	644	# Check to see how 'make' treats includes. -- Autoconf --
603	645
604		# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
605		#
606		# This file is free software; the Free Software Foundation
607		# gives unlimited permission to copy and/or distribute it,
608		# with or without modifications, as long as this notice is preserved.
609
610		# serial 4
	646	# Copyright (C) 2001-2013 Free Software Foundation, Inc.
	647	#
	648	# This file is free software; the Free Software Foundation
	649	# gives unlimited permission to copy and/or distribute it,
	650	# with or without modifications, as long as this notice is preserved.
611	651
612	652	# AM_MAKE_INCLUDE()
613	653	# -----------------

626	666	_am_result=none
627	667	# First try GNU make style include.
628	668	echo "include confinc" > confmf
629		# Ignore all kinds of additional output from `make'.
	669	# Ignore all kinds of additional output from 'make'.
630	670	case `$am_make -s -f confmf 2> /dev/null` in #(
631	671	the\ am__doit\ target)
632	672	am__include=include

653	693
654	694	# Fake the existence of programs that GNU maintainers use. -- Autoconf --
655	695
656		# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
657		# Free Software Foundation, Inc.
658		#
659		# This file is free software; the Free Software Foundation
660		# gives unlimited permission to copy and/or distribute it,
661		# with or without modifications, as long as this notice is preserved.
662
663		# serial 6
	696	# Copyright (C) 1997-2013 Free Software Foundation, Inc.
	697	#
	698	# This file is free software; the Free Software Foundation
	699	# gives unlimited permission to copy and/or distribute it,
	700	# with or without modifications, as long as this notice is preserved.
664	701
665	702	# AM_MISSING_PROG(NAME, PROGRAM)
666	703	# ------------------------------

669	706	$1=${$1-"${am_missing_run}$2"}
670	707	AC_SUBST($1)])
671	708
672
673	709	# AM_MISSING_HAS_RUN
674	710	# ------------------
675		# Define MISSING if not defined so far and test if it supports --run.
676		# If it does, set am_missing_run to use it, otherwise, to nothing.
	711	# Define MISSING if not defined so far and test if it is modern enough.
	712	# If it is, set am_missing_run to use it, otherwise, to nothing.
677	713	AC_DEFUN([AM_MISSING_HAS_RUN],
678	714	[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
679	715	AC_REQUIRE_AUX_FILE([missing])dnl

686	722	esac
687	723	fi
688	724	# Use eval to expand $SHELL
689		if eval "$MISSING --run true"; then
690		am_missing_run="$MISSING --run "
	725	if eval "$MISSING --is-lightweight"; then
	726	am_missing_run="$MISSING "
691	727	else
692	728	am_missing_run=
693		AC_MSG_WARN([`missing' script is too old or missing])
694		fi
695		])
696
697		# Copyright (C) 2003, 2004, 2005, 2006, 2011 Free Software Foundation,
698		# Inc.
699		#
700		# This file is free software; the Free Software Foundation
701		# gives unlimited permission to copy and/or distribute it,
702		# with or without modifications, as long as this notice is preserved.
703
704		# serial 1
705
706		# AM_PROG_MKDIR_P
707		# ---------------
708		# Check for `mkdir -p'.
709		AC_DEFUN([AM_PROG_MKDIR_P],
710		[AC_PREREQ([2.60])dnl
711		AC_REQUIRE([AC_PROG_MKDIR_P])dnl
712		dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
713		dnl while keeping a definition of mkdir_p for backward compatibility.
714		dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
715		dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
716		dnl Makefile.ins that do not define MKDIR_P, so we do our own
717		dnl adjustment using top_builddir (which is defined more often than
718		dnl MKDIR_P).
719		AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
720		case $mkdir_p in
721		[[\\/$]]* \| ?:[[\\/]]*) ;;
722		/) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
723		esac
	729	AC_MSG_WARN(['missing' script is too old or missing])
	730	fi
724	731	])
725	732
726	733	# Helper functions for option handling. -- Autoconf --
727	734
728		# Copyright (C) 2001, 2002, 2003, 2005, 2008, 2010 Free Software
729		# Foundation, Inc.
730		#
731		# This file is free software; the Free Software Foundation
732		# gives unlimited permission to copy and/or distribute it,
733		# with or without modifications, as long as this notice is preserved.
734
735		# serial 5
	735	# Copyright (C) 2001-2013 Free Software Foundation, Inc.
	736	#
	737	# This file is free software; the Free Software Foundation
	738	# gives unlimited permission to copy and/or distribute it,
	739	# with or without modifications, as long as this notice is preserved.
736	740
737	741	# _AM_MANGLE_OPTION(NAME)
738	742	# -----------------------

743	747	# --------------------
744	748	# Set option NAME. Presently that only means defining a flag for this option.
745	749	AC_DEFUN([_AM_SET_OPTION],
746		[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
	750	[m4_define(_AM_MANGLE_OPTION([$1]), [1])])
747	751
748	752	# _AM_SET_OPTIONS(OPTIONS)
749	753	# ------------------------

757	761	AC_DEFUN([_AM_IF_OPTION],
758	762	[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
759	763
	764	# Copyright (C) 1999-2013 Free Software Foundation, Inc.
	765	#
	766	# This file is free software; the Free Software Foundation
	767	# gives unlimited permission to copy and/or distribute it,
	768	# with or without modifications, as long as this notice is preserved.
	769
	770	# _AM_PROG_CC_C_O
	771	# ---------------
	772	# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
	773	# to automatically call this.
	774	AC_DEFUN([_AM_PROG_CC_C_O],
	775	[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
	776	AC_REQUIRE_AUX_FILE([compile])dnl
	777	AC_LANG_PUSH([C])dnl
	778	AC_CACHE_CHECK(
	779	[whether $CC understands -c and -o together],
	780	[am_cv_prog_cc_c_o],
	781	[AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
	782	# Make sure it works both with $CC and with simple cc.
	783	# Following AC_PROG_CC_C_O, we do the test twice because some
	784	# compilers refuse to overwrite an existing .o file with -o,
	785	# though they will create one.
	786	am_cv_prog_cc_c_o=yes
	787	for am_i in 1 2; do
	788	if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
	789	&& test -f conftest2.$ac_objext; then
	790	: OK
	791	else
	792	am_cv_prog_cc_c_o=no
	793	break
	794	fi
	795	done
	796	rm -f core conftest*
	797	unset am_i])
	798	if test "$am_cv_prog_cc_c_o" != yes; then
	799	# Losing compiler, so override with the script.
	800	# FIXME: It is wrong to rewrite CC.
	801	# But if we don't then we get into trouble of one sort or another.
	802	# A longer-term fix would be to have automake use am__CC in this case,
	803	# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
	804	CC="$am_aux_dir/compile $CC"
	805	fi
	806	AC_LANG_POP([C])])
	807
	808	# For backward compatibility.
	809	AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
	810
	811	# Copyright (C) 2001-2013 Free Software Foundation, Inc.
	812	#
	813	# This file is free software; the Free Software Foundation
	814	# gives unlimited permission to copy and/or distribute it,
	815	# with or without modifications, as long as this notice is preserved.
	816
	817	# AM_RUN_LOG(COMMAND)
	818	# -------------------
	819	# Run COMMAND, save the exit status in ac_status, and log it.
	820	# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
	821	AC_DEFUN([AM_RUN_LOG],
	822	[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
	823	($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
	824	ac_status=$?
	825	echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
	826	(exit $ac_status); }])
	827
760	828	# Check to make sure that the build environment is sane. -- Autoconf --
761	829
762		# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
763		# Free Software Foundation, Inc.
764		#
765		# This file is free software; the Free Software Foundation
766		# gives unlimited permission to copy and/or distribute it,
767		# with or without modifications, as long as this notice is preserved.
768
769		# serial 5
	830	# Copyright (C) 1996-2013 Free Software Foundation, Inc.
	831	#
	832	# This file is free software; the Free Software Foundation
	833	# gives unlimited permission to copy and/or distribute it,
	834	# with or without modifications, as long as this notice is preserved.
770	835
771	836	# AM_SANITY_CHECK
772	837	# ---------------
773	838	AC_DEFUN([AM_SANITY_CHECK],
774	839	[AC_MSG_CHECKING([whether build environment is sane])
775		# Just in case
776		sleep 1
777		echo timestamp > conftest.file
778	840	# Reject unsafe characters in $srcdir or the absolute working directory
779	841	# name. Accept space and tab only in the latter.
780	842	am_lf='

785	847	esac
786	848	case $srcdir in
787	849	[[\\\"\#\$\&\'\`$am_lf\ \ ]])
788		AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
	850	AC_MSG_ERROR([unsafe srcdir value: '$srcdir']);;
789	851	esac
790	852
791		# Do `set' in a subshell so we don't clobber the current shell's
	853	# Do 'set' in a subshell so we don't clobber the current shell's
792	854	# arguments. Must try -L first in case configure is actually a
793	855	# symlink; some systems play weird games with the mod time of symlinks
794	856	# (eg FreeBSD returns the mod time of the symlink's containing
795	857	# directory).
796	858	if (
797		set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
798		if test "$[*]" = "X"; then
799		# -L didn't work.
800		set X `ls -t "$srcdir/configure" conftest.file`
801		fi
802		rm -f conftest.file
803		if test "$[*]" != "X $srcdir/configure conftest.file" \
804		&& test "$[*]" != "X conftest.file $srcdir/configure"; then
805
806		# If neither matched, then we have a broken ls. This can happen
807		# if, for instance, CONFIG_SHELL is bash and it inherits a
808		# broken ls alias from the environment. This has actually
809		# happened. Such a system could not be considered "sane".
810		AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
811		alias in your environment])
812		fi
813
	859	am_has_slept=no
	860	for am_try in 1 2; do
	861	echo "timestamp, slept: $am_has_slept" > conftest.file
	862	set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
	863	if test "$[*]" = "X"; then
	864	# -L didn't work.
	865	set X `ls -t "$srcdir/configure" conftest.file`
	866	fi
	867	if test "$[*]" != "X $srcdir/configure conftest.file" \
	868	&& test "$[*]" != "X conftest.file $srcdir/configure"; then
	869
	870	# If neither matched, then we have a broken ls. This can happen
	871	# if, for instance, CONFIG_SHELL is bash and it inherits a
	872	# broken ls alias from the environment. This has actually
	873	# happened. Such a system could not be considered "sane".
	874	AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
	875	alias in your environment])
	876	fi
	877	if test "$[2]" = conftest.file \|\| test $am_try -eq 2; then
	878	break
	879	fi
	880	# Just in case.
	881	sleep 1
	882	am_has_slept=yes
	883	done
814	884	test "$[2]" = conftest.file
815	885	)
816	886	then

820	890	AC_MSG_ERROR([newly created file is older than distributed files!
821	891	Check your system clock])
822	892	fi
823		AC_MSG_RESULT(yes)])
824
825		# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
826		#
827		# This file is free software; the Free Software Foundation
828		# gives unlimited permission to copy and/or distribute it,
829		# with or without modifications, as long as this notice is preserved.
830
831		# serial 1
	893	AC_MSG_RESULT([yes])
	894	# If we didn't sleep, we still need to ensure time stamps of config.status and
	895	# generated files are strictly newer.
	896	am_sleep_pid=
	897	if grep 'slept: no' conftest.file >/dev/null 2>&1; then
	898	( sleep 1 ) &
	899	am_sleep_pid=$!
	900	fi
	901	AC_CONFIG_COMMANDS_PRE(
	902	[AC_MSG_CHECKING([that generated files are newer than configure])
	903	if test -n "$am_sleep_pid"; then
	904	# Hide warnings about reused PIDs.
	905	wait $am_sleep_pid 2>/dev/null
	906	fi
	907	AC_MSG_RESULT([done])])
	908	rm -f conftest.file
	909	])
	910
	911	# Copyright (C) 2009-2013 Free Software Foundation, Inc.
	912	#
	913	# This file is free software; the Free Software Foundation
	914	# gives unlimited permission to copy and/or distribute it,
	915	# with or without modifications, as long as this notice is preserved.
	916
	917	# AM_SILENT_RULES([DEFAULT])
	918	# --------------------------
	919	# Enable less verbose build rules; with the default set to DEFAULT
	920	# ("yes" being less verbose, "no" or empty being verbose).
	921	AC_DEFUN([AM_SILENT_RULES],
	922	[AC_ARG_ENABLE([silent-rules], [dnl
	923	AS_HELP_STRING(
	924	[--enable-silent-rules],
	925	[less verbose build output (undo: "make V=1")])
	926	AS_HELP_STRING(
	927	[--disable-silent-rules],
	928	[verbose build output (undo: "make V=0")])dnl
	929	])
	930	case $enable_silent_rules in @%:@ (((
	931	yes) AM_DEFAULT_VERBOSITY=0;;
	932	no) AM_DEFAULT_VERBOSITY=1;;
	933	*) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
	934	esac
	935	dnl
	936	dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
	937	dnl do not support nested variable expansions.
	938	dnl See automake bug#9928 and bug#10237.
	939	am_make=${MAKE-make}
	940	AC_CACHE_CHECK([whether $am_make supports nested variables],
	941	[am_cv_make_support_nested_variables],
	942	[if AS_ECHO([['TRUE=$(BAR$(V))
	943	BAR0=false
	944	BAR1=true
	945	V=1
	946	am__doit:
	947	@$(TRUE)
	948	.PHONY: am__doit']]) \| $am_make -f - >/dev/null 2>&1; then
	949	am_cv_make_support_nested_variables=yes
	950	else
	951	am_cv_make_support_nested_variables=no
	952	fi])
	953	if test $am_cv_make_support_nested_variables = yes; then
	954	dnl Using '$V' instead of '$(V)' breaks IRIX make.
	955	AM_V='$(V)'
	956	AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
	957	else
	958	AM_V=$AM_DEFAULT_VERBOSITY
	959	AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
	960	fi
	961	AC_SUBST([AM_V])dnl
	962	AM_SUBST_NOTMAKE([AM_V])dnl
	963	AC_SUBST([AM_DEFAULT_V])dnl
	964	AM_SUBST_NOTMAKE([AM_DEFAULT_V])dnl
	965	AC_SUBST([AM_DEFAULT_VERBOSITY])dnl
	966	AM_BACKSLASH='\'
	967	AC_SUBST([AM_BACKSLASH])dnl
	968	_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
	969	])
	970
	971	# Copyright (C) 2001-2013 Free Software Foundation, Inc.
	972	#
	973	# This file is free software; the Free Software Foundation
	974	# gives unlimited permission to copy and/or distribute it,
	975	# with or without modifications, as long as this notice is preserved.
832	976
833	977	# AM_PROG_INSTALL_STRIP
834	978	# ---------------------
835		# One issue with vendor `install' (even GNU) is that you can't
	979	# One issue with vendor 'install' (even GNU) is that you can't
836	980	# specify the program used to strip binaries. This is especially
837	981	# annoying in cross-compiling environments, where the build's strip
838	982	# is unlikely to handle the host's binaries.
839	983	# Fortunately install-sh will honor a STRIPPROG variable, so we
840		# always use install-sh in `make install-strip', and initialize
	984	# always use install-sh in "make install-strip", and initialize
841	985	# STRIPPROG with the value of the STRIP variable (set by the user).
842	986	AC_DEFUN([AM_PROG_INSTALL_STRIP],
843	987	[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
844		# Installed binaries are usually stripped using `strip' when the user
845		# run `make install-strip'. However `strip' might not be the right
	988	# Installed binaries are usually stripped using 'strip' when the user
	989	# run "make install-strip". However 'strip' might not be the right
846	990	# tool to use in cross-compilation environments, therefore Automake
847		# will honor the `STRIP' environment variable to overrule this program.
848		dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
	991	# will honor the 'STRIP' environment variable to overrule this program.
	992	dnl Don't test for $cross_compiling = yes, because it might be 'maybe'.
849	993	if test "$cross_compiling" != no; then
850	994	AC_CHECK_TOOL([STRIP], [strip], :)
851	995	fi
852	996	INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
853	997	AC_SUBST([INSTALL_STRIP_PROGRAM])])
854	998
855		# Copyright (C) 2006, 2008, 2010 Free Software Foundation, Inc.
856		#
857		# This file is free software; the Free Software Foundation
858		# gives unlimited permission to copy and/or distribute it,
859		# with or without modifications, as long as this notice is preserved.
860
861		# serial 3
	999	# Copyright (C) 2006-2013 Free Software Foundation, Inc.
	1000	#
	1001	# This file is free software; the Free Software Foundation
	1002	# gives unlimited permission to copy and/or distribute it,
	1003	# with or without modifications, as long as this notice is preserved.
862	1004
863	1005	# _AM_SUBST_NOTMAKE(VARIABLE)
864	1006	# ---------------------------

873	1015
874	1016	# Check how to create a tarball. -- Autoconf --
875	1017
876		# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
877		#
878		# This file is free software; the Free Software Foundation
879		# gives unlimited permission to copy and/or distribute it,
880		# with or without modifications, as long as this notice is preserved.
881
882		# serial 2
	1018	# Copyright (C) 2004-2013 Free Software Foundation, Inc.
	1019	#
	1020	# This file is free software; the Free Software Foundation
	1021	# gives unlimited permission to copy and/or distribute it,
	1022	# with or without modifications, as long as this notice is preserved.
883	1023
884	1024	# _AM_PROG_TAR(FORMAT)
885	1025	# --------------------
886	1026	# Check how to create a tarball in format FORMAT.
887		# FORMAT should be one of `v7', `ustar', or `pax'.
	1027	# FORMAT should be one of 'v7', 'ustar', or 'pax'.
888	1028	#
889	1029	# Substitute a variable $(am__tar) that is a command
890	1030	# writing to stdout a FORMAT-tarball containing the directory

894	1034	# Substitute a variable $(am__untar) that extract such
895	1035	# a tarball read from stdin.
896	1036	# $(am__untar) < result.tar
	1037	#
897	1038	AC_DEFUN([_AM_PROG_TAR],
898	1039	[# Always define AMTAR for backward compatibility. Yes, it's still used
899	1040	# in the wild :-( We should find a proper way to deprecate it ...
900	1041	AC_SUBST([AMTAR], ['$${TAR-tar}'])
	1042
	1043	# We'll loop over all known methods to create a tar archive until one works.
	1044	_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
	1045
901	1046	m4_if([$1], [v7],
902		[am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
903		[m4_case([$1], [ustar],, [pax],,
904		[m4_fatal([Unknown tar format])])
905		AC_MSG_CHECKING([how to create a $1 tar archive])
906		# Loop over all known methods to create a tar archive until one works.
907		_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
908		_am_tools=${am_cv_prog_tar_$1-$_am_tools}
909		# Do not fold the above two line into one, because Tru64 sh and
910		# Solaris sh will not grok spaces in the rhs of `-'.
911		for _am_tool in $_am_tools
912		do
913		case $_am_tool in
914		gnutar)
915		for _am_tar in tar gnutar gtar;
916		do
917		AM_RUN_LOG([$_am_tar --version]) && break
918		done
919		am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
920		am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
921		am__untar="$_am_tar -xf -"
922		;;
923		plaintar)
924		# Must skip GNU tar: if it does not support --format= it doesn't create
925		# ustar tarball either.
926		(tar --version) >/dev/null 2>&1 && continue
927		am__tar='tar chf - "$$tardir"'
928		am__tar_='tar chf - "$tardir"'
929		am__untar='tar xf -'
930		;;
931		pax)
932		am__tar='pax -L -x $1 -w "$$tardir"'
933		am__tar_='pax -L -x $1 -w "$tardir"'
934		am__untar='pax -r'
935		;;
936		cpio)
937		am__tar='find "$$tardir" -print \| cpio -o -H $1 -L'
938		am__tar_='find "$tardir" -print \| cpio -o -H $1 -L'
939		am__untar='cpio -i -H $1 -d'
940		;;
941		none)
942		am__tar=false
943		am__tar_=false
944		am__untar=false
945		;;
946		esac
947
948		# If the value was cached, stop now. We just wanted to have am__tar
949		# and am__untar set.
950		test -n "${am_cv_prog_tar_$1}" && break
951
952		# tar/untar a dummy directory, and stop if the command works
	1047	[am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
	1048
	1049	[m4_case([$1],
	1050	[ustar],
	1051	[# The POSIX 1988 'ustar' format is defined with fixed-size fields.
	1052	# There is notably a 21 bits limit for the UID and the GID. In fact,
	1053	# the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
	1054	# and bug#13588).
	1055	am_max_uid=2097151 # 2^21 - 1
	1056	am_max_gid=$am_max_uid
	1057	# The $UID and $GID variables are not portable, so we need to resort
	1058	# to the POSIX-mandated id(1) utility. Errors in the 'id' calls
	1059	# below are definitely unexpected, so allow the users to see them
	1060	# (that is, avoid stderr redirection).
	1061	am_uid=`id -u \|\| echo unknown`
	1062	am_gid=`id -g \|\| echo unknown`
	1063	AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
	1064	if test $am_uid -le $am_max_uid; then
	1065	AC_MSG_RESULT([yes])
	1066	else
	1067	AC_MSG_RESULT([no])
	1068	_am_tools=none
	1069	fi
	1070	AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
	1071	if test $am_gid -le $am_max_gid; then
	1072	AC_MSG_RESULT([yes])
	1073	else
	1074	AC_MSG_RESULT([no])
	1075	_am_tools=none
	1076	fi],
	1077
	1078	[pax],
	1079	[],
	1080
	1081	[m4_fatal([Unknown tar format])])
	1082
	1083	AC_MSG_CHECKING([how to create a $1 tar archive])
	1084
	1085	# Go ahead even if we have the value already cached. We do so because we
	1086	# need to set the values for the 'am__tar' and 'am__untar' variables.
	1087	_am_tools=${am_cv_prog_tar_$1-$_am_tools}
	1088
	1089	for _am_tool in $_am_tools; do
	1090	case $_am_tool in
	1091	gnutar)
	1092	for _am_tar in tar gnutar gtar; do
	1093	AM_RUN_LOG([$_am_tar --version]) && break
	1094	done
	1095	am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
	1096	am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
	1097	am__untar="$_am_tar -xf -"
	1098	;;
	1099	plaintar)
	1100	# Must skip GNU tar: if it does not support --format= it doesn't create
	1101	# ustar tarball either.
	1102	(tar --version) >/dev/null 2>&1 && continue
	1103	am__tar='tar chf - "$$tardir"'
	1104	am__tar_='tar chf - "$tardir"'
	1105	am__untar='tar xf -'
	1106	;;
	1107	pax)
	1108	am__tar='pax -L -x $1 -w "$$tardir"'
	1109	am__tar_='pax -L -x $1 -w "$tardir"'
	1110	am__untar='pax -r'
	1111	;;
	1112	cpio)
	1113	am__tar='find "$$tardir" -print \| cpio -o -H $1 -L'
	1114	am__tar_='find "$tardir" -print \| cpio -o -H $1 -L'
	1115	am__untar='cpio -i -H $1 -d'
	1116	;;
	1117	none)
	1118	am__tar=false
	1119	am__tar_=false
	1120	am__untar=false
	1121	;;
	1122	esac
	1123
	1124	# If the value was cached, stop now. We just wanted to have am__tar
	1125	# and am__untar set.
	1126	test -n "${am_cv_prog_tar_$1}" && break
	1127
	1128	# tar/untar a dummy directory, and stop if the command works.
	1129	rm -rf conftest.dir
	1130	mkdir conftest.dir
	1131	echo GrepMe > conftest.dir/file
	1132	AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
	1133	rm -rf conftest.dir
	1134	if test -s conftest.tar; then
	1135	AM_RUN_LOG([$am__untar <conftest.tar])
	1136	AM_RUN_LOG([cat conftest.dir/file])
	1137	grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
	1138	fi
	1139	done
953	1140	rm -rf conftest.dir
954		mkdir conftest.dir
955		echo GrepMe > conftest.dir/file
956		AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
957		rm -rf conftest.dir
958		if test -s conftest.tar; then
959		AM_RUN_LOG([$am__untar <conftest.tar])
960		grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
961		fi
962		done
963		rm -rf conftest.dir
964
965		AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
966		AC_MSG_RESULT([$am_cv_prog_tar_$1])])
	1141
	1142	AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
	1143	AC_MSG_RESULT([$am_cv_prog_tar_$1])])
	1144
967	1145	AC_SUBST([am__tar])
968	1146	AC_SUBST([am__untar])
969	1147	]) # _AM_PROG_TAR

+518

-390

bin/Makefile.in less more

0		# Makefile.in generated by automake 1.11.3 from Makefile.am.
	0	# Makefile.in generated by automake 1.14.1 from Makefile.am.
1	1	# @configure_input@
2	2
3		# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
4		# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
5		# Foundation, Inc.
	3	# Copyright (C) 1994-2013 Free Software Foundation, Inc.
	4
6	5	# This Makefile.in is free software; the Free Software Foundation
7	6	# gives unlimited permission to copy and/or distribute it,
8	7	# with or without modifications, as long as this notice is preserved.

15	14	@SET_MAKE@
16	15
17	16	VPATH = @srcdir@
	17	am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
	18	am__make_running_with_option = \
	19	case $${target_option-} in \
	20	?) ;; \
	21	*) echo "am__make_running_with_option: internal error: invalid" \
	22	"target option '$${target_option-}' specified" >&2; \
	23	exit 1;; \
	24	esac; \
	25	has_opt=no; \
	26	sane_makeflags=$$MAKEFLAGS; \
	27	if $(am__is_gnu_make); then \
	28	sane_makeflags=$$MFLAGS; \
	29	else \
	30	case $$MAKEFLAGS in \
	31	\\[\ \ ]) \
	32	bs=\\; \
	33	sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
	34	\| sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
	35	esac; \
	36	fi; \
	37	skip_next=no; \
	38	strip_trailopt () \
	39	{ \
	40	flg=`printf '%s\n' "$$flg" \| sed "s/$$1.*$$//"`; \
	41	}; \
	42	for flg in $$sane_makeflags; do \
	43	test $$skip_next = yes && { skip_next=no; continue; }; \
	44	case $$flg in \
	45	=\|--*) continue;; \
	46	-*I) strip_trailopt 'I'; skip_next=yes;; \
	47	-I?) strip_trailopt 'I';; \
	48	-*O) strip_trailopt 'O'; skip_next=yes;; \
	49	-O?) strip_trailopt 'O';; \
	50	-*l) strip_trailopt 'l'; skip_next=yes;; \
	51	-l?) strip_trailopt 'l';; \
	52	-[dEDm]) skip_next=yes;; \
	53	-[JT]) skip_next=yes;; \
	54	esac; \
	55	case $$flg in \
	56	$$target_option) has_opt=yes; break;; \
	57	esac; \
	58	done; \
	59	test $$has_opt = yes
	60	am__make_dryrun = (target_option=n; $(am__make_running_with_option))
	61	am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
18	62	pkgdatadir = $(datadir)/@PACKAGE@
19	63	pkgincludedir = $(includedir)/@PACKAGE@
20	64	pkglibdir = $(libdir)/@PACKAGE@

45	89	sim_reads_tran$(EXEEXT) filterfa$(EXEEXT) idba$(EXEEXT) \
46	90	split_scaffold$(EXEEXT) sim_reads$(EXEEXT)
47	91	subdir = bin
48		DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
	92	DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
	93	$(top_srcdir)/depcomp
49	94	ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
50	95	am__aclocal_m4_deps = $(top_srcdir)/configure.ac
51	96	am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \

148	193	am_validate_rna_OBJECTS = validate_rna.$(OBJEXT)
149	194	validate_rna_OBJECTS = $(am_validate_rna_OBJECTS)
150	195	validate_rna_LDADD = $(LDADD)
	196	AM_V_P = $(am__v_P_@AM_V@)
	197	am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
	198	am__v_P_0 = false
	199	am__v_P_1 = :
	200	AM_V_GEN = $(am__v_GEN_@AM_V@)
	201	am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
	202	am__v_GEN_0 = @echo " GEN " $@;
	203	am__v_GEN_1 =
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	205	am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
	206	am__v_at_0 = @
	207	am__v_at_1 =
151	208	DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
152	209	depcomp = $(SHELL) $(top_srcdir)/depcomp
153	210	am__depfiles_maybe = depfiles
154	211	am__mv = mv -f
	212	AM_V_lt = $(am__v_lt_@AM_V@)
	213	am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
	214	am__v_lt_0 = --silent
	215	am__v_lt_1 =
155	216	CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
156	217	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
	218	AM_V_CXX = $(am__v_CXX_@AM_V@)
	219	am__v_CXX_ = $(am__v_CXX_@AM_DEFAULT_V@)
	220	am__v_CXX_0 = @echo " CXX " $@;
	221	am__v_CXX_1 =
157	222	CXXLD = $(CXX)
158	223	CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
159	224	-o $@
	225	AM_V_CXXLD = $(am__v_CXXLD_@AM_V@)
	226	am__v_CXXLD_ = $(am__v_CXXLD_@AM_DEFAULT_V@)
	227	am__v_CXXLD_0 = @echo " CXXLD " $@;
	228	am__v_CXXLD_1 =
160	229	SOURCES = $(fa2fq_SOURCES) $(filter_blat_SOURCES) \
161	230	$(filter_contigs_SOURCES) $(filterfa_SOURCES) $(fq2fa_SOURCES) \
162	231	$(idba_SOURCES) $(idba_hybrid_SOURCES) $(idba_tran_SOURCES) \

185	254	$(validate_component_SOURCES) $(validate_contigs_blat_SOURCES) \
186	255	$(validate_contigs_mummer_SOURCES) \
187	256	$(validate_reads_blat_SOURCES) $(validate_rna_SOURCES)
	257	am__can_run_installinfo = \
	258	case $$AM_UPDATE_INFO_DIR in \
	259	n\|no\|NO) false;; \
	260	*) (install-info --version) >/dev/null 2>&1;; \
	261	esac
	262	am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
	263	# Read a list of newline-separated strings from the standard input,
	264	# and print each of them once, without duplicates. Input order is
	265	# not preserved.
	266	am__uniquify_input = $(AWK) '\
	267	BEGIN { nonempty = 0; } \
	268	{ items[$$0] = 1; nonempty = 1; } \
	269	END { if (nonempty) { for (i in items) print i; }; } \
	270	'
	271	# Make sure the list of sources is unique. This is necessary because,
	272	# e.g., the same source file might be shared among _SOURCES variables
	273	# for different programs/libraries.
	274	am__define_uniq_tagged_files = \
	275	list='$(am__tagged_files)'; \
	276	unique=`for i in $$list; do \
	277	if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
	278	done \| $(am__uniquify_input)`
188	279	ETAGS = etags
189	280	CTAGS = ctags
190	281	DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
191	282	ACLOCAL = @ACLOCAL@
192	283	AMTAR = @AMTAR@
	284	AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
193	285	AUTOCONF = @AUTOCONF@
194	286	AUTOHEADER = @AUTOHEADER@
195	287	AUTOMAKE = @AUTOMAKE@

348	440	$(am__aclocal_m4_deps):
349	441	install-binPROGRAMS: $(bin_PROGRAMS)
350	442	@$(NORMAL_INSTALL)
351		test -z "$(bindir)" \|\| $(MKDIR_P) "$(DESTDIR)$(bindir)"
352	443	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" \|\| list=; \
	444	if test -n "$$list"; then \
	445	echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
	446	$(MKDIR_P) "$(DESTDIR)$(bindir)" \|\| exit 1; \
	447	fi; \
353	448	for p in $$list; do echo "$$p $$p"; done \| \
354	449	sed 's/$(EXEEXT)$$//' \| \
355		while read p p1; do if test -f $$p; \
356		then echo "$$p"; echo "$$p"; else :; fi; \
	450	while read p p1; do if test -f $$p \
	451	; then echo "$$p"; echo "$$p"; else :; fi; \
357	452	done \| \
358		sed -e 'p;s,./,,;n;h' -e 's\|.\|.\|' \
	453	sed -e 'p;s,.*/,,;n;h' \
	454	-e 's\|.*\|.\|' \
359	455	-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' \| \
360	456	sed 'N;N;N;s,\n, ,g' \| \
361	457	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \

376	472	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" \|\| list=; \
377	473	files=`for p in $$list; do echo "$$p"; done \| \
378	474	sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
379		-e 's/$$/$(EXEEXT)/' `; \
	475	-e 's/$$/$(EXEEXT)/' \
	476	`; \
380	477	test -n "$$list" \|\| exit 0; \
381	478	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
382	479	cd "$(DESTDIR)$(bindir)" && rm -f $$files

386	483
387	484	clean-noinstPROGRAMS:
388	485	-test -z "$(noinst_PROGRAMS)" \|\| rm -f $(noinst_PROGRAMS)
	486
389	487	fa2fq$(EXEEXT): $(fa2fq_OBJECTS) $(fa2fq_DEPENDENCIES) $(EXTRA_fa2fq_DEPENDENCIES)
390	488	@rm -f fa2fq$(EXEEXT)
391		$(CXXLINK) $(fa2fq_OBJECTS) $(fa2fq_LDADD) $(LIBS)
	489	$(AM_V_CXXLD)$(CXXLINK) $(fa2fq_OBJECTS) $(fa2fq_LDADD) $(LIBS)
	490
392	491	filter_blat$(EXEEXT): $(filter_blat_OBJECTS) $(filter_blat_DEPENDENCIES) $(EXTRA_filter_blat_DEPENDENCIES)
393	492	@rm -f filter_blat$(EXEEXT)
394		$(CXXLINK) $(filter_blat_OBJECTS) $(filter_blat_LDADD) $(LIBS)
	493	$(AM_V_CXXLD)$(CXXLINK) $(filter_blat_OBJECTS) $(filter_blat_LDADD) $(LIBS)
	494
395	495	filter_contigs$(EXEEXT): $(filter_contigs_OBJECTS) $(filter_contigs_DEPENDENCIES) $(EXTRA_filter_contigs_DEPENDENCIES)
396	496	@rm -f filter_contigs$(EXEEXT)
397		$(CXXLINK) $(filter_contigs_OBJECTS) $(filter_contigs_LDADD) $(LIBS)
	497	$(AM_V_CXXLD)$(CXXLINK) $(filter_contigs_OBJECTS) $(filter_contigs_LDADD) $(LIBS)
	498
398	499	filterfa$(EXEEXT): $(filterfa_OBJECTS) $(filterfa_DEPENDENCIES) $(EXTRA_filterfa_DEPENDENCIES)
399	500	@rm -f filterfa$(EXEEXT)
400		$(CXXLINK) $(filterfa_OBJECTS) $(filterfa_LDADD) $(LIBS)
	501	$(AM_V_CXXLD)$(CXXLINK) $(filterfa_OBJECTS) $(filterfa_LDADD) $(LIBS)
	502
401	503	fq2fa$(EXEEXT): $(fq2fa_OBJECTS) $(fq2fa_DEPENDENCIES) $(EXTRA_fq2fa_DEPENDENCIES)
402	504	@rm -f fq2fa$(EXEEXT)
403		$(CXXLINK) $(fq2fa_OBJECTS) $(fq2fa_LDADD) $(LIBS)
	505	$(AM_V_CXXLD)$(CXXLINK) $(fq2fa_OBJECTS) $(fq2fa_LDADD) $(LIBS)
	506
404	507	idba$(EXEEXT): $(idba_OBJECTS) $(idba_DEPENDENCIES) $(EXTRA_idba_DEPENDENCIES)
405	508	@rm -f idba$(EXEEXT)
406		$(CXXLINK) $(idba_OBJECTS) $(idba_LDADD) $(LIBS)
	509	$(AM_V_CXXLD)$(CXXLINK) $(idba_OBJECTS) $(idba_LDADD) $(LIBS)
	510
407	511	idba_hybrid$(EXEEXT): $(idba_hybrid_OBJECTS) $(idba_hybrid_DEPENDENCIES) $(EXTRA_idba_hybrid_DEPENDENCIES)
408	512	@rm -f idba_hybrid$(EXEEXT)
409		$(CXXLINK) $(idba_hybrid_OBJECTS) $(idba_hybrid_LDADD) $(LIBS)
	513	$(AM_V_CXXLD)$(CXXLINK) $(idba_hybrid_OBJECTS) $(idba_hybrid_LDADD) $(LIBS)
	514
410	515	idba_tran$(EXEEXT): $(idba_tran_OBJECTS) $(idba_tran_DEPENDENCIES) $(EXTRA_idba_tran_DEPENDENCIES)
411	516	@rm -f idba_tran$(EXEEXT)
412		$(CXXLINK) $(idba_tran_OBJECTS) $(idba_tran_LDADD) $(LIBS)
	517	$(AM_V_CXXLD)$(CXXLINK) $(idba_tran_OBJECTS) $(idba_tran_LDADD) $(LIBS)
	518
413	519	idba_tran_test$(EXEEXT): $(idba_tran_test_OBJECTS) $(idba_tran_test_DEPENDENCIES) $(EXTRA_idba_tran_test_DEPENDENCIES)
414	520	@rm -f idba_tran_test$(EXEEXT)
415		$(CXXLINK) $(idba_tran_test_OBJECTS) $(idba_tran_test_LDADD) $(LIBS)
	521	$(AM_V_CXXLD)$(CXXLINK) $(idba_tran_test_OBJECTS) $(idba_tran_test_LDADD) $(LIBS)
	522
416	523	idba_ud$(EXEEXT): $(idba_ud_OBJECTS) $(idba_ud_DEPENDENCIES) $(EXTRA_idba_ud_DEPENDENCIES)
417	524	@rm -f idba_ud$(EXEEXT)
418		$(CXXLINK) $(idba_ud_OBJECTS) $(idba_ud_LDADD) $(LIBS)
	525	$(AM_V_CXXLD)$(CXXLINK) $(idba_ud_OBJECTS) $(idba_ud_LDADD) $(LIBS)
	526
419	527	parallel_blat$(EXEEXT): $(parallel_blat_OBJECTS) $(parallel_blat_DEPENDENCIES) $(EXTRA_parallel_blat_DEPENDENCIES)
420	528	@rm -f parallel_blat$(EXEEXT)
421		$(CXXLINK) $(parallel_blat_OBJECTS) $(parallel_blat_LDADD) $(LIBS)
	529	$(AM_V_CXXLD)$(CXXLINK) $(parallel_blat_OBJECTS) $(parallel_blat_LDADD) $(LIBS)
	530
422	531	parallel_rna_blat$(EXEEXT): $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_DEPENDENCIES) $(EXTRA_parallel_rna_blat_DEPENDENCIES)
423	532	@rm -f parallel_rna_blat$(EXEEXT)
424		$(CXXLINK) $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_LDADD) $(LIBS)
	533	$(AM_V_CXXLD)$(CXXLINK) $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_LDADD) $(LIBS)
	534
425	535	print_graph$(EXEEXT): $(print_graph_OBJECTS) $(print_graph_DEPENDENCIES) $(EXTRA_print_graph_DEPENDENCIES)
426	536	@rm -f print_graph$(EXEEXT)
427		$(CXXLINK) $(print_graph_OBJECTS) $(print_graph_LDADD) $(LIBS)
	537	$(AM_V_CXXLD)$(CXXLINK) $(print_graph_OBJECTS) $(print_graph_LDADD) $(LIBS)
	538
428	539	raw_n50$(EXEEXT): $(raw_n50_OBJECTS) $(raw_n50_DEPENDENCIES) $(EXTRA_raw_n50_DEPENDENCIES)
429	540	@rm -f raw_n50$(EXEEXT)
430		$(CXXLINK) $(raw_n50_OBJECTS) $(raw_n50_LDADD) $(LIBS)
	541	$(AM_V_CXXLD)$(CXXLINK) $(raw_n50_OBJECTS) $(raw_n50_LDADD) $(LIBS)
	542
431	543	sample_reads$(EXEEXT): $(sample_reads_OBJECTS) $(sample_reads_DEPENDENCIES) $(EXTRA_sample_reads_DEPENDENCIES)
432	544	@rm -f sample_reads$(EXEEXT)
433		$(CXXLINK) $(sample_reads_OBJECTS) $(sample_reads_LDADD) $(LIBS)
	545	$(AM_V_CXXLD)$(CXXLINK) $(sample_reads_OBJECTS) $(sample_reads_LDADD) $(LIBS)
	546
434	547	scaffold$(EXEEXT): $(scaffold_OBJECTS) $(scaffold_DEPENDENCIES) $(EXTRA_scaffold_DEPENDENCIES)
435	548	@rm -f scaffold$(EXEEXT)
436		$(CXXLINK) $(scaffold_OBJECTS) $(scaffold_LDADD) $(LIBS)
	549	$(AM_V_CXXLD)$(CXXLINK) $(scaffold_OBJECTS) $(scaffold_LDADD) $(LIBS)
	550
437	551	shuffle_reads$(EXEEXT): $(shuffle_reads_OBJECTS) $(shuffle_reads_DEPENDENCIES) $(EXTRA_shuffle_reads_DEPENDENCIES)
438	552	@rm -f shuffle_reads$(EXEEXT)
439		$(CXXLINK) $(shuffle_reads_OBJECTS) $(shuffle_reads_LDADD) $(LIBS)
	553	$(AM_V_CXXLD)$(CXXLINK) $(shuffle_reads_OBJECTS) $(shuffle_reads_LDADD) $(LIBS)
	554
440	555	sim_reads$(EXEEXT): $(sim_reads_OBJECTS) $(sim_reads_DEPENDENCIES) $(EXTRA_sim_reads_DEPENDENCIES)
441	556	@rm -f sim_reads$(EXEEXT)
442		$(CXXLINK) $(sim_reads_OBJECTS) $(sim_reads_LDADD) $(LIBS)
	557	$(AM_V_CXXLD)$(CXXLINK) $(sim_reads_OBJECTS) $(sim_reads_LDADD) $(LIBS)
	558
443	559	sim_reads_tran$(EXEEXT): $(sim_reads_tran_OBJECTS) $(sim_reads_tran_DEPENDENCIES) $(EXTRA_sim_reads_tran_DEPENDENCIES)
444	560	@rm -f sim_reads_tran$(EXEEXT)
445		$(CXXLINK) $(sim_reads_tran_OBJECTS) $(sim_reads_tran_LDADD) $(LIBS)
	561	$(AM_V_CXXLD)$(CXXLINK) $(sim_reads_tran_OBJECTS) $(sim_reads_tran_LDADD) $(LIBS)
	562
446	563	sort_psl$(EXEEXT): $(sort_psl_OBJECTS) $(sort_psl_DEPENDENCIES) $(EXTRA_sort_psl_DEPENDENCIES)
447	564	@rm -f sort_psl$(EXEEXT)
448		$(CXXLINK) $(sort_psl_OBJECTS) $(sort_psl_LDADD) $(LIBS)
	565	$(AM_V_CXXLD)$(CXXLINK) $(sort_psl_OBJECTS) $(sort_psl_LDADD) $(LIBS)
	566
449	567	sort_reads$(EXEEXT): $(sort_reads_OBJECTS) $(sort_reads_DEPENDENCIES) $(EXTRA_sort_reads_DEPENDENCIES)
450	568	@rm -f sort_reads$(EXEEXT)
451		$(CXXLINK) $(sort_reads_OBJECTS) $(sort_reads_LDADD) $(LIBS)
	569	$(AM_V_CXXLD)$(CXXLINK) $(sort_reads_OBJECTS) $(sort_reads_LDADD) $(LIBS)
	570
452	571	split_fa$(EXEEXT): $(split_fa_OBJECTS) $(split_fa_DEPENDENCIES) $(EXTRA_split_fa_DEPENDENCIES)
453	572	@rm -f split_fa$(EXEEXT)
454		$(CXXLINK) $(split_fa_OBJECTS) $(split_fa_LDADD) $(LIBS)
	573	$(AM_V_CXXLD)$(CXXLINK) $(split_fa_OBJECTS) $(split_fa_LDADD) $(LIBS)
	574
455	575	split_fq$(EXEEXT): $(split_fq_OBJECTS) $(split_fq_DEPENDENCIES) $(EXTRA_split_fq_DEPENDENCIES)
456	576	@rm -f split_fq$(EXEEXT)
457		$(CXXLINK) $(split_fq_OBJECTS) $(split_fq_LDADD) $(LIBS)
	577	$(AM_V_CXXLD)$(CXXLINK) $(split_fq_OBJECTS) $(split_fq_LDADD) $(LIBS)
	578
458	579	split_scaffold$(EXEEXT): $(split_scaffold_OBJECTS) $(split_scaffold_DEPENDENCIES) $(EXTRA_split_scaffold_DEPENDENCIES)
459	580	@rm -f split_scaffold$(EXEEXT)
460		$(CXXLINK) $(split_scaffold_OBJECTS) $(split_scaffold_LDADD) $(LIBS)
	581	$(AM_V_CXXLD)$(CXXLINK) $(split_scaffold_OBJECTS) $(split_scaffold_LDADD) $(LIBS)
	582
461	583	test$(EXEEXT): $(test_OBJECTS) $(test_DEPENDENCIES) $(EXTRA_test_DEPENDENCIES)
462	584	@rm -f test$(EXEEXT)
463		$(CXXLINK) $(test_OBJECTS) $(test_LDADD) $(LIBS)
	585	$(AM_V_CXXLD)$(CXXLINK) $(test_OBJECTS) $(test_LDADD) $(LIBS)
	586
464	587	validate_component$(EXEEXT): $(validate_component_OBJECTS) $(validate_component_DEPENDENCIES) $(EXTRA_validate_component_DEPENDENCIES)
465	588	@rm -f validate_component$(EXEEXT)
466		$(CXXLINK) $(validate_component_OBJECTS) $(validate_component_LDADD) $(LIBS)
	589	$(AM_V_CXXLD)$(CXXLINK) $(validate_component_OBJECTS) $(validate_component_LDADD) $(LIBS)
	590
467	591	validate_contigs_blat$(EXEEXT): $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_DEPENDENCIES) $(EXTRA_validate_contigs_blat_DEPENDENCIES)
468	592	@rm -f validate_contigs_blat$(EXEEXT)
469		$(CXXLINK) $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_LDADD) $(LIBS)
	593	$(AM_V_CXXLD)$(CXXLINK) $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_LDADD) $(LIBS)
	594
470	595	validate_contigs_mummer$(EXEEXT): $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_DEPENDENCIES) $(EXTRA_validate_contigs_mummer_DEPENDENCIES)
471	596	@rm -f validate_contigs_mummer$(EXEEXT)
472		$(CXXLINK) $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_LDADD) $(LIBS)
	597	$(AM_V_CXXLD)$(CXXLINK) $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_LDADD) $(LIBS)
	598
473	599	validate_reads_blat$(EXEEXT): $(validate_reads_blat_OBJECTS) $(validate_reads_blat_DEPENDENCIES) $(EXTRA_validate_reads_blat_DEPENDENCIES)
474	600	@rm -f validate_reads_blat$(EXEEXT)
475		$(CXXLINK) $(validate_reads_blat_OBJECTS) $(validate_reads_blat_LDADD) $(LIBS)
	601	$(AM_V_CXXLD)$(CXXLINK) $(validate_reads_blat_OBJECTS) $(validate_reads_blat_LDADD) $(LIBS)
	602
476	603	validate_rna$(EXEEXT): $(validate_rna_OBJECTS) $(validate_rna_DEPENDENCIES) $(EXTRA_validate_rna_DEPENDENCIES)
477	604	@rm -f validate_rna$(EXEEXT)
478		$(CXXLINK) $(validate_rna_OBJECTS) $(validate_rna_LDADD) $(LIBS)
	605	$(AM_V_CXXLD)$(CXXLINK) $(validate_rna_OBJECTS) $(validate_rna_LDADD) $(LIBS)
479	606
480	607	mostlyclean-compile:
481	608	-rm -f *.$(OBJEXT)

515	642	@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/validate_rna.Po@am__quote@
516	643
517	644	.cpp.o:
518		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
519		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
520		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
521		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
522		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
	645	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
	646	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
	647	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
	648	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	649	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ $<
523	650
524	651	.cpp.obj:
525		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
526		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
527		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
528		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
529		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
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	653	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
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530	657
531	658	fa2fq.o: $(top_srcdir)/src/tools/fa2fq.cpp
532		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fa2fq.o -MD -MP -MF $(DEPDIR)/fa2fq.Tpo -c -o fa2fq.o `test -f '$(top_srcdir)/src/tools/fa2fq.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/fa2fq.cpp
533		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/fa2fq.Tpo $(DEPDIR)/fa2fq.Po
534		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/tools/fa2fq.cpp' object='fa2fq.o' libtool=no @AMDEPBACKSLASH@
535		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
536		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fa2fq.o `test -f '$(top_srcdir)/src/tools/fa2fq.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/fa2fq.cpp
	659	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fa2fq.o -MD -MP -MF $(DEPDIR)/fa2fq.Tpo -c -o fa2fq.o `test -f '$(top_srcdir)/src/tools/fa2fq.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/fa2fq.cpp
	660	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/fa2fq.Tpo $(DEPDIR)/fa2fq.Po
	661	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$(top_srcdir)/src/tools/fa2fq.cpp' object='fa2fq.o' libtool=no @AMDEPBACKSLASH@
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	663	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fa2fq.o `test -f '$(top_srcdir)/src/tools/fa2fq.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/fa2fq.cpp
537	664
538	665	fa2fq.obj: $(top_srcdir)/src/tools/fa2fq.cpp
539		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fa2fq.obj -MD -MP -MF $(DEPDIR)/fa2fq.Tpo -c -o fa2fq.obj `if test -f '$(top_srcdir)/src/tools/fa2fq.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/tools/fa2fq.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/tools/fa2fq.cpp'; fi`
540		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/fa2fq.Tpo $(DEPDIR)/fa2fq.Po
541		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/tools/fa2fq.cpp' object='fa2fq.obj' libtool=no @AMDEPBACKSLASH@
542		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
543		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fa2fq.obj `if test -f '$(top_srcdir)/src/tools/fa2fq.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/tools/fa2fq.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/tools/fa2fq.cpp'; fi`
	666	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fa2fq.obj -MD -MP -MF $(DEPDIR)/fa2fq.Tpo -c -o fa2fq.obj `if test -f '$(top_srcdir)/src/tools/fa2fq.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/tools/fa2fq.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/tools/fa2fq.cpp'; fi`
	667	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/fa2fq.Tpo $(DEPDIR)/fa2fq.Po
	668	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$(top_srcdir)/src/tools/fa2fq.cpp' object='fa2fq.obj' libtool=no @AMDEPBACKSLASH@
	669	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	670	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fa2fq.obj `if test -f '$(top_srcdir)/src/tools/fa2fq.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/tools/fa2fq.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/tools/fa2fq.cpp'; fi`
544	671
545	672	filter_blat.o: $(top_srcdir)/src/tools/filter_blat.cpp
546		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT filter_blat.o -MD -MP -MF $(DEPDIR)/filter_blat.Tpo -c -o filter_blat.o `test -f '$(top_srcdir)/src/tools/filter_blat.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/filter_blat.cpp
547		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/filter_blat.Tpo $(DEPDIR)/filter_blat.Po
548		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/tools/filter_blat.cpp' object='filter_blat.o' libtool=no @AMDEPBACKSLASH@
549		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
550		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o filter_blat.o `test -f '$(top_srcdir)/src/tools/filter_blat.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/filter_blat.cpp
	673	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT filter_blat.o -MD -MP -MF $(DEPDIR)/filter_blat.Tpo -c -o filter_blat.o `test -f '$(top_srcdir)/src/tools/filter_blat.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/filter_blat.cpp
	674	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/filter_blat.Tpo $(DEPDIR)/filter_blat.Po
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909	1036	validate_contigs_mummer.o: $(top_srcdir)/src/tools/validate_contigs_mummer.cpp
910		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT validate_contigs_mummer.o -MD -MP -MF $(DEPDIR)/validate_contigs_mummer.Tpo -c -o validate_contigs_mummer.o `test -f '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/tools/validate_contigs_mummer.cpp
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915	1042
916	1043	validate_contigs_mummer.obj: $(top_srcdir)/src/tools/validate_contigs_mummer.cpp
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922	1049
923	1050	validate_reads_blat.o: $(top_srcdir)/src/tools/validate_reads_blat.cpp
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929	1056
930	1057	validate_reads_blat.obj: $(top_srcdir)/src/tools/validate_reads_blat.cpp
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936	1063
937	1064	validate_rna.o: $(top_srcdir)/src/tools/validate_rna.cpp
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1154	1282
1155	1283
1156	1284	# Tell versions [3.59,3.63) of GNU make to not export all variables.

+347

-0

compile less more

	0	#! /bin/sh
	1	# Wrapper for compilers which do not understand '-c -o'.
	2
	3	scriptversion=2012-10-14.11; # UTC
	4
	5	# Copyright (C) 1999-2013 Free Software Foundation, Inc.
	6	# Written by Tom Tromey <tromey@cygnus.com>.
	7	#
	8	# This program is free software; you can redistribute it and/or modify
	9	# it under the terms of the GNU General Public License as published by
	10	# the Free Software Foundation; either version 2, or (at your option)
	11	# any later version.
	12	#
	13	# This program is distributed in the hope that it will be useful,
	14	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	15	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	16	# GNU General Public License for more details.
	17	#
	18	# You should have received a copy of the GNU General Public License
	19	# along with this program. If not, see <http://www.gnu.org/licenses/>.
	20
	21	# As a special exception to the GNU General Public License, if you
	22	# distribute this file as part of a program that contains a
	23	# configuration script generated by Autoconf, you may include it under
	24	# the same distribution terms that you use for the rest of that program.
	25
	26	# This file is maintained in Automake, please report
	27	# bugs to <bug-automake@gnu.org> or send patches to
	28	# <automake-patches@gnu.org>.
	29
	30	nl='
	31	'
	32
	33	# We need space, tab and new line, in precisely that order. Quoting is
	34	# there to prevent tools from complaining about whitespace usage.
	35	IFS=" "" $nl"
	36
	37	file_conv=
	38
	39	# func_file_conv build_file lazy
	40	# Convert a $build file to $host form and store it in $file
	41	# Currently only supports Windows hosts. If the determined conversion
	42	# type is listed in (the comma separated) LAZY, no conversion will
	43	# take place.
	44	func_file_conv ()
	45	{
	46	file=$1
	47	case $file in
	48	/ \| /[!/]*) # absolute file, and not a UNC file
	49	if test -z "$file_conv"; then
	50	# lazily determine how to convert abs files
	51	case `uname -s` in
	52	MINGW*)
	53	file_conv=mingw
	54	;;
	55	CYGWIN*)
	56	file_conv=cygwin
	57	;;
	58	*)
	59	file_conv=wine
	60	;;
	61	esac
	62	fi
	63	case $file_conv/,$2, in
	64	,$file_conv,)
	65	;;
	66	mingw/*)
	67	file=`cmd //C echo "$file " \| sed -e 's/"$.$ " $/\1/'`
	68	;;
	69	cygwin/*)
	70	file=`cygpath -m "$file" \|\| echo "$file"`
	71	;;
	72	wine/*)
	73	file=`winepath -w "$file" \|\| echo "$file"`
	74	;;
	75	esac
	76	;;
	77	esac
	78	}
	79
	80	# func_cl_dashL linkdir
	81	# Make cl look for libraries in LINKDIR
	82	func_cl_dashL ()
	83	{
	84	func_file_conv "$1"
	85	if test -z "$lib_path"; then
	86	lib_path=$file
	87	else
	88	lib_path="$lib_path;$file"
	89	fi
	90	linker_opts="$linker_opts -LIBPATH:$file"
	91	}
	92
	93	# func_cl_dashl library
	94	# Do a library search-path lookup for cl
	95	func_cl_dashl ()
	96	{
	97	lib=$1
	98	found=no
	99	save_IFS=$IFS
	100	IFS=';'
	101	for dir in $lib_path $LIB
	102	do
	103	IFS=$save_IFS
	104	if $shared && test -f "$dir/$lib.dll.lib"; then
	105	found=yes
	106	lib=$dir/$lib.dll.lib
	107	break
	108	fi
	109	if test -f "$dir/$lib.lib"; then
	110	found=yes
	111	lib=$dir/$lib.lib
	112	break
	113	fi
	114	if test -f "$dir/lib$lib.a"; then
	115	found=yes
	116	lib=$dir/lib$lib.a
	117	break
	118	fi
	119	done
	120	IFS=$save_IFS
	121
	122	if test "$found" != yes; then
	123	lib=$lib.lib
	124	fi
	125	}
	126
	127	# func_cl_wrapper cl arg...
	128	# Adjust compile command to suit cl
	129	func_cl_wrapper ()
	130	{
	131	# Assume a capable shell
	132	lib_path=
	133	shared=:
	134	linker_opts=
	135	for arg
	136	do
	137	if test -n "$eat"; then
	138	eat=
	139	else
	140	case $1 in
	141	-o)
	142	# configure might choose to run compile as 'compile cc -o foo foo.c'.
	143	eat=1
	144	case $2 in
	145	.o \| .[oO][bB][jJ])
	146	func_file_conv "$2"
	147	set x "$@" -Fo"$file"
	148	shift
	149	;;
	150	*)
	151	func_file_conv "$2"
	152	set x "$@" -Fe"$file"
	153	shift
	154	;;
	155	esac
	156	;;
	157	-I)
	158	eat=1
	159	func_file_conv "$2" mingw
	160	set x "$@" -I"$file"
	161	shift
	162	;;
	163	-I*)
	164	func_file_conv "${1#-I}" mingw
	165	set x "$@" -I"$file"
	166	shift
	167	;;
	168	-l)
	169	eat=1
	170	func_cl_dashl "$2"
	171	set x "$@" "$lib"
	172	shift
	173	;;
	174	-l*)
	175	func_cl_dashl "${1#-l}"
	176	set x "$@" "$lib"
	177	shift
	178	;;
	179	-L)
	180	eat=1
	181	func_cl_dashL "$2"
	182	;;
	183	-L*)
	184	func_cl_dashL "${1#-L}"
	185	;;
	186	-static)
	187	shared=false
	188	;;
	189	-Wl,*)
	190	arg=${1#-Wl,}
	191	save_ifs="$IFS"; IFS=','
	192	for flag in $arg; do
	193	IFS="$save_ifs"
	194	linker_opts="$linker_opts $flag"
	195	done
	196	IFS="$save_ifs"
	197	;;
	198	-Xlinker)
	199	eat=1
	200	linker_opts="$linker_opts $2"
	201	;;
	202	-*)
	203	set x "$@" "$1"
	204	shift
	205	;;
	206	.cc \| .CC \| .cxx \| .CXX \| *.[cC]++)
	207	func_file_conv "$1"
	208	set x "$@" -Tp"$file"
	209	shift
	210	;;
	211	.c \| .cpp \| .CPP \| .lib \| .LIB \| .Lib \| .OBJ \| .obj \| *.[oO])
	212	func_file_conv "$1" mingw
	213	set x "$@" "$file"
	214	shift
	215	;;
	216	*)
	217	set x "$@" "$1"
	218	shift
	219	;;
	220	esac
	221	fi
	222	shift
	223	done
	224	if test -n "$linker_opts"; then
	225	linker_opts="-link$linker_opts"
	226	fi
	227	exec "$@" $linker_opts
	228	exit 1
	229	}
	230
	231	eat=
	232
	233	case $1 in
	234	'')
	235	echo "$0: No command. Try '$0 --help' for more information." 1>&2
	236	exit 1;
	237	;;
	238	-h \| --h*)
	239	cat <<\EOF
	240	Usage: compile [--help] [--version] PROGRAM [ARGS]
	241
	242	Wrapper for compilers which do not understand '-c -o'.
	243	Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
	244	arguments, and rename the output as expected.
	245
	246	If you are trying to build a whole package this is not the
	247	right script to run: please start by reading the file 'INSTALL'.
	248
	249	Report bugs to <bug-automake@gnu.org>.
	250	EOF
	251	exit $?
	252	;;
	253	-v \| --v*)
	254	echo "compile $scriptversion"
	255	exit $?
	256	;;
	257	cl \| [/\\]cl \| cl.exe \| [/\\]cl.exe )
	258	func_cl_wrapper "$@" # Doesn't return...
	259	;;
	260	esac
	261
	262	ofile=
	263	cfile=
	264
	265	for arg
	266	do
	267	if test -n "$eat"; then
	268	eat=
	269	else
	270	case $1 in
	271	-o)
	272	# configure might choose to run compile as 'compile cc -o foo foo.c'.
	273	# So we strip '-o arg' only if arg is an object.
	274	eat=1
	275	case $2 in
	276	.o \| .obj)
	277	ofile=$2
	278	;;
	279	*)
	280	set x "$@" -o "$2"
	281	shift
	282	;;
	283	esac
	284	;;
	285	*.c)
	286	cfile=$1
	287	set x "$@" "$1"
	288	shift
	289	;;
	290	*)
	291	set x "$@" "$1"
	292	shift
	293	;;
	294	esac
	295	fi
	296	shift
	297	done
	298
	299	if test -z "$ofile" \|\| test -z "$cfile"; then
	300	# If no '-o' option was seen then we might have been invoked from a
	301	# pattern rule where we don't need one. That is ok -- this is a
	302	# normal compilation that the losing compiler can handle. If no
	303	# '.c' file was seen then we are probably linking. That is also
	304	# ok.
	305	exec "$@"
	306	fi
	307
	308	# Name of file we expect compiler to create.
	309	cofile=`echo "$cfile" \| sed 's\|^.*[\\/]\|\|; s\|^[a-zA-Z]:\|\|; s/\.c$/.o/'`
	310
	311	# Create the lock directory.
	312	# Note: use '[/\\:.-]' here to ensure that we don't use the same name
	313	# that we are using for the .o file. Also, base the name on the expected
	314	# object file name, since that is what matters with a parallel build.
	315	lockdir=`echo "$cofile" \| sed -e 's\|[/\\:.-]\|_\|g'`.d
	316	while true; do
	317	if mkdir "$lockdir" >/dev/null 2>&1; then
	318	break
	319	fi
	320	sleep 1
	321	done
	322	# FIXME: race condition here if user kills between mkdir and trap.
	323	trap "rmdir '$lockdir'; exit 1" 1 2 15
	324
	325	# Run the compile.
	326	"$@"
	327	ret=$?
	328
	329	if test -f "$cofile"; then
	330	test "$cofile" = "$ofile" \|\| mv "$cofile" "$ofile"
	331	elif test -f "${cofile}bj"; then
	332	test "${cofile}bj" = "$ofile" \|\| mv "${cofile}bj" "$ofile"
	333	fi
	334
	335	rmdir "$lockdir"
	336	exit $ret
	337
	338	# Local Variables:
	339	# mode: shell-script
	340	# sh-indentation: 2
	341	# eval: (add-hook 'write-file-hooks 'time-stamp)
	342	# time-stamp-start: "scriptversion="
	343	# time-stamp-format: "%:y-%02m-%02d.%02H"
	344	# time-stamp-time-zone: "UTC"
	345	# time-stamp-end: "; # UTC"
	346	# End:

+419

-237

configure less more

0	0	#! /bin/sh
1	1	# Guess values for system-dependent variables and create Makefiles.
2		# Generated by GNU Autoconf 2.68 for idba 1.1.2.
	2	# Generated by GNU Autoconf 2.69 for idba 1.1.3.
3	3	#
4	4	# Report bugs to <loneknightpy@gmail.com>.
5	5	#
6	6	#
7		# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
8		# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
9		# Foundation, Inc.
	7	# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
10	8	#
11	9	#
12	10	# This configure script is free software; the Free Software Foundation

135	133	# CDPATH.
136	134	(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
137	135
	136	# Use a proper internal environment variable to ensure we don't fall
	137	# into an infinite loop, continuously re-executing ourselves.
	138	if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
	139	_as_can_reexec=no; export _as_can_reexec;
	140	# We cannot yet assume a decent shell, so we have to provide a
	141	# neutralization value for shells without unset; and this also
	142	# works around shells that cannot unset nonexistent variables.
	143	# Preserve -v and -x to the replacement shell.
	144	BASH_ENV=/dev/null
	145	ENV=/dev/null
	146	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
	147	case $- in # ((((
	148	vx* \| xv* ) as_opts=-vx ;;
	149	v ) as_opts=-v ;;
	150	x ) as_opts=-x ;;
	151	* ) as_opts= ;;
	152	esac
	153	exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
	154	# Admittedly, this is quite paranoid, since all the known shells bail
	155	# out after a failed `exec'.
	156	$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
	157	as_fn_exit 255
	158	fi
	159	# We don't want this to propagate to other subprocesses.
	160	{ _as_can_reexec=; unset _as_can_reexec;}
138	161	if test "x$CONFIG_SHELL" = x; then
139	162	as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
140	163	emulate sh

168	191	else
169	192	exitcode=1; echo positional parameters were not saved.
170	193	fi
171		test x\$exitcode = x0 \|\| exit 1"
	194	test x\$exitcode = x0 \|\| exit 1
	195	test -x / \|\| exit 1"
172	196	as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
173	197	as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
174	198	eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&

213	237
214	238
215	239	if test "x$CONFIG_SHELL" != x; then :
216		# We cannot yet assume a decent shell, so we have to provide a
217		# neutralization value for shells without unset; and this also
218		# works around shells that cannot unset nonexistent variables.
219		# Preserve -v and -x to the replacement shell.
220		BASH_ENV=/dev/null
221		ENV=/dev/null
222		(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
223		export CONFIG_SHELL
224		case $- in # ((((
225		vx* \| xv* ) as_opts=-vx ;;
226		v ) as_opts=-v ;;
227		x ) as_opts=-x ;;
228		* ) as_opts= ;;
229		esac
230		exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
	240	export CONFIG_SHELL
	241	# We cannot yet assume a decent shell, so we have to provide a
	242	# neutralization value for shells without unset; and this also
	243	# works around shells that cannot unset nonexistent variables.
	244	# Preserve -v and -x to the replacement shell.
	245	BASH_ENV=/dev/null
	246	ENV=/dev/null
	247	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
	248	case $- in # ((((
	249	vx* \| xv* ) as_opts=-vx ;;
	250	v ) as_opts=-v ;;
	251	x ) as_opts=-x ;;
	252	* ) as_opts= ;;
	253	esac
	254	exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
	255	# Admittedly, this is quite paranoid, since all the known shells bail
	256	# out after a failed `exec'.
	257	$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
	258	exit 255
231	259	fi
232	260
233	261	if test x$as_have_required = xno; then :

330	358
331	359
332	360	} # as_fn_mkdir_p
	361
	362	# as_fn_executable_p FILE
	363	# -----------------------
	364	# Test if FILE is an executable regular file.
	365	as_fn_executable_p ()
	366	{
	367	test -f "$1" && test -x "$1"
	368	} # as_fn_executable_p
333	369	# as_fn_append VAR VALUE
334	370	# ----------------------
335	371	# Append the text in VALUE to the end of the definition contained in VAR. Take

451	487	chmod +x "$as_me.lineno" \|\|
452	488	{ $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
453	489
	490	# If we had to re-execute with $CONFIG_SHELL, we're ensured to have
	491	# already done that, so ensure we don't try to do so again and fall
	492	# in an infinite loop. This has already happened in practice.
	493	_as_can_reexec=no; export _as_can_reexec
454	494	# Don't try to exec as it changes $[0], causing all sort of problems
455	495	# (the dirname of $[0] is not the place where we might find the
456	496	# original and so on. Autoconf is especially sensitive to this).

485	525	# ... but there are two gotchas:
486	526	# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
487	527	# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
488		# In both cases, we have to default to `cp -p'.
	528	# In both cases, we have to default to `cp -pR'.
489	529	ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe \|\|
490		as_ln_s='cp -p'
	530	as_ln_s='cp -pR'
491	531	elif ln conf$$.file conf$$ 2>/dev/null; then
492	532	as_ln_s=ln
493	533	else
494		as_ln_s='cp -p'
	534	as_ln_s='cp -pR'
495	535	fi
496	536	else
497		as_ln_s='cp -p'
	537	as_ln_s='cp -pR'
498	538	fi
499	539	rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
500	540	rmdir conf$$.dir 2>/dev/null

506	546	as_mkdir_p=false
507	547	fi
508	548
509		if test -x / >/dev/null 2>&1; then
510		as_test_x='test -x'
511		else
512		if ls -dL / >/dev/null 2>&1; then
513		as_ls_L_option=L
514		else
515		as_ls_L_option=
516		fi
517		as_test_x='
518		eval sh -c '\''
519		if test -d "$1"; then
520		test -d "$1/.";
521		else
522		case $1 in #(
523		-*)set "./$1";;
524		esac;
525		case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
526		???[sx]):;;)false;;esac;fi
527		'\'' sh
528		'
529		fi
530		as_executable_p=$as_test_x
	549	as_test_x='test -x'
	550	as_executable_p=as_fn_executable_p
531	551
532	552	# Sed expression to map a string onto a valid CPP name.
533	553	as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"

559	579	# Identity of this package.
560	580	PACKAGE_NAME='idba'
561	581	PACKAGE_TARNAME='idba'
562		PACKAGE_VERSION='1.1.2'
563		PACKAGE_STRING='idba 1.1.2'
	582	PACKAGE_VERSION='1.1.3'
	583	PACKAGE_STRING='idba 1.1.3'
564	584	PACKAGE_BUGREPORT='loneknightpy@gmail.com'
565	585	PACKAGE_URL=''
566	586

632	652	LDFLAGS
633	653	CXXFLAGS
634	654	CXX
	655	AM_BACKSLASH
	656	AM_DEFAULT_VERBOSITY
	657	AM_DEFAULT_V
	658	AM_V
635	659	am__untar
636	660	am__tar
637	661	AMTAR

696	720	ac_subst_files=''
697	721	ac_user_opts='
698	722	enable_option_checking
	723	enable_silent_rules
699	724	enable_dependency_tracking
700	725	'
701	726	ac_precious_vars='build_alias

1165	1190	if test "x$host_alias" != x; then
1166	1191	if test "x$build_alias" = x; then
1167	1192	cross_compiling=maybe
1168		$as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
1169		If a cross compiler is detected then cross compile mode will be used" >&2
1170	1193	elif test "x$build_alias" != "x$host_alias"; then
1171	1194	cross_compiling=yes
1172	1195	fi

1252	1275	# Omit some internal or obsolete options to make the list less imposing.
1253	1276	# This message is too long to be a string in the A/UX 3.1 sh.
1254	1277	cat <<_ACEOF
1255		\`configure' configures idba 1.1.2 to adapt to many kinds of systems.
	1278	\`configure' configures idba 1.1.3 to adapt to many kinds of systems.
1256	1279
1257	1280	Usage: $0 [OPTION]... [VAR=VALUE]...
1258	1281

1318	1341
1319	1342	if test -n "$ac_init_help"; then
1320	1343	case $ac_init_help in
1321		short \| recursive ) echo "Configuration of idba 1.1.2:";;
	1344	short \| recursive ) echo "Configuration of idba 1.1.3:";;
1322	1345	esac
1323	1346	cat <<\_ACEOF
1324	1347

1326	1349	--disable-option-checking ignore unrecognized --enable/--with options
1327	1350	--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
1328	1351	--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
1329		--disable-dependency-tracking speeds up one-time build
1330		--enable-dependency-tracking do not reject slow dependency extractors
	1352	--enable-silent-rules less verbose build output (undo: "make V=1")
	1353	--disable-silent-rules verbose build output (undo: "make V=0")
	1354	--enable-dependency-tracking
	1355	do not reject slow dependency extractors
	1356	--disable-dependency-tracking
	1357	speeds up one-time build
1331	1358
1332	1359	Some influential environment variables:
1333	1360	CXX C++ compiler command

1407	1434	test -n "$ac_init_help" && exit $ac_status
1408	1435	if $ac_init_version; then
1409	1436	cat <<\_ACEOF
1410		idba configure 1.1.2
1411		generated by GNU Autoconf 2.68
1412
1413		Copyright (C) 2010 Free Software Foundation, Inc.
	1437	idba configure 1.1.3
	1438	generated by GNU Autoconf 2.69
	1439
	1440	Copyright (C) 2012 Free Software Foundation, Inc.
1414	1441	This configure script is free software; the Free Software Foundation
1415	1442	gives unlimited permission to copy, distribute and modify it.
1416	1443	_ACEOF

1688	1715	test ! -s conftest.err
1689	1716	} && test -s conftest$ac_exeext && {
1690	1717	test "$cross_compiling" = yes \|\|
1691		$as_test_x conftest$ac_exeext
	1718	test -x conftest$ac_exeext
1692	1719	}; then :
1693	1720	ac_retval=0
1694	1721	else

1777	1804	This file contains any messages produced by compilers while
1778	1805	running configure, to aid debugging if configure makes a mistake.
1779	1806
1780		It was created by idba $as_me 1.1.2, which was
1781		generated by GNU Autoconf 2.68. Invocation command line was
	1807	It was created by idba $as_me 1.1.3, which was
	1808	generated by GNU Autoconf 2.69. Invocation command line was
1782	1809
1783	1810	$ $0 $@
1784	1811

2128	2155
2129	2156	ac_config_headers="$ac_config_headers config.h"
2130	2157
2131		am__api_version='1.11'
	2158	am__api_version='1.14'
2132	2159
2133	2160	ac_aux_dir=
2134	2161	for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do

2196	2223	# by default.
2197	2224	for ac_prog in ginstall scoinst install; do
2198	2225	for ac_exec_ext in '' $ac_executable_extensions; do
2199		if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
	2226	if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
2200	2227	if test $ac_prog = install &&
2201	2228	grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
2202	2229	# AIX install. It has an incompatible calling convention.

2254	2281
2255	2282	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
2256	2283	$as_echo_n "checking whether build environment is sane... " >&6; }
2257		# Just in case
2258		sleep 1
2259		echo timestamp > conftest.file
2260	2284	# Reject unsafe characters in $srcdir or the absolute working directory
2261	2285	# name. Accept space and tab only in the latter.
2262	2286	am_lf='

2267	2291	esac
2268	2292	case $srcdir in
2269	2293	[\\\"\#\$\&\'\`$am_lf\ \ ])
2270		as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
	2294	as_fn_error $? "unsafe srcdir value: '$srcdir'" "$LINENO" 5;;
2271	2295	esac
2272	2296
2273		# Do `set' in a subshell so we don't clobber the current shell's
	2297	# Do 'set' in a subshell so we don't clobber the current shell's
2274	2298	# arguments. Must try -L first in case configure is actually a
2275	2299	# symlink; some systems play weird games with the mod time of symlinks
2276	2300	# (eg FreeBSD returns the mod time of the symlink's containing
2277	2301	# directory).
2278	2302	if (
2279		set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
2280		if test "$*" = "X"; then
2281		# -L didn't work.
2282		set X `ls -t "$srcdir/configure" conftest.file`
2283		fi
2284		rm -f conftest.file
2285		if test "$*" != "X $srcdir/configure conftest.file" \
2286		&& test "$*" != "X conftest.file $srcdir/configure"; then
2287
2288		# If neither matched, then we have a broken ls. This can happen
2289		# if, for instance, CONFIG_SHELL is bash and it inherits a
2290		# broken ls alias from the environment. This has actually
2291		# happened. Such a system could not be considered "sane".
2292		as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
2293		alias in your environment" "$LINENO" 5
2294		fi
2295
	2303	am_has_slept=no
	2304	for am_try in 1 2; do
	2305	echo "timestamp, slept: $am_has_slept" > conftest.file
	2306	set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
	2307	if test "$*" = "X"; then
	2308	# -L didn't work.
	2309	set X `ls -t "$srcdir/configure" conftest.file`
	2310	fi
	2311	if test "$*" != "X $srcdir/configure conftest.file" \
	2312	&& test "$*" != "X conftest.file $srcdir/configure"; then
	2313
	2314	# If neither matched, then we have a broken ls. This can happen
	2315	# if, for instance, CONFIG_SHELL is bash and it inherits a
	2316	# broken ls alias from the environment. This has actually
	2317	# happened. Such a system could not be considered "sane".
	2318	as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
	2319	alias in your environment" "$LINENO" 5
	2320	fi
	2321	if test "$2" = conftest.file \|\| test $am_try -eq 2; then
	2322	break
	2323	fi
	2324	# Just in case.
	2325	sleep 1
	2326	am_has_slept=yes
	2327	done
2296	2328	test "$2" = conftest.file
2297	2329	)
2298	2330	then

2304	2336	fi
2305	2337	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
2306	2338	$as_echo "yes" >&6; }
	2339	# If we didn't sleep, we still need to ensure time stamps of config.status and
	2340	# generated files are strictly newer.
	2341	am_sleep_pid=
	2342	if grep 'slept: no' conftest.file >/dev/null 2>&1; then
	2343	( sleep 1 ) &
	2344	am_sleep_pid=$!
	2345	fi
	2346
	2347	rm -f conftest.file
	2348
2307	2349	test "$program_prefix" != NONE &&
2308	2350	program_transform_name="s&^&$program_prefix&;$program_transform_name"
2309	2351	# Use a double $ so make ignores it.

2326	2368	esac
2327	2369	fi
2328	2370	# Use eval to expand $SHELL
2329		if eval "$MISSING --run true"; then
2330		am_missing_run="$MISSING --run "
	2371	if eval "$MISSING --is-lightweight"; then
	2372	am_missing_run="$MISSING "
2331	2373	else
2332	2374	am_missing_run=
2333		{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
2334		$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
	2375	{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
	2376	$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
2335	2377	fi
2336	2378
2337	2379	if test x"${install_sh}" != xset; then

2343	2385	esac
2344	2386	fi
2345	2387
2346		# Installed binaries are usually stripped using `strip' when the user
2347		# run `make install-strip'. However `strip' might not be the right
	2388	# Installed binaries are usually stripped using 'strip' when the user
	2389	# run "make install-strip". However 'strip' might not be the right
2348	2390	# tool to use in cross-compilation environments, therefore Automake
2349		# will honor the `STRIP' environment variable to overrule this program.
	2391	# will honor the 'STRIP' environment variable to overrule this program.
2350	2392	if test "$cross_compiling" != no; then
2351	2393	if test -n "$ac_tool_prefix"; then
2352	2394	# Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.

2365	2407	IFS=$as_save_IFS
2366	2408	test -z "$as_dir" && as_dir=.
2367	2409	for ac_exec_ext in '' $ac_executable_extensions; do
2368		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	2410	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
2369	2411	ac_cv_prog_STRIP="${ac_tool_prefix}strip"
2370	2412	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
2371	2413	break 2

2405	2447	IFS=$as_save_IFS
2406	2448	test -z "$as_dir" && as_dir=.
2407	2449	for ac_exec_ext in '' $ac_executable_extensions; do
2408		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	2450	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
2409	2451	ac_cv_prog_ac_ct_STRIP="strip"
2410	2452	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
2411	2453	break 2

2456	2498	test -z "$as_dir" && as_dir=.
2457	2499	for ac_prog in mkdir gmkdir; do
2458	2500	for ac_exec_ext in '' $ac_executable_extensions; do
2459		{ test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } \|\| continue
	2501	as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext" \|\| continue
2460	2502	case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
2461	2503	'mkdir (GNU coreutils) '* \| \
2462	2504	'mkdir (coreutils) '* \| \

2485	2527	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
2486	2528	$as_echo "$MKDIR_P" >&6; }
2487	2529
2488		mkdir_p="$MKDIR_P"
2489		case $mkdir_p in
2490		[\\/$]* \| ?:[\\/]*) ;;
2491		/) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
2492		esac
2493
2494	2530	for ac_prog in gawk mawk nawk awk
2495	2531	do
2496	2532	# Extract the first word of "$ac_prog", so it can be a program name with args.

2509	2545	IFS=$as_save_IFS
2510	2546	test -z "$as_dir" && as_dir=.
2511	2547	for ac_exec_ext in '' $ac_executable_extensions; do
2512		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	2548	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
2513	2549	ac_cv_prog_AWK="$ac_prog"
2514	2550	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
2515	2551	break 2

2573	2609	fi
2574	2610	rmdir .tst 2>/dev/null
2575	2611
	2612	# Check whether --enable-silent-rules was given.
	2613	if test "${enable_silent_rules+set}" = set; then :
	2614	enableval=$enable_silent_rules;
	2615	fi
	2616
	2617	case $enable_silent_rules in # (((
	2618	yes) AM_DEFAULT_VERBOSITY=0;;
	2619	no) AM_DEFAULT_VERBOSITY=1;;
	2620	*) AM_DEFAULT_VERBOSITY=1;;
	2621	esac
	2622	am_make=${MAKE-make}
	2623	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
	2624	$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
	2625	if ${am_cv_make_support_nested_variables+:} false; then :
	2626	$as_echo_n "(cached) " >&6
	2627	else
	2628	if $as_echo 'TRUE=$(BAR$(V))
	2629	BAR0=false
	2630	BAR1=true
	2631	V=1
	2632	am__doit:
	2633	@$(TRUE)
	2634	.PHONY: am__doit' \| $am_make -f - >/dev/null 2>&1; then
	2635	am_cv_make_support_nested_variables=yes
	2636	else
	2637	am_cv_make_support_nested_variables=no
	2638	fi
	2639	fi
	2640	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
	2641	$as_echo "$am_cv_make_support_nested_variables" >&6; }
	2642	if test $am_cv_make_support_nested_variables = yes; then
	2643	AM_V='$(V)'
	2644	AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
	2645	else
	2646	AM_V=$AM_DEFAULT_VERBOSITY
	2647	AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
	2648	fi
	2649	AM_BACKSLASH='\'
	2650
2576	2651	if test "`cd $srcdir && pwd`" != "`pwd`"; then
2577	2652	# Use -I$(srcdir) only when $(srcdir) != ., so that make's output
2578	2653	# is not polluted with repeated "-I."

2594	2669
2595	2670
2596	2671	# Define the identity of the package.
	2672
2597	2673	PACKAGE=idba
2598		VERSION=1.1.2
	2674	VERSION=1.1.3
2599	2675
2600	2676
2601	2677	cat >>confdefs.h <<_ACEOF

2622	2698
2623	2699
2624	2700	MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
	2701
	2702	# For better backward compatibility. To be removed once Automake 1.9.x
	2703	# dies out for good. For more background, see:
	2704	# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
	2705	# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
	2706	mkdir_p='$(MKDIR_P)'
2625	2707
2626	2708	# We need awk for the "check" target. The system "awk" is bad on
2627	2709	# some platforms.

2629	2711	# in the wild :-( We should find a proper way to deprecate it ...
2630	2712	AMTAR='$${TAR-tar}'
2631	2713
	2714
	2715	# We'll loop over all known methods to create a tar archive until one works.
	2716	_am_tools='gnutar pax cpio none'
	2717
2632	2718	am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
2633	2719
2634	2720
2635	2721
2636	2722
2637	2723
	2724
	2725	# POSIX will say in a future version that running "rm -f" with no argument
	2726	# is OK; and we want to be able to make that assumption in our Makefile
	2727	# recipes. So use an aggressive probe to check that the usage we want is
	2728	# actually supported "in the wild" to an acceptable degree.
	2729	# See automake bug#10828.
	2730	# To make any issue more visible, cause the running configure to be aborted
	2731	# by default if the 'rm' program in use doesn't match our expectations; the
	2732	# user can still override this though.
	2733	if rm -f && rm -fr && rm -rf; then : OK; else
	2734	cat >&2 <<'END'
	2735	Oops!
	2736
	2737	Your 'rm' program seems unable to run without file operands specified
	2738	on the command line, even when the '-f' option is present. This is contrary
	2739	to the behaviour of most rm programs out there, and not conforming with
	2740	the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
	2741
	2742	Please tell bug-automake@gnu.org about your system, including the value
	2743	of your $PATH and any error possibly output before this message. This
	2744	can help us improve future automake versions.
	2745
	2746	END
	2747	if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
	2748	echo 'Configuration will proceed anyway, since you have set the' >&2
	2749	echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
	2750	echo >&2
	2751	else
	2752	cat >&2 <<'END'
	2753	Aborting the configuration process, to ensure you take notice of the issue.
	2754
	2755	You can download and install GNU coreutils to get an 'rm' implementation
	2756	that behaves properly: <http://www.gnu.org/software/coreutils/>.
	2757
	2758	If you want to complete the configuration process using your problematic
	2759	'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
	2760	to "yes", and re-run configure.
	2761
	2762	END
	2763	as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
	2764	fi
	2765	fi
2638	2766
2639	2767	# Checks for programs.
2640	2768	ac_ext=cpp

2665	2793	IFS=$as_save_IFS
2666	2794	test -z "$as_dir" && as_dir=.
2667	2795	for ac_exec_ext in '' $ac_executable_extensions; do
2668		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	2796	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
2669	2797	ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
2670	2798	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
2671	2799	break 2

2709	2837	IFS=$as_save_IFS
2710	2838	test -z "$as_dir" && as_dir=.
2711	2839	for ac_exec_ext in '' $ac_executable_extensions; do
2712		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	2840	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
2713	2841	ac_cv_prog_ac_ct_CXX="$ac_prog"
2714	2842	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
2715	2843	break 2

3162	3290	_am_result=none
3163	3291	# First try GNU make style include.
3164	3292	echo "include confinc" > confmf
3165		# Ignore all kinds of additional output from `make'.
	3293	# Ignore all kinds of additional output from 'make'.
3166	3294	case `$am_make -s -f confmf 2> /dev/null` in #(
3167	3295	the\ am__doit\ target)
3168	3296	am__include=include

3218	3346	# We make a subdir and do the tests there. Otherwise we can end up
3219	3347	# making bogus files that we don't know about and never remove. For
3220	3348	# instance it was reported that on HP-UX the gcc test will end up
3221		# making a dummy file named `D' -- because `-MD' means `put the output
3222		# in D'.
	3349	# making a dummy file named 'D' -- because '-MD' means "put the output
	3350	# in D".
3223	3351	rm -rf conftest.dir
3224	3352	mkdir conftest.dir
3225	3353	# Copy depcomp to subdir because otherwise we won't find it if we're

3254	3382	: > sub/conftest.c
3255	3383	for i in 1 2 3 4 5 6; do
3256	3384	echo '#include "conftst'$i'.h"' >> sub/conftest.c
3257		# Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
3258		# Solaris 8's {/usr,}/bin/sh.
3259		touch sub/conftst$i.h
	3385	# Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
	3386	# Solaris 10 /bin/sh.
	3387	echo '/* dummy */' > sub/conftst$i.h
3260	3388	done
3261	3389	echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
3262	3390
3263		# We check with `-c' and `-o' for the sake of the "dashmstdout"
	3391	# We check with '-c' and '-o' for the sake of the "dashmstdout"
3264	3392	# mode. It turns out that the SunPro C++ compiler does not properly
3265		# handle `-M -o', and we need to detect this. Also, some Intel
3266		# versions had trouble with output in subdirs
	3393	# handle '-M -o', and we need to detect this. Also, some Intel
	3394	# versions had trouble with output in subdirs.
3267	3395	am__obj=sub/conftest.${OBJEXT-o}
3268	3396	am__minus_obj="-o $am__obj"
3269	3397	case $depmode in

3272	3400	test "$am__universal" = false \|\| continue
3273	3401	;;
3274	3402	nosideeffect)
3275		# after this tag, mechanisms are not by side-effect, so they'll
3276		# only be used when explicitly requested
	3403	# After this tag, mechanisms are not by side-effect, so they'll
	3404	# only be used when explicitly requested.
3277	3405	if test "x$enable_dependency_tracking" = xyes; then
3278	3406	continue
3279	3407	else

3281	3409	fi
3282	3410	;;
3283	3411	msvc7 \| msvc7msys \| msvisualcpp \| msvcmsys)
3284		# This compiler won't grok `-c -o', but also, the minuso test has
	3412	# This compiler won't grok '-c -o', but also, the minuso test has
3285	3413	# not run yet. These depmodes are late enough in the game, and
3286	3414	# so weak that their functioning should not be impacted.
3287	3415	am__obj=conftest.${OBJEXT-o}

3357	3485	IFS=$as_save_IFS
3358	3486	test -z "$as_dir" && as_dir=.
3359	3487	for ac_exec_ext in '' $ac_executable_extensions; do
3360		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3488	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3361	3489	ac_cv_prog_CC="${ac_tool_prefix}gcc"
3362	3490	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
3363	3491	break 2

3397	3525	IFS=$as_save_IFS
3398	3526	test -z "$as_dir" && as_dir=.
3399	3527	for ac_exec_ext in '' $ac_executable_extensions; do
3400		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3528	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3401	3529	ac_cv_prog_ac_ct_CC="gcc"
3402	3530	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
3403	3531	break 2

3450	3578	IFS=$as_save_IFS
3451	3579	test -z "$as_dir" && as_dir=.
3452	3580	for ac_exec_ext in '' $ac_executable_extensions; do
3453		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3581	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3454	3582	ac_cv_prog_CC="${ac_tool_prefix}cc"
3455	3583	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
3456	3584	break 2

3491	3619	IFS=$as_save_IFS
3492	3620	test -z "$as_dir" && as_dir=.
3493	3621	for ac_exec_ext in '' $ac_executable_extensions; do
3494		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3622	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3495	3623	if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
3496	3624	ac_prog_rejected=yes
3497	3625	continue

3549	3677	IFS=$as_save_IFS
3550	3678	test -z "$as_dir" && as_dir=.
3551	3679	for ac_exec_ext in '' $ac_executable_extensions; do
3552		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3680	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3553	3681	ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
3554	3682	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
3555	3683	break 2

3593	3721	IFS=$as_save_IFS
3594	3722	test -z "$as_dir" && as_dir=.
3595	3723	for ac_exec_ext in '' $ac_executable_extensions; do
3596		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	3724	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
3597	3725	ac_cv_prog_ac_ct_CC="$ac_prog"
3598	3726	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
3599	3727	break 2

3789	3917	/* end confdefs.h. */
3790	3918	#include <stdarg.h>
3791	3919	#include <stdio.h>
3792		#include <sys/types.h>
3793		#include <sys/stat.h>
	3920	struct stat;
3794	3921	/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
3795	3922	struct buf { int x; };
3796	3923	FILE * (rcsopen) (struct buf , struct stat *, int);

3875	4002	ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
3876	4003	ac_compiler_gnu=$ac_cv_c_compiler_gnu
3877	4004
	4005	ac_ext=c
	4006	ac_cpp='$CPP $CPPFLAGS'
	4007	ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
	4008	ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
	4009	ac_compiler_gnu=$ac_cv_c_compiler_gnu
	4010	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
	4011	$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
	4012	if ${am_cv_prog_cc_c_o+:} false; then :
	4013	$as_echo_n "(cached) " >&6
	4014	else
	4015	cat confdefs.h - <<_ACEOF >conftest.$ac_ext
	4016	/* end confdefs.h. */
	4017
	4018	int
	4019	main ()
	4020	{
	4021
	4022	;
	4023	return 0;
	4024	}
	4025	_ACEOF
	4026	# Make sure it works both with $CC and with simple cc.
	4027	# Following AC_PROG_CC_C_O, we do the test twice because some
	4028	# compilers refuse to overwrite an existing .o file with -o,
	4029	# though they will create one.
	4030	am_cv_prog_cc_c_o=yes
	4031	for am_i in 1 2; do
	4032	if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
	4033	($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
	4034	ac_status=$?
	4035	echo "$as_me:$LINENO: \$? = $ac_status" >&5
	4036	(exit $ac_status); } \
	4037	&& test -f conftest2.$ac_objext; then
	4038	: OK
	4039	else
	4040	am_cv_prog_cc_c_o=no
	4041	break
	4042	fi
	4043	done
	4044	rm -f core conftest*
	4045	unset am_i
	4046	fi
	4047	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
	4048	$as_echo "$am_cv_prog_cc_c_o" >&6; }
	4049	if test "$am_cv_prog_cc_c_o" != yes; then
	4050	# Losing compiler, so override with the script.
	4051	# FIXME: It is wrong to rewrite CC.
	4052	# But if we don't then we get into trouble of one sort or another.
	4053	# A longer-term fix would be to have automake use am__CC in this case,
	4054	# and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
	4055	CC="$am_aux_dir/compile $CC"
	4056	fi
	4057	ac_ext=c
	4058	ac_cpp='$CPP $CPPFLAGS'
	4059	ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
	4060	ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
	4061	ac_compiler_gnu=$ac_cv_c_compiler_gnu
	4062
	4063
3878	4064	depcc="$CC" am_compiler_list=
3879	4065
3880	4066	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5

3886	4072	# We make a subdir and do the tests there. Otherwise we can end up
3887	4073	# making bogus files that we don't know about and never remove. For
3888	4074	# instance it was reported that on HP-UX the gcc test will end up
3889		# making a dummy file named `D' -- because `-MD' means `put the output
3890		# in D'.
	4075	# making a dummy file named 'D' -- because '-MD' means "put the output
	4076	# in D".
3891	4077	rm -rf conftest.dir
3892	4078	mkdir conftest.dir
3893	4079	# Copy depcomp to subdir because otherwise we won't find it if we're

3922	4108	: > sub/conftest.c
3923	4109	for i in 1 2 3 4 5 6; do
3924	4110	echo '#include "conftst'$i'.h"' >> sub/conftest.c
3925		# Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
3926		# Solaris 8's {/usr,}/bin/sh.
3927		touch sub/conftst$i.h
	4111	# Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
	4112	# Solaris 10 /bin/sh.
	4113	echo '/* dummy */' > sub/conftst$i.h
3928	4114	done
3929	4115	echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
3930	4116
3931		# We check with `-c' and `-o' for the sake of the "dashmstdout"
	4117	# We check with '-c' and '-o' for the sake of the "dashmstdout"
3932	4118	# mode. It turns out that the SunPro C++ compiler does not properly
3933		# handle `-M -o', and we need to detect this. Also, some Intel
3934		# versions had trouble with output in subdirs
	4119	# handle '-M -o', and we need to detect this. Also, some Intel
	4120	# versions had trouble with output in subdirs.
3935	4121	am__obj=sub/conftest.${OBJEXT-o}
3936	4122	am__minus_obj="-o $am__obj"
3937	4123	case $depmode in

3940	4126	test "$am__universal" = false \|\| continue
3941	4127	;;
3942	4128	nosideeffect)
3943		# after this tag, mechanisms are not by side-effect, so they'll
3944		# only be used when explicitly requested
	4129	# After this tag, mechanisms are not by side-effect, so they'll
	4130	# only be used when explicitly requested.
3945	4131	if test "x$enable_dependency_tracking" = xyes; then
3946	4132	continue
3947	4133	else

3949	4135	fi
3950	4136	;;
3951	4137	msvc7 \| msvc7msys \| msvisualcpp \| msvcmsys)
3952		# This compiler won't grok `-c -o', but also, the minuso test has
	4138	# This compiler won't grok '-c -o', but also, the minuso test has
3953	4139	# not run yet. These depmodes are late enough in the game, and
3954	4140	# so weak that their functioning should not be impacted.
3955	4141	am__obj=conftest.${OBJEXT-o}

4024	4210	IFS=$as_save_IFS
4025	4211	test -z "$as_dir" && as_dir=.
4026	4212	for ac_exec_ext in '' $ac_executable_extensions; do
4027		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	4213	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
4028	4214	ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
4029	4215	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
4030	4216	break 2

4064	4250	IFS=$as_save_IFS
4065	4251	test -z "$as_dir" && as_dir=.
4066	4252	for ac_exec_ext in '' $ac_executable_extensions; do
4067		if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
	4253	if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
4068	4254	ac_cv_prog_ac_ct_RANLIB="ranlib"
4069	4255	$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
4070	4256	break 2

4258	4444	for ac_prog in grep ggrep; do
4259	4445	for ac_exec_ext in '' $ac_executable_extensions; do
4260	4446	ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
4261		{ test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } \|\| continue
	4447	as_fn_executable_p "$ac_path_GREP" \|\| continue
4262	4448	# Check for GNU ac_path_GREP and select it if it is found.
4263	4449	# Check for GNU $ac_path_GREP
4264	4450	case `"$ac_path_GREP" --version 2>&1` in

4324	4510	for ac_prog in egrep; do
4325	4511	for ac_exec_ext in '' $ac_executable_extensions; do
4326	4512	ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
4327		{ test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } \|\| continue
	4513	as_fn_executable_p "$ac_path_EGREP" \|\| continue
4328	4514	# Check for GNU ac_path_EGREP and select it if it is found.
4329	4515	# Check for GNU $ac_path_EGREP
4330	4516	case `"$ac_path_EGREP" --version 2>&1` in

4509	4695	cat confdefs.h - <<_ACEOF >conftest.$ac_ext
4510	4696	/* end confdefs.h. */
4511	4697
4512		#include <stdbool.h>
4513		#ifndef bool
4514		"error: bool is not defined"
4515		#endif
4516		#ifndef false
4517		"error: false is not defined"
4518		#endif
4519		#if false
4520		"error: false is not 0"
4521		#endif
4522		#ifndef true
4523		"error: true is not defined"
4524		#endif
4525		#if true != 1
4526		"error: true is not 1"
4527		#endif
4528		#ifndef __bool_true_false_are_defined
4529		"error: __bool_true_false_are_defined is not defined"
4530		#endif
4531
4532		struct s { _Bool s: 1; _Bool t; } s;
4533
4534		char a[true == 1 ? 1 : -1];
4535		char b[false == 0 ? 1 : -1];
4536		char c[__bool_true_false_are_defined == 1 ? 1 : -1];
4537		char d[(bool) 0.5 == true ? 1 : -1];
4538		/* See body of main program for 'e'. */
4539		char f[(_Bool) 0.0 == false ? 1 : -1];
4540		char g[true];
4541		char h[sizeof (_Bool)];
4542		char i[sizeof s.t];
4543		enum { j = false, k = true, l = false * true, m = true * 256 };
4544		/* The following fails for
4545		HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
4546		_Bool n[m];
4547		char o[sizeof n == m * sizeof n[0] ? 1 : -1];
4548		char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
4549		/* Catch a bug in an HP-UX C compiler. See
4550		http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
4551		http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
4552		*/
4553		_Bool q = true;
4554		_Bool *pq = &q;
	4698	#include <stdbool.h>
	4699	#ifndef bool
	4700	"error: bool is not defined"
	4701	#endif
	4702	#ifndef false
	4703	"error: false is not defined"
	4704	#endif
	4705	#if false
	4706	"error: false is not 0"
	4707	#endif
	4708	#ifndef true
	4709	"error: true is not defined"
	4710	#endif
	4711	#if true != 1
	4712	"error: true is not 1"
	4713	#endif
	4714	#ifndef __bool_true_false_are_defined
	4715	"error: __bool_true_false_are_defined is not defined"
	4716	#endif
	4717
	4718	struct s { _Bool s: 1; _Bool t; } s;
	4719
	4720	char a[true == 1 ? 1 : -1];
	4721	char b[false == 0 ? 1 : -1];
	4722	char c[__bool_true_false_are_defined == 1 ? 1 : -1];
	4723	char d[(bool) 0.5 == true ? 1 : -1];
	4724	/* See body of main program for 'e'. */
	4725	char f[(_Bool) 0.0 == false ? 1 : -1];
	4726	char g[true];
	4727	char h[sizeof (_Bool)];
	4728	char i[sizeof s.t];
	4729	enum { j = false, k = true, l = false * true, m = true * 256 };
	4730	/* The following fails for
	4731	HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
	4732	_Bool n[m];
	4733	char o[sizeof n == m * sizeof n[0] ? 1 : -1];
	4734	char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
	4735	/* Catch a bug in an HP-UX C compiler. See
	4736	http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
	4737	http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
	4738	*/
	4739	_Bool q = true;
	4740	_Bool *pq = &q;
4555	4741
4556	4742	int
4557	4743	main ()
4558	4744	{
4559	4745
4560		bool e = &s;
4561		*pq \|= q;
4562		*pq \|= ! q;
4563		/* Refer to every declared value, to avoid compiler optimizations. */
4564		return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
4565		+ !m + !n + !o + !p + !q + !pq);
	4746	bool e = &s;
	4747	*pq \|= q;
	4748	*pq \|= ! q;
	4749	/* Refer to every declared value, to avoid compiler optimizations. */
	4750	return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
	4751	+ !m + !n + !o + !p + !q + !pq);
4566	4752
4567	4753	;
4568	4754	return 0;

4577	4763	fi
4578	4764	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
4579	4765	$as_echo "$ac_cv_header_stdbool_h" >&6; }
4580		ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
	4766	ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
4581	4767	if test "x$ac_cv_type__Bool" = xyes; then :
4582	4768
4583	4769	cat >>confdefs.h <<_ACEOF

4586	4772
4587	4773
4588	4774	fi
	4775
4589	4776
4590	4777	if test $ac_cv_header_stdbool_h = yes; then
4591	4778

4604	4791	int
4605	4792	main ()
4606	4793	{
4607		/* FIXME: Include the comments suggested by Paul. */
	4794
4608	4795	#ifndef __cplusplus
4609		/* Ultrix mips cc rejects this. */
	4796	/* Ultrix mips cc rejects this sort of thing. */
4610	4797	typedef int charset[2];
4611		const charset cs;
	4798	const charset cs = { 0, 0 };
4612	4799	/* SunOS 4.1.1 cc rejects this. */
4613	4800	char const const pcpcc;
4614	4801	char **ppc;

4625	4812	++pcpcc;
4626	4813	ppc = (char**) pcpcc;
4627	4814	pcpcc = (char const const ) ppc;
4628		{ /* SCO 3.2v4 cc rejects this. */
4629		char *t;
	4815	{ /* SCO 3.2v4 cc rejects this sort of thing. */
	4816	char tx;
	4817	char *t = &tx;
4630	4818	char const s = 0 ? (char ) 0 : (char const *) 0;
4631	4819
4632	4820	*t++ = 0;

4642	4830	iptr p = 0;
4643	4831	++p;
4644	4832	}
4645		{ /* AIX XL C 1.02.0.0 rejects this saying
	4833	{ /* AIX XL C 1.02.0.0 rejects this sort of thing, saying
4646	4834	"k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
4647		struct s { int j; const int *ap[3]; };
4648		struct s *b; b->j = 5;
	4835	struct s { int j; const int *ap[3]; } bx;
	4836	struct s *b = &bx; b->j = 5;
4649	4837	}
4650	4838	{ /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
4651	4839	const int foo = 10;

4879	5067	LTLIBOBJS=$ac_ltlibobjs
4880	5068
4881	5069
	5070	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking that generated files are newer than configure" >&5
	5071	$as_echo_n "checking that generated files are newer than configure... " >&6; }
	5072	if test -n "$am_sleep_pid"; then
	5073	# Hide warnings about reused PIDs.
	5074	wait $am_sleep_pid 2>/dev/null
	5075	fi
	5076	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
	5077	$as_echo "done" >&6; }
4882	5078	if test -n "$EXEEXT"; then
4883	5079	am__EXEEXT_TRUE=
4884	5080	am__EXEEXT_FALSE='#'

5197	5393	# ... but there are two gotchas:
5198	5394	# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
5199	5395	# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
5200		# In both cases, we have to default to `cp -p'.
	5396	# In both cases, we have to default to `cp -pR'.
5201	5397	ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe \|\|
5202		as_ln_s='cp -p'
	5398	as_ln_s='cp -pR'
5203	5399	elif ln conf$$.file conf$$ 2>/dev/null; then
5204	5400	as_ln_s=ln
5205	5401	else
5206		as_ln_s='cp -p'
	5402	as_ln_s='cp -pR'
5207	5403	fi
5208	5404	else
5209		as_ln_s='cp -p'
	5405	as_ln_s='cp -pR'
5210	5406	fi
5211	5407	rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
5212	5408	rmdir conf$$.dir 2>/dev/null

5266	5462	as_mkdir_p=false
5267	5463	fi
5268	5464
5269		if test -x / >/dev/null 2>&1; then
5270		as_test_x='test -x'
5271		else
5272		if ls -dL / >/dev/null 2>&1; then
5273		as_ls_L_option=L
5274		else
5275		as_ls_L_option=
5276		fi
5277		as_test_x='
5278		eval sh -c '\''
5279		if test -d "$1"; then
5280		test -d "$1/.";
5281		else
5282		case $1 in #(
5283		-*)set "./$1";;
5284		esac;
5285		case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
5286		???[sx]):;;)false;;esac;fi
5287		'\'' sh
5288		'
5289		fi
5290		as_executable_p=$as_test_x
	5465
	5466	# as_fn_executable_p FILE
	5467	# -----------------------
	5468	# Test if FILE is an executable regular file.
	5469	as_fn_executable_p ()
	5470	{
	5471	test -f "$1" && test -x "$1"
	5472	} # as_fn_executable_p
	5473	as_test_x='test -x'
	5474	as_executable_p=as_fn_executable_p
5291	5475
5292	5476	# Sed expression to map a string onto a valid CPP name.
5293	5477	as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"

5308	5492	# report actual input values of CONFIG_FILES etc. instead of their
5309	5493	# values after options handling.
5310	5494	ac_log="
5311		This file was extended by idba $as_me 1.1.2, which was
5312		generated by GNU Autoconf 2.68. Invocation command line was
	5495	This file was extended by idba $as_me 1.1.3, which was
	5496	generated by GNU Autoconf 2.69. Invocation command line was
5313	5497
5314	5498	CONFIG_FILES = $CONFIG_FILES
5315	5499	CONFIG_HEADERS = $CONFIG_HEADERS

5374	5558	cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
5375	5559	ac_cs_config="`$as_echo "$ac_configure_args" \| sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
5376	5560	ac_cs_version="\\
5377		idba config.status 1.1.2
5378		configured by $0, generated by GNU Autoconf 2.68,
	5561	idba config.status 1.1.3
	5562	configured by $0, generated by GNU Autoconf 2.69,
5379	5563	with options \\"\$ac_cs_config\\"
5380	5564
5381		Copyright (C) 2010 Free Software Foundation, Inc.
	5565	Copyright (C) 2012 Free Software Foundation, Inc.
5382	5566	This config.status script is free software; the Free Software Foundation
5383	5567	gives unlimited permission to copy, distribute and modify it."
5384	5568

5469	5653	_ACEOF
5470	5654	cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
5471	5655	if \$ac_cs_recheck; then
5472		set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
	5656	set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
5473	5657	shift
5474	5658	\$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
5475	5659	CONFIG_SHELL='$SHELL'

6106	6290
6107	6291	case $ac_file$ac_mode in
6108	6292	"depfiles":C) test x"$AMDEP_TRUE" != x"" \|\| {
6109		# Autoconf 2.62 quotes --file arguments for eval, but not when files
	6293	# Older Autoconf quotes --file arguments for eval, but not when files
6110	6294	# are listed without --file. Let's play safe and only enable the eval
6111	6295	# if we detect the quoting.
6112	6296	case $CONFIG_FILES in

6119	6303	# Strip MF so we end up with the name of the file.
6120	6304	mf=`echo "$mf" \| sed -e 's/:.*$//'`
6121	6305	# Check whether this is an Automake generated Makefile or not.
6122		# We used to match only the files named `Makefile.in', but
	6306	# We used to match only the files named 'Makefile.in', but
6123	6307	# some people rename them; so instead we look at the file content.
6124	6308	# Grep'ing the first line is not enough: some people post-process
6125	6309	# each Makefile.in and add a new line on top of each file to say so.

6153	6337	continue
6154	6338	fi
6155	6339	# Extract the definition of DEPDIR, am__include, and am__quote
6156		# from the Makefile without running `make'.
	6340	# from the Makefile without running 'make'.
6157	6341	DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
6158	6342	test -z "$DEPDIR" && continue
6159	6343	am__include=`sed -n 's/^am__include = //p' < "$mf"`
6160		test -z "am__include" && continue
	6344	test -z "$am__include" && continue
6161	6345	am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
6162		# When using ansi2knr, U may be empty or an underscore; expand it
6163		U=`sed -n 's/^U = //p' < "$mf"`
6164	6346	# Find all dependency output files, they are included files with
6165	6347	# $(DEPDIR) in their names. We invoke sed twice because it is the
6166	6348	# simplest approach to changing $(DEPDIR) to its actual value in the
6167	6349	# expansion.
6168	6350	for file in `sed -n "
6169	6351	s/^$am__include $am__quote$.(DEPDIR).$$am__quote"'$/\1/p' <"$mf" \| \
6170		sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
	6352	sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
6171	6353	# Make sure the directory exists.
6172	6354	test -f "$dirpart/$file" && continue
6173	6355	fdir=`$as_dirname -- "$file" \|\|

-2

configure.ac less more

1	1	# Process this file with autoconf to produce a configure script.
2	2
3	3	AC_PREREQ(2.59)
4		AC_INIT(idba, 1.1.2, loneknightpy@gmail.com)
	4	AC_INIT(idba, 1.1.3, loneknightpy@gmail.com)
5	5	AC_CONFIG_SRCDIR([src/basic/kmer.h])
6	6	AC_CONFIG_HEADER([config.h])
7		AM_INIT_AUTOMAKE(idba, 1.1.2)
	7	AM_INIT_AUTOMAKE(idba, 1.1.3)
8	8
9	9	# Checks for programs.
10	10	AC_PROG_CXX

+395

-289

lib/Makefile.in less more

0		# Makefile.in generated by automake 1.11.3 from Makefile.am.
	0	# Makefile.in generated by automake 1.14.1 from Makefile.am.
1	1	# @configure_input@
2	2
3		# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
4		# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
5		# Foundation, Inc.
	3	# Copyright (C) 1994-2013 Free Software Foundation, Inc.
	4
6	5	# This Makefile.in is free software; the Free Software Foundation
7	6	# gives unlimited permission to copy and/or distribute it,
8	7	# with or without modifications, as long as this notice is preserved.

15	14	@SET_MAKE@
16	15
17	16	VPATH = @srcdir@
	17	am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
	18	am__make_running_with_option = \
	19	case $${target_option-} in \
	20	?) ;; \
	21	*) echo "am__make_running_with_option: internal error: invalid" \
	22	"target option '$${target_option-}' specified" >&2; \
	23	exit 1;; \
	24	esac; \
	25	has_opt=no; \
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	30	case $$MAKEFLAGS in \
	31	\\[\ \ ]) \
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	33	sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
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	35	esac; \
	36	fi; \
	37	skip_next=no; \
	38	strip_trailopt () \
	39	{ \
	40	flg=`printf '%s\n' "$$flg" \| sed "s/$$1.*$$//"`; \
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	46	-*I) strip_trailopt 'I'; skip_next=yes;; \
	47	-I?) strip_trailopt 'I';; \
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	49	-O?) strip_trailopt 'O';; \
	50	-*l) strip_trailopt 'l'; skip_next=yes;; \
	51	-l?) strip_trailopt 'l';; \
	52	-[dEDm]) skip_next=yes;; \
	53	-[JT]) skip_next=yes;; \
	54	esac; \
	55	case $$flg in \
	56	$$target_option) has_opt=yes; break;; \
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	60	am__make_dryrun = (target_option=n; $(am__make_running_with_option))
	61	am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
18	62	pkgdatadir = $(datadir)/@PACKAGE@
19	63	pkgincludedir = $(includedir)/@PACKAGE@
20	64	pkglibdir = $(libdir)/@PACKAGE@

32	76	PRE_UNINSTALL = :
33	77	POST_UNINSTALL = :
34	78	subdir = lib
35		DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
	79	DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
	80	$(top_srcdir)/depcomp
36	81	ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
37	82	am__aclocal_m4_deps = $(top_srcdir)/configure.ac
38	83	am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \

44	89	LIBRARIES = $(noinst_LIBRARIES)
45	90	AR = ar
46	91	ARFLAGS = cru
	92	AM_V_AR = $(am__v_AR_@AM_V@)
	93	am__v_AR_ = $(am__v_AR_@AM_DEFAULT_V@)
	94	am__v_AR_0 = @echo " AR " $@;
	95	am__v_AR_1 =
47	96	libassembly_a_AR = $(AR) $(ARFLAGS)
48	97	libassembly_a_LIBADD =
49	98	am_libassembly_a_OBJECTS = math.$(OBJEXT) hash_aligner.$(OBJEXT) \

61	110	libgtest_a_LIBADD =
62	111	am_libgtest_a_OBJECTS = gtest_main.$(OBJEXT) gtest-all.$(OBJEXT)
63	112	libgtest_a_OBJECTS = $(am_libgtest_a_OBJECTS)
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	118	am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
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	121	AM_V_at = $(am__v_at_@AM_V@)
	122	am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
	123	am__v_at_0 = @
	124	am__v_at_1 =
64	125	DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
65	126	depcomp = $(SHELL) $(top_srcdir)/depcomp
66	127	am__depfiles_maybe = depfiles
67	128	am__mv = mv -f
	129	AM_V_lt = $(am__v_lt_@AM_V@)
	130	am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
	131	am__v_lt_0 = --silent
	132	am__v_lt_1 =
68	133	CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
69	134	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
	135	AM_V_CXX = $(am__v_CXX_@AM_V@)
	136	am__v_CXX_ = $(am__v_CXX_@AM_DEFAULT_V@)
	137	am__v_CXX_0 = @echo " CXX " $@;
	138	am__v_CXX_1 =
70	139	CXXLD = $(CXX)
71	140	CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
72	141	-o $@
	142	AM_V_CXXLD = $(am__v_CXXLD_@AM_V@)
	143	am__v_CXXLD_ = $(am__v_CXXLD_@AM_DEFAULT_V@)
	144	am__v_CXXLD_0 = @echo " CXXLD " $@;
	145	am__v_CXXLD_1 =
73	146	COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
74	147	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
	148	AM_V_CC = $(am__v_CC_@AM_V@)
	149	am__v_CC_ = $(am__v_CC_@AM_DEFAULT_V@)
	150	am__v_CC_0 = @echo " CC " $@;
	151	am__v_CC_1 =
75	152	CCLD = $(CC)
76	153	LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
	154	AM_V_CCLD = $(am__v_CCLD_@AM_V@)
	155	am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
	156	am__v_CCLD_0 = @echo " CCLD " $@;
	157	am__v_CCLD_1 =
77	158	SOURCES = $(libassembly_a_SOURCES) $(libgtest_a_SOURCES)
78	159	DIST_SOURCES = $(libassembly_a_SOURCES) $(libgtest_a_SOURCES)
	160	am__can_run_installinfo = \
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	162	n\|no\|NO) false;; \
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	169	am__uniquify_input = $(AWK) '\
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	178	list='$(am__tagged_files)'; \
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79	182	ETAGS = etags
80	183	CTAGS = ctags
81	184	DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
82	185	ACLOCAL = @ACLOCAL@
83	186	AMTAR = @AMTAR@
	187	AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
84	188	AUTOCONF = @AUTOCONF@
85	189	AUTOHEADER = @AUTOHEADER@
86	190	AUTOMAKE = @AUTOMAKE@

282	386
283	387	clean-noinstLIBRARIES:
284	388	-test -z "$(noinst_LIBRARIES)" \|\| rm -f $(noinst_LIBRARIES)
	389
285	390	libassembly.a: $(libassembly_a_OBJECTS) $(libassembly_a_DEPENDENCIES) $(EXTRA_libassembly_a_DEPENDENCIES)
286		-rm -f libassembly.a
287		$(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
288		$(RANLIB) libassembly.a
	391	$(AM_V_at)-rm -f libassembly.a
	392	$(AM_V_AR)$(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
	393	$(AM_V_at)$(RANLIB) libassembly.a
	394
289	395	libgtest.a: $(libgtest_a_OBJECTS) $(libgtest_a_DEPENDENCIES) $(EXTRA_libgtest_a_DEPENDENCIES)
290		-rm -f libgtest.a
291		$(libgtest_a_AR) libgtest.a $(libgtest_a_OBJECTS) $(libgtest_a_LIBADD)
292		$(RANLIB) libgtest.a
	396	$(AM_V_at)-rm -f libgtest.a
	397	$(AM_V_AR)$(libgtest_a_AR) libgtest.a $(libgtest_a_OBJECTS) $(libgtest_a_LIBADD)
	398	$(AM_V_at)$(RANLIB) libgtest.a
293	399
294	400	mostlyclean-compile:
295	401	-rm -f *.$(OBJEXT)

321	427	@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
322	428
323	429	.cc.o:
324		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
325		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
326		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
327		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
328		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
	430	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
	431	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
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	433	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	434	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ $<
329	435
330	436	.cc.obj:
331		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
332		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
333		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
334		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
335		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
	437	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
	438	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
	439	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
	440	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	441	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
336	442
337	443	math.o: $(top_srcdir)/src/basic/math.cpp
338		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT math.o -MD -MP -MF $(DEPDIR)/math.Tpo -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
339		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/math.Tpo $(DEPDIR)/math.Po
340		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/basic/math.cpp' object='math.o' libtool=no @AMDEPBACKSLASH@
341		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
342		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
	444	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT math.o -MD -MP -MF $(DEPDIR)/math.Tpo -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
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	447	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	448	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
343	449
344	450	math.obj: $(top_srcdir)/src/basic/math.cpp
345		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT math.obj -MD -MP -MF $(DEPDIR)/math.Tpo -c -o math.obj `if test -f '$(top_srcdir)/src/basic/math.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/basic/math.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/basic/math.cpp'; fi`
346		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/math.Tpo $(DEPDIR)/math.Po
347		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/basic/math.cpp' object='math.obj' libtool=no @AMDEPBACKSLASH@
348		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
349		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o math.obj `if test -f '$(top_srcdir)/src/basic/math.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/basic/math.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/basic/math.cpp'; fi`
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	452	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/math.Tpo $(DEPDIR)/math.Po
	453	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$(top_srcdir)/src/basic/math.cpp' object='math.obj' libtool=no @AMDEPBACKSLASH@
	454	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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350	456
351	457	hash_aligner.o: $(top_srcdir)/src/misc/hash_aligner.cpp
352		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT hash_aligner.o -MD -MP -MF $(DEPDIR)/hash_aligner.Tpo -c -o hash_aligner.o `test -f '$(top_srcdir)/src/misc/hash_aligner.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/misc/hash_aligner.cpp
353		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/hash_aligner.Tpo $(DEPDIR)/hash_aligner.Po
354		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/misc/hash_aligner.cpp' object='hash_aligner.o' libtool=no @AMDEPBACKSLASH@
355		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
356		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o hash_aligner.o `test -f '$(top_srcdir)/src/misc/hash_aligner.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/misc/hash_aligner.cpp
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357	463
358	464	hash_aligner.obj: $(top_srcdir)/src/misc/hash_aligner.cpp
359		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT hash_aligner.obj -MD -MP -MF $(DEPDIR)/hash_aligner.Tpo -c -o hash_aligner.obj `if test -f '$(top_srcdir)/src/misc/hash_aligner.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/misc/hash_aligner.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/misc/hash_aligner.cpp'; fi`
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	953	clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
	954	distclean-compile distclean-generic distclean-tags distdir dvi \
	955	dvi-am html html-am info info-am install install-am \
	956	install-data install-data-am install-dvi install-dvi-am \
	957	install-exec install-exec-am install-html install-html-am \
	958	install-info install-info-am install-man install-pdf \
	959	install-pdf-am install-ps install-ps-am install-strip \
	960	installcheck installcheck-am installdirs maintainer-clean \
855	961	maintainer-clean-generic mostlyclean mostlyclean-compile \
856		mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
	962	mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
857	963	uninstall-am
858	964
859	965

+89

-23

script/Makefile.in less more

0		# Makefile.in generated by automake 1.11.3 from Makefile.am.
	0	# Makefile.in generated by automake 1.14.1 from Makefile.am.
1	1	# @configure_input@
2	2
3		# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
4		# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
5		# Foundation, Inc.
	3	# Copyright (C) 1994-2013 Free Software Foundation, Inc.
	4
6	5	# This Makefile.in is free software; the Free Software Foundation
7	6	# gives unlimited permission to copy and/or distribute it,
8	7	# with or without modifications, as long as this notice is preserved.

15	14	@SET_MAKE@
16	15
17	16	VPATH = @srcdir@
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	19	case $${target_option-} in \
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	49	-O?) strip_trailopt 'O';; \
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	60	am__make_dryrun = (target_option=n; $(am__make_running_with_option))
	61	am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
18	62	pkgdatadir = $(datadir)/@PACKAGE@
19	63	pkgincludedir = $(includedir)/@PACKAGE@
20	64	pkglibdir = $(libdir)/@PACKAGE@

32	76	PRE_UNINSTALL = :
33	77	POST_UNINSTALL = :
34	78	subdir = script
35		DIST_COMMON = $(dist_bin_SCRIPTS) $(srcdir)/Makefile.am \
36		$(srcdir)/Makefile.in
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37	81	ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
38	82	am__aclocal_m4_deps = $(top_srcdir)/configure.ac
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71	115	}
72	116	am__installdirs = "$(DESTDIR)$(bindir)"
73	117	SCRIPTS = $(dist_bin_SCRIPTS)
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76	138	DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
77	139	ACLOCAL = @ACLOCAL@
78	140	AMTAR = @AMTAR@
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79	142	AUTOCONF = @AUTOCONF@
80	143	AUTOHEADER = @AUTOHEADER@
81	144	AUTOMAKE = @AUTOMAKE@

206	269	$(am__aclocal_m4_deps):
207	270	install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
208	271	@$(NORMAL_INSTALL)
209		test -z "$(bindir)" \|\| $(MKDIR_P) "$(DESTDIR)$(bindir)"
210	272	@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" \|\| list=; \
	273	if test -n "$$list"; then \
	274	echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
	275	$(MKDIR_P) "$(DESTDIR)$(bindir)" \|\| exit 1; \
	276	fi; \
211	277	for p in $$list; do \
212	278	if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
213	279	if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \

236	302	files=`for p in $$list; do echo "$$p"; done \| \
237	303	sed -e 's,.*/,,;$(transform)'`; \
238	304	dir='$(DESTDIR)$(bindir)'; $(am__uninstall_files_from_dir)
239		tags: TAGS
240		TAGS:
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242		ctags: CTAGS
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244	310
245	311
246	312	distdir: $(DISTFILES)

378	444
379	445	.MAKE: install-am install-strip
380	446
381		.PHONY: all all-am check check-am clean clean-generic distclean \
382		distclean-generic distdir dvi dvi-am html html-am info info-am \
383		install install-am install-data install-data-am \
384		install-dist_binSCRIPTS install-dvi install-dvi-am \
385		install-exec install-exec-am install-html install-html-am \
386		install-info install-info-am install-man install-pdf \
387		install-pdf-am install-ps install-ps-am install-strip \
388		installcheck installcheck-am installdirs maintainer-clean \
389		maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
390		pdf-am ps ps-am uninstall uninstall-am \
391		uninstall-dist_binSCRIPTS
	447	.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
	448	ctags-am distclean distclean-generic distdir dvi dvi-am html \
	449	html-am info info-am install install-am install-data \
	450	install-data-am install-dist_binSCRIPTS install-dvi \
	451	install-dvi-am install-exec install-exec-am install-html \
	452	install-html-am install-info install-info-am install-man \
	453	install-pdf install-pdf-am install-ps install-ps-am \
	454	install-strip installcheck installcheck-am installdirs \
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	456	mostlyclean-generic pdf pdf-am ps ps-am tags-am uninstall \
	457	uninstall-am uninstall-dist_binSCRIPTS
392	458
393	459
394	460	# Tell versions [3.59,3.63) of GNU make to not export all variables.

-3

src/graph/contig_graph.cpp less more

36	36	const double err = 0.01;
37	37	double p_err = err/3 * pow(1-err, double(kmer_size_-1));
38	38
	39	p_table.resize(10);
	40	for (unsigned i = 0; i < 10; ++i) {
	41	p_table.resize(1000);
	42	}
	43
39	44	for (int m = 1; m < 10; ++m)
40	45	{
41	46	for (int x = 1; x < 1000; ++x)

218	223
219	224	if (current.out_edges().size() > 1)
220	225	{
221		ContigGraphVertexAdaptor end(NULL);
222	226	deque<ContigGraphVertexAdaptor> neighbors;
223	227	GetNeighbors(current, neighbors);
224	228	sort(neighbors.begin(), neighbors.end(), CompareContigCoverage);

246	250	}
247	251	Refresh();
248	252	MergeSimplePaths();
249
250	253	}
251	254
252	255	int64_t ContigGraph::Prune(int min_length)

1243	1246
1244	1247	double ContigGraph::GetSimilarity(const Sequence &a, const Sequence &b)
1245	1248	{
	1249	if (a.size() >= kMaxCheckSimilarity \|\| b.size() > kMaxCheckSimilarity)
	1250	return 0;
	1251
1246	1252	vector<vector<int> > table;
1247	1253	table.resize(a.size() + 1);
1248	1254	for (unsigned i = 0; i < table.size(); ++i)

1470	1476	}
1471	1477	}
1472	1478
1473

-2

src/graph/contig_graph.h less more

259	259	double FindSimilarPath(ContigGraphVertexAdaptor target, ContigGraphVertexAdaptor start);
260	260	double FindSimilarPath(ContigGraphVertexAdaptor target, ContigGraphPath &path, int &time);
261	261
	262	static const uint32_t kMaxCheckSimilarity = 1024;
	263
262	264	HashMap<Kmer, uint32_t> begin_kmer_map_;
263	265	std::deque<ContigGraphVertex> vertices_;
264	266	uint64_t num_edges_;

267	269	HashMap<Kmer, uint32_t> in_kmer_count_table_;
268	270	HashGraph edge_count_table_;
269	271
270		double p_table[10][10000];
	272	std::vector<std::vector<double> > p_table;
271	273	};
272	274
273	275	#endif
274

-1

src/graph/hash_graph.h less more

187	187	void clear() { vertex_table_.clear(); num_edges_ = 0; }
188	188
189	189	private:
	190	#if __cplusplus >= 201103L
	191	HashGraph(const HashGraph &) = delete;
	192	const HashGraph &operator =(const HashGraph &) = delete;
	193	#else
190	194	HashGraph(const HashGraph &);
191	195	const HashGraph &operator =(const HashGraph &);
	196	#endif
192	197
193	198	bool GetNextVertexAdaptor(const HashGraphVertexAdaptor &current, HashGraphVertexAdaptor &next)
194	199	{

427	432
428	433	namespace std
429	434	{
430		template <> inline void swap(HashGraph &x, HashGraph &y)
	435	inline void swap(HashGraph &x, HashGraph &y)
431	436	{ x.swap(y); }
432	437	}
433	438

-3

src/misc/log.cpp less more

47	47	dup2(pipe_fds[0], STDIN_FILENO);
48	48	close(pipe_fds[0]);
49	49
50		char line[kMaxLine];
	50	char *line = new char[kMaxLine];
51	51	FILE *flog = OpenFile(log_file, "wb");
52	52	while (fgets(line, kMaxLine, stdin) != NULL)
53	53	{

56	56	fflush(NULL);
57	57	}
58	58
	59	delete[] line;
59	60	exit(0);
60	61	}
61	62	else

113	114
114	115	FILE *flog = OpenFile(log_thread.log_file_, "wb");
115	116
116		char line[kMaxLine];
	117	char *line = new char[kMaxLine];
117	118	int len = 0;
118	119	while ((len = read(log_thread.in_fd, line, kMaxLine)) > 0)
119	120	{

123	124	}
124	125	fclose(flog);
125	126
	127	delete[] line;
126	128	return p;
127	129	}
128

-1

src/release/filterfa.cpp less more

43	43	cerr << "fq2fa - Filter out fasta sequence containing N." << endl;
44	44	cerr << "Usage: filterfa tmp.fa out.fa " << endl;
45	45	cerr << " filterfa --paired tmp.fa out.fa" << endl;
46		cerr << " filterfa --merged tmp_1.fa tmp_2.fa out.fa" << endl;
	46	cerr << " filterfa --merge tmp_1.fa tmp_2.fa out.fa" << endl;
47	47	cerr << "Allowed Options: " << endl;
48	48	cerr << desc << endl;
49	49	exit(1);

-2

src/release/idba_tran.cpp less more

48	48	int min_count;
49	49	int min_support;
50	50	int min_contig;
	51	int min_transcript;
51	52	double similar;
52	53	int max_mismatch;
53	54	int seed_kmer_size;

74	75	min_count = 2;
75	76	min_support = 1;
76	77	min_contig = 200;
	78	min_transcript = 300;
77	79	similar = 0.95;
78	80	max_mismatch = 3;
79	81	seed_kmer_size = 30;

235	237	{
236	238	bool flag = true;
237	239
238		if (flag && path.size() > 300)
	240	if (flag && path.size() > option.min_transcript)
239	241	{
240	242	isoforms.push_back(path);
241	243	}

299	301	desc.AddOption("num_threads", "", option.num_threads, "number of threads");
300	302	desc.AddOption("seed_kmer", "", option.seed_kmer_size, "seed kmer size for alignment");
301	303	desc.AddOption("min_contig", "", option.min_contig, "minimum size of contig");
	304	desc.AddOption("min_transcript", "", option.min_transcript, "minimum size of transcript");
302	305	desc.AddOption("similar", "", option.similar, "similarity for alignment");
303	306	desc.AddOption("max_mismatch", "", option.max_mismatch, "max mismatch of error correction");
304	307	//desc.AddOption("min_pairs", "", option.min_pairs, "minimum number of pairs");

516	519	int index = 0;
517	520	for (unsigned i = 0; i < transcripts.size(); ++i)
518	521	{
519		if (transcripts[i].size() >= 300)
	522	if (transcripts[i].size() >= option.min_transcript)
520	523	{
521	524	transcript_paths[index] = transcript_paths[i];
522	525	transcripts[index++] = transcripts[i];

-2

src/sequence/sequence_reader.cpp less more

46	46
47	47	bool FastaReader::ReadRecord(Sequence &seq, string &comment, string &quality)
48	48	{
49		return ReadFasta(*is_, seq, comment);
	49	return ReadFasta(*is_, seq, comment).good();
50	50	}
51	51
52	52	bool FastqReader::ReadRecord(Sequence &seq, string &comment, string &quality)
53	53	{
54		return ReadFastq(*is_, seq, comment, quality);
	54	return ReadFastq(*is_, seq, comment, quality).good();
55	55	}
56	56

-2

src/sequence/sequence_writer.cpp less more

45	45
46	46	bool FastaWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
47	47	{
48		return WriteFasta(*os_, seq, comment);
	48	return WriteFasta(*os_, seq, comment).good();
49	49	}
50	50
51	51	bool FastqWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
52	52	{
53		return WriteFastq(*os_, seq, comment, quality);
	53	return WriteFastq(*os_, seq, comment, quality).good();
54	54	}
55	55

-1

test/Makefile.am less more

15	15	short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
16	16	hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
17	17
18		noinst_PROGRAMS = \
	18	check_PROGRAMS = \
19	19	compact_sequence_unittest \
20	20	hash_table_unittest \
21	21	bit_edges_unittest \

29	29	short_sequence_unittest \
30	30	hash_map_unittest
31	31
	32	TESTS=$(check_PROGRAMS)

+749

-197

test/Makefile.in less more

0		# Makefile.in generated by automake 1.11.3 from Makefile.am.
	0	# Makefile.in generated by automake 1.14.1 from Makefile.am.
1	1	# @configure_input@
2	2
3		# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
4		# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
5		# Foundation, Inc.
	3	# Copyright (C) 1994-2013 Free Software Foundation, Inc.
	4
6	5	# This Makefile.in is free software; the Free Software Foundation
7	6	# gives unlimited permission to copy and/or distribute it,
8	7	# with or without modifications, as long as this notice is preserved.

13	12	# PARTICULAR PURPOSE.
14	13
15	14	@SET_MAKE@
16
17	15	VPATH = @srcdir@
	16	am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
	17	am__make_running_with_option = \
	18	case $${target_option-} in \
	19	?) ;; \
	20	*) echo "am__make_running_with_option: internal error: invalid" \
	21	"target option '$${target_option-}' specified" >&2; \
	22	exit 1;; \
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	24	has_opt=no; \
	25	sane_makeflags=$$MAKEFLAGS; \
	26	if $(am__is_gnu_make); then \
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	29	case $$MAKEFLAGS in \
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	32	sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
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	34	esac; \
	35	fi; \
	36	skip_next=no; \
	37	strip_trailopt () \
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	39	flg=`printf '%s\n' "$$flg" \| sed "s/$$1.*$$//"`; \
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	52	-[JT]) skip_next=yes;; \
	53	esac; \
	54	case $$flg in \
	55	$$target_option) has_opt=yes; break;; \
	56	esac; \
	57	done; \
	58	test $$has_opt = yes
	59	am__make_dryrun = (target_option=n; $(am__make_running_with_option))
	60	am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
18	61	pkgdatadir = $(datadir)/@PACKAGE@
19	62	pkgincludedir = $(includedir)/@PACKAGE@
20	63	pkglibdir = $(libdir)/@PACKAGE@

31	74	NORMAL_UNINSTALL = :
32	75	PRE_UNINSTALL = :
33	76	POST_UNINSTALL = :
34		noinst_PROGRAMS = compact_sequence_unittest$(EXEEXT) \
	77	check_PROGRAMS = compact_sequence_unittest$(EXEEXT) \
35	78	hash_table_unittest$(EXEEXT) bit_edges_unittest$(EXEEXT) \
36	79	kmer_unittest$(EXEEXT) hash_set_unittest$(EXEEXT) \
37	80	atomic_integer_unittest$(EXEEXT) \

39	82	managed_list_unittest$(EXEEXT) sequence_unittest$(EXEEXT) \
40	83	short_sequence_unittest$(EXEEXT) hash_map_unittest$(EXEEXT)
41	84	subdir = test
42		DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
	85	DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
	86	$(top_srcdir)/depcomp $(top_srcdir)/test-driver
43	87	ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
44	88	am__aclocal_m4_deps = $(top_srcdir)/configure.ac
45	89	am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \

48	92	CONFIG_HEADER = $(top_builddir)/config.h
49	93	CONFIG_CLEAN_FILES =
50	94	CONFIG_CLEAN_VPATH_FILES =
51		PROGRAMS = $(noinst_PROGRAMS)
52	95	am_atomic_integer_unittest_OBJECTS = \
53	96	atomic_integer_unittest.$(OBJEXT)
54	97	atomic_integer_unittest_OBJECTS = \

91	134	am_vertex_status_unittest_OBJECTS = vertex_status_unittest.$(OBJEXT)
92	135	vertex_status_unittest_OBJECTS = $(am_vertex_status_unittest_OBJECTS)
93	136	vertex_status_unittest_LDADD = $(LDADD)
	137	AM_V_P = $(am__v_P_@AM_V@)
	138	am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
	139	am__v_P_0 = false
	140	am__v_P_1 = :
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	147	am__v_at_0 = @
	148	am__v_at_1 =
94	149	DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
95	150	depcomp = $(SHELL) $(top_srcdir)/depcomp
96	151	am__depfiles_maybe = depfiles
97	152	am__mv = mv -f
	153	AM_V_lt = $(am__v_lt_@AM_V@)
	154	am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
	155	am__v_lt_0 = --silent
	156	am__v_lt_1 =
98	157	CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
99	158	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
	159	AM_V_CXX = $(am__v_CXX_@AM_V@)
	160	am__v_CXX_ = $(am__v_CXX_@AM_DEFAULT_V@)
	161	am__v_CXX_0 = @echo " CXX " $@;
	162	am__v_CXX_1 =
100	163	CXXLD = $(CXX)
101	164	CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
102	165	-o $@
	166	AM_V_CXXLD = $(am__v_CXXLD_@AM_V@)
	167	am__v_CXXLD_ = $(am__v_CXXLD_@AM_DEFAULT_V@)
	168	am__v_CXXLD_0 = @echo " CXXLD " $@;
	169	am__v_CXXLD_1 =
103	170	SOURCES = $(atomic_integer_unittest_SOURCES) \
104	171	$(bit_edges_unittest_SOURCES) \
105	172	$(compact_sequence_unittest_SOURCES) \

118	185	$(sequence_unittest_SOURCES) \
119	186	$(short_sequence_unittest_SOURCES) \
120	187	$(vertex_status_unittest_SOURCES)
	188	am__can_run_installinfo = \
	189	case $$AM_UPDATE_INFO_DIR in \
	190	n\|no\|NO) false;; \
	191	*) (install-info --version) >/dev/null 2>&1;; \
	192	esac
	193	am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
	194	# Read a list of newline-separated strings from the standard input,
	195	# and print each of them once, without duplicates. Input order is
	196	# not preserved.
	197	am__uniquify_input = $(AWK) '\
	198	BEGIN { nonempty = 0; } \
	199	{ items[$$0] = 1; nonempty = 1; } \
	200	END { if (nonempty) { for (i in items) print i; }; } \
	201	'
	202	# Make sure the list of sources is unique. This is necessary because,
	203	# e.g., the same source file might be shared among _SOURCES variables
	204	# for different programs/libraries.
	205	am__define_uniq_tagged_files = \
	206	list='$(am__tagged_files)'; \
	207	unique=`for i in $$list; do \
	208	if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
	209	done \| $(am__uniquify_input)`
121	210	ETAGS = etags
122	211	CTAGS = ctags
	212	am__tty_colors_dummy = \
	213	mgn= red= grn= lgn= blu= brg= std=; \
	214	am__color_tests=no
	215	am__tty_colors = { \
	216	$(am__tty_colors_dummy); \
	217	if test "X$(AM_COLOR_TESTS)" = Xno; then \
	218	am__color_tests=no; \
	219	elif test "X$(AM_COLOR_TESTS)" = Xalways; then \
	220	am__color_tests=yes; \
	221	elif test "X$$TERM" != Xdumb && { test -t 1; } 2>/dev/null; then \
	222	am__color_tests=yes; \
	223	fi; \
	224	if test $$am__color_tests = yes; then \
	225	red='[0;31m'; \
	226	grn='[0;32m'; \
	227	lgn='[1;32m'; \
	228	blu='[1;34m'; \
	229	mgn='[0;35m'; \
	230	brg='[1m'; \
	231	std='[m'; \
	232	fi; \
	233	}
	234	am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" \| sed 's\|.\|.\|g'`;
	235	am__vpath_adj = case $$p in \
	236	$(srcdir)/*) f=`echo "$$p" \| sed "s\|^$$srcdirstrip/\|\|"`;; \
	237	*) f=$$p;; \
	238	esac;
	239	am__strip_dir = f=`echo $$p \| sed -e 's\|^.*/\|\|'`;
	240	am__install_max = 40
	241	am__nobase_strip_setup = \
	242	srcdirstrip=`echo "$(srcdir)" \| sed 's/[].[^$$\\*\|]/\\\\&/g'`
	243	am__nobase_strip = \
	244	for p in $$list; do echo "$$p"; done \| sed -e "s\|$$srcdirstrip/\|\|"
	245	am__nobase_list = $(am__nobase_strip_setup); \
	246	for p in $$list; do echo "$$p $$p"; done \| \
	247	sed "s\| $$srcdirstrip/\| \|;"' / .\//!s/ ./ ./; s,$ .$/[^/]$$,\1,' \| \
	248	$(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
	249	if (++n[$$2] == $(am__install_max)) \
	250	{ print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
	251	END { for (dir in files) print dir, files[dir] }'
	252	am__base_list = \
	253	sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' \| \
	254	sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
	255	am__uninstall_files_from_dir = { \
	256	test -z "$$files" \
	257	\|\| { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
	258	\|\| { echo " ( cd '$$dir' && rm -f" $$files ")"; \
	259	$(am__cd) "$$dir" && rm -f $$files; }; \
	260	}
	261	am__recheck_rx = ^[ ]:recheck:[ ]
	262	am__global_test_result_rx = ^[ ]:global-test-result:[ ]
	263	am__copy_in_global_log_rx = ^[ ]:copy-in-global-log:[ ]
	264	# A command that, given a newline-separated list of test names on the
	265	# standard input, print the name of the tests that are to be re-run
	266	# upon "make recheck".
	267	am__list_recheck_tests = $(AWK) '{ \
	268	recheck = 1; \
	269	while ((rc = (getline line < ($$0 ".trs"))) != 0) \
	270	{ \
	271	if (rc < 0) \
	272	{ \
	273	if ((getline line2 < ($$0 ".log")) < 0) \
	274	recheck = 0; \
	275	break; \
	276	} \
	277	else if (line ~ /$(am__recheck_rx)[nN][Oo]/) \
	278	{ \
	279	recheck = 0; \
	280	break; \
	281	} \
	282	else if (line ~ /$(am__recheck_rx)[yY][eE][sS]/) \
	283	{ \
	284	break; \
	285	} \
	286	}; \
	287	if (recheck) \
	288	print $$0; \
	289	close ($$0 ".trs"); \
	290	close ($$0 ".log"); \
	291	}'
	292	# A command that, given a newline-separated list of test names on the
	293	# standard input, create the global log from their .trs and .log files.
	294	am__create_global_log = $(AWK) ' \
	295	function fatal(msg) \
	296	{ \
	297	print "fatal: making $@: " msg \| "cat >&2"; \
	298	exit 1; \
	299	} \
	300	function rst_section(header) \
	301	{ \
	302	print header; \
	303	len = length(header); \
	304	for (i = 1; i <= len; i = i + 1) \
	305	printf "="; \
	306	printf "\n\n"; \
	307	} \
	308	{ \
	309	copy_in_global_log = 1; \
	310	global_test_result = "RUN"; \
	311	while ((rc = (getline line < ($$0 ".trs"))) != 0) \
	312	{ \
	313	if (rc < 0) \
	314	fatal("failed to read from " $$0 ".trs"); \
	315	if (line ~ /$(am__global_test_result_rx)/) \
	316	{ \
	317	sub("$(am__global_test_result_rx)", "", line); \
	318	sub("[ ]*$$", "", line); \
	319	global_test_result = line; \
	320	} \
	321	else if (line ~ /$(am__copy_in_global_log_rx)[nN][oO]/) \
	322	copy_in_global_log = 0; \
	323	}; \
	324	if (copy_in_global_log) \
	325	{ \
	326	rst_section(global_test_result ": " $$0); \
	327	while ((rc = (getline line < ($$0 ".log"))) != 0) \
	328	{ \
	329	if (rc < 0) \
	330	fatal("failed to read from " $$0 ".log"); \
	331	print line; \
	332	}; \
	333	printf "\n"; \
	334	}; \
	335	close ($$0 ".trs"); \
	336	close ($$0 ".log"); \
	337	}'
	338	# Restructured Text title.
	339	am__rst_title = { sed 's/./ & /;h;s/./=/g;p;x;s/ $$//;p;g' && echo; }
	340	# Solaris 10 'make', and several other traditional 'make' implementations,
	341	# pass "-e" to $(SHELL), and POSIX 2008 even requires this. Work around it
	342	# by disabling -e (using the XSI extension "set +e") if it's set.
	343	am__sh_e_setup = case $$- in e) set +e;; esac
	344	# Default flags passed to test drivers.
	345	am__common_driver_flags = \
	346	--color-tests "$$am__color_tests" \
	347	--enable-hard-errors "$$am__enable_hard_errors" \
	348	--expect-failure "$$am__expect_failure"
	349	# To be inserted before the command running the test. Creates the
	350	# directory for the log if needed. Stores in $dir the directory
	351	# containing $f, in $tst the test, in $log the log. Executes the
	352	# developer- defined test setup AM_TESTS_ENVIRONMENT (if any), and
	353	# passes TESTS_ENVIRONMENT. Set up options for the wrapper that
	354	# will run the test scripts (or their associated LOG_COMPILER, if
	355	# thy have one).
	356	am__check_pre = \
	357	$(am__sh_e_setup); \
	358	$(am__vpath_adj_setup) $(am__vpath_adj) \
	359	$(am__tty_colors); \
	360	srcdir=$(srcdir); export srcdir; \
	361	case "$@" in \
	362	/) am__odir=`echo "./$@" \| sed 's\|/[^/]*$$\|\|'`;; \
	363	*) am__odir=.;; \
	364	esac; \
	365	test "x$$am__odir" = x"." \|\| test -d "$$am__odir" \
	366	\|\| $(MKDIR_P) "$$am__odir" \|\| exit $$?; \
	367	if test -f "./$$f"; then dir=./; \
	368	elif test -f "$$f"; then dir=; \
	369	else dir="$(srcdir)/"; fi; \
	370	tst=$$dir$$f; log='$@'; \
	371	if test -n '$(DISABLE_HARD_ERRORS)'; then \
	372	am__enable_hard_errors=no; \
	373	else \
	374	am__enable_hard_errors=yes; \
	375	fi; \
	376	case " $(XFAIL_TESTS) " in \
	377	[\ \ ]$$f[\ \ ] \| [\ \ ]$$dir$$f[\ \ ]) \
	378	am__expect_failure=yes;; \
	379	*) \
	380	am__expect_failure=no;; \
	381	esac; \
	382	$(AM_TESTS_ENVIRONMENT) $(TESTS_ENVIRONMENT)
	383	# A shell command to get the names of the tests scripts with any registered
	384	# extension removed (i.e., equivalently, the names of the test logs, with
	385	# the '.log' extension removed). The result is saved in the shell variable
	386	# '$bases'. This honors runtime overriding of TESTS and TEST_LOGS. Sadly,
	387	# we cannot use something simpler, involving e.g., "$(TEST_LOGS:.log=)",
	388	# since that might cause problem with VPATH rewrites for suffix-less tests.
	389	# See also 'test-harness-vpath-rewrite.sh' and 'test-trs-basic.sh'.
	390	am__set_TESTS_bases = \
	391	bases='$(TEST_LOGS)'; \
	392	bases=`for i in $$bases; do echo $$i; done \| sed 's/\.log$$//'`; \
	393	bases=`echo $$bases`
	394	RECHECK_LOGS = $(TEST_LOGS)
	395	AM_RECURSIVE_TARGETS = check recheck
	396	TEST_SUITE_LOG = test-suite.log
	397	TEST_EXTENSIONS = @EXEEXT@ .test
	398	LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
	399	LOG_COMPILE = $(LOG_COMPILER) $(AM_LOG_FLAGS) $(LOG_FLAGS)
	400	am__set_b = \
	401	case '$@' in \
	402	/) \
	403	case '$*' in \
	404	/) b='$*';; \
	405	*) b=`echo '$@' \| sed 's/\.log$$//'`; \
	406	esac;; \
	407	*) \
	408	b='$*';; \
	409	esac
	410	am__test_logs1 = $(TESTS:=.log)
	411	am__test_logs2 = $(am__test_logs1:@EXEEXT@.log=.log)
	412	TEST_LOGS = $(am__test_logs2:.test.log=.log)
	413	TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
	414	TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
	415	$(TEST_LOG_FLAGS)
123	416	DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
124	417	ACLOCAL = @ACLOCAL@
125	418	AMTAR = @AMTAR@
	419	AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
126	420	AUTOCONF = @AUTOCONF@
127	421	AUTOHEADER = @AUTOHEADER@
128	422	AUTOMAKE = @AUTOMAKE@

227	521	sequence_unittest_SOURCES = $(top_srcdir)/src/test/sequence_unittest.cpp
228	522	short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
229	523	hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
	524	TESTS = $(check_PROGRAMS)
230	525	all: all-am
231	526
232	527	.SUFFIXES:
233		.SUFFIXES: .cpp .o .obj
	528	.SUFFIXES: .cpp .log .o .obj .test .test$(EXEEXT) .trs
234	529	$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
235	530	@for dep in $?; do \
236	531	case '$(am__configure_deps)' in \

262	557	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
263	558	$(am__aclocal_m4_deps):
264	559
265		clean-noinstPROGRAMS:
266		-test -z "$(noinst_PROGRAMS)" \|\| rm -f $(noinst_PROGRAMS)
	560	clean-checkPROGRAMS:
	561	-test -z "$(check_PROGRAMS)" \|\| rm -f $(check_PROGRAMS)
	562
267	563	atomic_integer_unittest$(EXEEXT): $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_DEPENDENCIES) $(EXTRA_atomic_integer_unittest_DEPENDENCIES)
268	564	@rm -f atomic_integer_unittest$(EXEEXT)
269		$(CXXLINK) $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_LDADD) $(LIBS)
	565	$(AM_V_CXXLD)$(CXXLINK) $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_LDADD) $(LIBS)
	566
270	567	bit_edges_unittest$(EXEEXT): $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_DEPENDENCIES) $(EXTRA_bit_edges_unittest_DEPENDENCIES)
271	568	@rm -f bit_edges_unittest$(EXEEXT)
272		$(CXXLINK) $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_LDADD) $(LIBS)
	569	$(AM_V_CXXLD)$(CXXLINK) $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_LDADD) $(LIBS)
	570
273	571	compact_sequence_unittest$(EXEEXT): $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_DEPENDENCIES) $(EXTRA_compact_sequence_unittest_DEPENDENCIES)
274	572	@rm -f compact_sequence_unittest$(EXEEXT)
275		$(CXXLINK) $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_LDADD) $(LIBS)
	573	$(AM_V_CXXLD)$(CXXLINK) $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_LDADD) $(LIBS)
	574
276	575	hash_map_unittest$(EXEEXT): $(hash_map_unittest_OBJECTS) $(hash_map_unittest_DEPENDENCIES) $(EXTRA_hash_map_unittest_DEPENDENCIES)
277	576	@rm -f hash_map_unittest$(EXEEXT)
278		$(CXXLINK) $(hash_map_unittest_OBJECTS) $(hash_map_unittest_LDADD) $(LIBS)
	577	$(AM_V_CXXLD)$(CXXLINK) $(hash_map_unittest_OBJECTS) $(hash_map_unittest_LDADD) $(LIBS)
	578
279	579	hash_set_unittest$(EXEEXT): $(hash_set_unittest_OBJECTS) $(hash_set_unittest_DEPENDENCIES) $(EXTRA_hash_set_unittest_DEPENDENCIES)
280	580	@rm -f hash_set_unittest$(EXEEXT)
281		$(CXXLINK) $(hash_set_unittest_OBJECTS) $(hash_set_unittest_LDADD) $(LIBS)
	581	$(AM_V_CXXLD)$(CXXLINK) $(hash_set_unittest_OBJECTS) $(hash_set_unittest_LDADD) $(LIBS)
	582
282	583	hash_table_unittest$(EXEEXT): $(hash_table_unittest_OBJECTS) $(hash_table_unittest_DEPENDENCIES) $(EXTRA_hash_table_unittest_DEPENDENCIES)
283	584	@rm -f hash_table_unittest$(EXEEXT)
284		$(CXXLINK) $(hash_table_unittest_OBJECTS) $(hash_table_unittest_LDADD) $(LIBS)
	585	$(AM_V_CXXLD)$(CXXLINK) $(hash_table_unittest_OBJECTS) $(hash_table_unittest_LDADD) $(LIBS)
	586
285	587	histgram_unittest$(EXEEXT): $(histgram_unittest_OBJECTS) $(histgram_unittest_DEPENDENCIES) $(EXTRA_histgram_unittest_DEPENDENCIES)
286	588	@rm -f histgram_unittest$(EXEEXT)
287		$(CXXLINK) $(histgram_unittest_OBJECTS) $(histgram_unittest_LDADD) $(LIBS)
	589	$(AM_V_CXXLD)$(CXXLINK) $(histgram_unittest_OBJECTS) $(histgram_unittest_LDADD) $(LIBS)
	590
288	591	kmer_unittest$(EXEEXT): $(kmer_unittest_OBJECTS) $(kmer_unittest_DEPENDENCIES) $(EXTRA_kmer_unittest_DEPENDENCIES)
289	592	@rm -f kmer_unittest$(EXEEXT)
290		$(CXXLINK) $(kmer_unittest_OBJECTS) $(kmer_unittest_LDADD) $(LIBS)
	593	$(AM_V_CXXLD)$(CXXLINK) $(kmer_unittest_OBJECTS) $(kmer_unittest_LDADD) $(LIBS)
	594
291	595	managed_list_unittest$(EXEEXT): $(managed_list_unittest_OBJECTS) $(managed_list_unittest_DEPENDENCIES) $(EXTRA_managed_list_unittest_DEPENDENCIES)
292	596	@rm -f managed_list_unittest$(EXEEXT)
293		$(CXXLINK) $(managed_list_unittest_OBJECTS) $(managed_list_unittest_LDADD) $(LIBS)
	597	$(AM_V_CXXLD)$(CXXLINK) $(managed_list_unittest_OBJECTS) $(managed_list_unittest_LDADD) $(LIBS)
	598
294	599	sequence_unittest$(EXEEXT): $(sequence_unittest_OBJECTS) $(sequence_unittest_DEPENDENCIES) $(EXTRA_sequence_unittest_DEPENDENCIES)
295	600	@rm -f sequence_unittest$(EXEEXT)
296		$(CXXLINK) $(sequence_unittest_OBJECTS) $(sequence_unittest_LDADD) $(LIBS)
	601	$(AM_V_CXXLD)$(CXXLINK) $(sequence_unittest_OBJECTS) $(sequence_unittest_LDADD) $(LIBS)
	602
297	603	short_sequence_unittest$(EXEEXT): $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_DEPENDENCIES) $(EXTRA_short_sequence_unittest_DEPENDENCIES)
298	604	@rm -f short_sequence_unittest$(EXEEXT)
299		$(CXXLINK) $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_LDADD) $(LIBS)
	605	$(AM_V_CXXLD)$(CXXLINK) $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_LDADD) $(LIBS)
	606
300	607	vertex_status_unittest$(EXEEXT): $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_DEPENDENCIES) $(EXTRA_vertex_status_unittest_DEPENDENCIES)
301	608	@rm -f vertex_status_unittest$(EXEEXT)
302		$(CXXLINK) $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_LDADD) $(LIBS)
	609	$(AM_V_CXXLD)$(CXXLINK) $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_LDADD) $(LIBS)
303	610
304	611	mostlyclean-compile:
305	612	-rm -f *.$(OBJEXT)

321	628	@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/vertex_status_unittest.Po@am__quote@
322	629
323	630	.cpp.o:
324		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
325		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
326		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
327		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
328		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
	631	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
	632	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
	633	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
	634	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	635	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ $<
329	636
330	637	.cpp.obj:
331		@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
332		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
333		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
334		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
335		@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
	638	@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
	639	@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$.Tpo $(DEPDIR)/$.Po
	640	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
	641	@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
	642	@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
336	643
337	644	atomic_integer_unittest.o: $(top_srcdir)/src/test/atomic_integer_unittest.cpp
338		@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT atomic_integer_unittest.o -MD -MP -MF $(DEPDIR)/atomic_integer_unittest.Tpo -c -o atomic_integer_unittest.o `test -f '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/test/atomic_integer_unittest.cpp
339		@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/atomic_integer_unittest.Tpo $(DEPDIR)/atomic_integer_unittest.Po
340		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/test/atomic_integer_unittest.cpp' object='atomic_integer_unittest.o' libtool=no @AMDEPBACKSLASH@
341		@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
342		@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o atomic_integer_unittest.o `test -f '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' \|\| echo '$(srcdir)/'`$(top_srcdir)/src/test/atomic_integer_unittest.cpp
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	834	CTAGS: ctags
	835	ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
	836	$(am__define_uniq_tagged_files); \
545	837	test -z "$(CTAGS_ARGS)$$unique" \
546	838	\|\| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
547	839	$$unique

550	842	here=`$(am__cd) $(top_builddir) && pwd` \
551	843	&& $(am__cd) $(top_srcdir) \
552	844	&& gtags -i $(GTAGS_ARGS) "$$here"
	845	cscopelist: cscopelist-am
	846
	847	cscopelist-am: $(am__tagged_files)
	848	list='$(am__tagged_files)'; \
	849	case "$(srcdir)" in \
	850	[\\/]* \| ?:[\\/]*) sdir="$(srcdir)" ;; \
	851	*) sdir=$(subdir)/$(srcdir) ;; \
	852	esac; \
	853	for i in $$list; do \
	854	if test -f "$$i"; then \
	855	echo "$(subdir)/$$i"; \
	856	else \
	857	echo "$$sdir/$$i"; \
	858	fi; \
	859	done >> $(top_builddir)/cscope.files
553	860
554	861	distclean-tags:
555	862	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
	863
	864	# Recover from deleted '.trs' file; this should ensure that
	865	# "rm -f foo.log; make foo.trs" re-run 'foo.test', and re-create
	866	# both 'foo.log' and 'foo.trs'. Break the recipe in two subshells
	867	# to avoid problems with "make -n".
	868	.log.trs:
	869	rm -f $< $@
	870	$(MAKE) $(AM_MAKEFLAGS) $<
	871
	872	# Leading 'am--fnord' is there to ensure the list of targets does not
	873	# expand to empty, as could happen e.g. with make check TESTS=''.
	874	am--fnord $(TEST_LOGS) $(TEST_LOGS:.log=.trs): $(am__force_recheck)
	875	am--force-recheck:
	876	@:
	877
	878	$(TEST_SUITE_LOG): $(TEST_LOGS)
	879	@$(am__set_TESTS_bases); \
	880	am__f_ok () { test -f "$$1" && test -r "$$1"; }; \
	881	redo_bases=`for i in $$bases; do \
	882	am__f_ok $$i.trs && am__f_ok $$i.log \|\| echo $$i; \
	883	done`; \
	884	if test -n "$$redo_bases"; then \
	885	redo_logs=`for i in $$redo_bases; do echo $$i.log; done`; \
	886	redo_results=`for i in $$redo_bases; do echo $$i.trs; done`; \
	887	if $(am__make_dryrun); then :; else \
	888	rm -f $$redo_logs && rm -f $$redo_results \|\| exit 1; \
	889	fi; \
	890	fi; \
	891	if test -n "$$am__remaking_logs"; then \
	892	echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \
	893	"recursion detected" >&2; \
	894	else \
	895	am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \
	896	fi; \
	897	if $(am__make_dryrun); then :; else \
	898	st=0; \
	899	errmsg="fatal: making $(TEST_SUITE_LOG): failed to create"; \
	900	for i in $$redo_bases; do \
	901	test -f $$i.trs && test -r $$i.trs \
	902	\|\| { echo "$$errmsg $$i.trs" >&2; st=1; }; \
	903	test -f $$i.log && test -r $$i.log \
	904	\|\| { echo "$$errmsg $$i.log" >&2; st=1; }; \
	905	done; \
	906	test $$st -eq 0 \|\| exit 1; \
	907	fi
	908	@$(am__sh_e_setup); $(am__tty_colors); $(am__set_TESTS_bases); \
	909	ws='[ ]'; \
	910	results=`for b in $$bases; do echo $$b.trs; done`; \
	911	test -n "$$results" \|\| results=/dev/null; \
	912	all=` grep "^$$ws*:test-result:" $$results \| wc -l`; \
	913	pass=` grep "^$$ws:test-result:$$wsPASS" $$results \| wc -l`; \
	914	fail=` grep "^$$ws:test-result:$$wsFAIL" $$results \| wc -l`; \
	915	skip=` grep "^$$ws:test-result:$$wsSKIP" $$results \| wc -l`; \
	916	xfail=`grep "^$$ws:test-result:$$wsXFAIL" $$results \| wc -l`; \
	917	xpass=`grep "^$$ws:test-result:$$wsXPASS" $$results \| wc -l`; \
	918	error=`grep "^$$ws:test-result:$$wsERROR" $$results \| wc -l`; \
	919	if test `expr $$fail + $$xpass + $$error` -eq 0; then \
	920	success=true; \
	921	else \
	922	success=false; \
	923	fi; \
	924	br='==================='; br=$$br$$br$$br$$br; \
	925	result_count () \
	926	{ \
	927	if test x"$$1" = x"--maybe-color"; then \
	928	maybe_colorize=yes; \
	929	elif test x"$$1" = x"--no-color"; then \
	930	maybe_colorize=no; \
	931	else \
	932	echo "$@: invalid 'result_count' usage" >&2; exit 4; \
	933	fi; \
	934	shift; \
	935	desc=$$1 count=$$2; \
	936	if test $$maybe_colorize = yes && test $$count -gt 0; then \
	937	color_start=$$3 color_end=$$std; \
	938	else \
	939	color_start= color_end=; \
	940	fi; \
	941	echo "$${color_start}# $$desc $$count$${color_end}"; \
	942	}; \
	943	create_testsuite_report () \
	944	{ \
	945	result_count $$1 "TOTAL:" $$all "$$brg"; \
	946	result_count $$1 "PASS: " $$pass "$$grn"; \
	947	result_count $$1 "SKIP: " $$skip "$$blu"; \
	948	result_count $$1 "XFAIL:" $$xfail "$$lgn"; \
	949	result_count $$1 "FAIL: " $$fail "$$red"; \
	950	result_count $$1 "XPASS:" $$xpass "$$red"; \
	951	result_count $$1 "ERROR:" $$error "$$mgn"; \
	952	}; \
	953	{ \
	954	echo "$(PACKAGE_STRING): $(subdir)/$(TEST_SUITE_LOG)" \| \
	955	$(am__rst_title); \
	956	create_testsuite_report --no-color; \
	957	echo; \
	958	echo ".. contents:: :depth: 2"; \
	959	echo; \
	960	for b in $$bases; do echo $$b; done \
	961	\| $(am__create_global_log); \
	962	} >$(TEST_SUITE_LOG).tmp \|\| exit 1; \
	963	mv $(TEST_SUITE_LOG).tmp $(TEST_SUITE_LOG); \
	964	if $$success; then \
	965	col="$$grn"; \
	966	else \
	967	col="$$red"; \
	968	test x"$$VERBOSE" = x \|\| cat $(TEST_SUITE_LOG); \
	969	fi; \
	970	echo "$${col}$$br$${std}"; \
	971	echo "$${col}Testsuite summary for $(PACKAGE_STRING)$${std}"; \
	972	echo "$${col}$$br$${std}"; \
	973	create_testsuite_report --maybe-color; \
	974	echo "$$col$$br$$std"; \
	975	if $$success; then :; else \
	976	echo "$${col}See $(subdir)/$(TEST_SUITE_LOG)$${std}"; \
	977	if test -n "$(PACKAGE_BUGREPORT)"; then \
	978	echo "$${col}Please report to $(PACKAGE_BUGREPORT)$${std}"; \
	979	fi; \
	980	echo "$$col$$br$$std"; \
	981	fi; \
	982	$$success \|\| exit 1
	983
	984	check-TESTS:
	985	@list='$(RECHECK_LOGS)'; test -z "$$list" \|\| rm -f $$list
	986	@list='$(RECHECK_LOGS:.log=.trs)'; test -z "$$list" \|\| rm -f $$list
	987	@test -z "$(TEST_SUITE_LOG)" \|\| rm -f $(TEST_SUITE_LOG)
	988	@set +e; $(am__set_TESTS_bases); \
	989	log_list=`for i in $$bases; do echo $$i.log; done`; \
	990	trs_list=`for i in $$bases; do echo $$i.trs; done`; \
	991	log_list=`echo $$log_list`; trs_list=`echo $$trs_list`; \
	992	$(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) TEST_LOGS="$$log_list"; \
	993	exit $$?;
	994	recheck: all $(check_PROGRAMS)
	995	@test -z "$(TEST_SUITE_LOG)" \|\| rm -f $(TEST_SUITE_LOG)
	996	@set +e; $(am__set_TESTS_bases); \
	997	bases=`for i in $$bases; do echo $$i; done \
	998	\| $(am__list_recheck_tests)` \|\| exit 1; \
	999	log_list=`for i in $$bases; do echo $$i.log; done`; \
	1000	log_list=`echo $$log_list`; \
	1001	$(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) \
	1002	am__force_recheck=am--force-recheck \
	1003	TEST_LOGS="$$log_list"; \
	1004	exit $$?
	1005	compact_sequence_unittest.log: compact_sequence_unittest$(EXEEXT)
	1006	@p='compact_sequence_unittest$(EXEEXT)'; \
	1007	b='compact_sequence_unittest'; \
	1008	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1009	--log-file $$b.log --trs-file $$b.trs \
	1010	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1011	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1012	hash_table_unittest.log: hash_table_unittest$(EXEEXT)
	1013	@p='hash_table_unittest$(EXEEXT)'; \
	1014	b='hash_table_unittest'; \
	1015	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1016	--log-file $$b.log --trs-file $$b.trs \
	1017	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1018	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1019	bit_edges_unittest.log: bit_edges_unittest$(EXEEXT)
	1020	@p='bit_edges_unittest$(EXEEXT)'; \
	1021	b='bit_edges_unittest'; \
	1022	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1023	--log-file $$b.log --trs-file $$b.trs \
	1024	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1025	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1026	kmer_unittest.log: kmer_unittest$(EXEEXT)
	1027	@p='kmer_unittest$(EXEEXT)'; \
	1028	b='kmer_unittest'; \
	1029	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1030	--log-file $$b.log --trs-file $$b.trs \
	1031	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1032	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1033	hash_set_unittest.log: hash_set_unittest$(EXEEXT)
	1034	@p='hash_set_unittest$(EXEEXT)'; \
	1035	b='hash_set_unittest'; \
	1036	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1037	--log-file $$b.log --trs-file $$b.trs \
	1038	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1039	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1040	atomic_integer_unittest.log: atomic_integer_unittest$(EXEEXT)
	1041	@p='atomic_integer_unittest$(EXEEXT)'; \
	1042	b='atomic_integer_unittest'; \
	1043	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1044	--log-file $$b.log --trs-file $$b.trs \
	1045	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1046	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1047	vertex_status_unittest.log: vertex_status_unittest$(EXEEXT)
	1048	@p='vertex_status_unittest$(EXEEXT)'; \
	1049	b='vertex_status_unittest'; \
	1050	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1051	--log-file $$b.log --trs-file $$b.trs \
	1052	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1053	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1054	histgram_unittest.log: histgram_unittest$(EXEEXT)
	1055	@p='histgram_unittest$(EXEEXT)'; \
	1056	b='histgram_unittest'; \
	1057	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1058	--log-file $$b.log --trs-file $$b.trs \
	1059	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1060	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1061	managed_list_unittest.log: managed_list_unittest$(EXEEXT)
	1062	@p='managed_list_unittest$(EXEEXT)'; \
	1063	b='managed_list_unittest'; \
	1064	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1065	--log-file $$b.log --trs-file $$b.trs \
	1066	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1067	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1068	sequence_unittest.log: sequence_unittest$(EXEEXT)
	1069	@p='sequence_unittest$(EXEEXT)'; \
	1070	b='sequence_unittest'; \
	1071	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1072	--log-file $$b.log --trs-file $$b.trs \
	1073	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1074	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1075	short_sequence_unittest.log: short_sequence_unittest$(EXEEXT)
	1076	@p='short_sequence_unittest$(EXEEXT)'; \
	1077	b='short_sequence_unittest'; \
	1078	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1079	--log-file $$b.log --trs-file $$b.trs \
	1080	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1081	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1082	hash_map_unittest.log: hash_map_unittest$(EXEEXT)
	1083	@p='hash_map_unittest$(EXEEXT)'; \
	1084	b='hash_map_unittest'; \
	1085	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
	1086	--log-file $$b.log --trs-file $$b.trs \
	1087	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
	1088	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1089	.test.log:
	1090	@p='$<'; \
	1091	$(am__set_b); \
	1092	$(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
	1093	--log-file $$b.log --trs-file $$b.trs \
	1094	$(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
	1095	"$$tst" $(AM_TESTS_FD_REDIRECT)
	1096	@am__EXEEXT_TRUE@.test$(EXEEXT).log:
	1097	@am__EXEEXT_TRUE@ @p='$<'; \
	1098	@am__EXEEXT_TRUE@ $(am__set_b); \
	1099	@am__EXEEXT_TRUE@ $(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
	1100	@am__EXEEXT_TRUE@ --log-file $$b.log --trs-file $$b.trs \
	1101	@am__EXEEXT_TRUE@ $(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
	1102	@am__EXEEXT_TRUE@ "$$tst" $(AM_TESTS_FD_REDIRECT)
556	1103
557	1104	distdir: $(DISTFILES)
558	1105	@srcdirstrip=`echo "$(srcdir)" \| sed 's/[].[^$$\\*]/\\\\&/g'`; \

585	1132	fi; \
586	1133	done
587	1134	check-am: all-am
	1135	$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
	1136	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
588	1137	check: check-am
589		all-am: Makefile $(PROGRAMS)
	1138	all-am: Makefile
590	1139	installdirs:
591	1140	install: install-am
592	1141	install-exec: install-exec-am

608	1157	"INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
609	1158	fi
610	1159	mostlyclean-generic:
	1160	-test -z "$(TEST_LOGS)" \|\| rm -f $(TEST_LOGS)
	1161	-test -z "$(TEST_LOGS:.log=.trs)" \|\| rm -f $(TEST_LOGS:.log=.trs)
	1162	-test -z "$(TEST_SUITE_LOG)" \|\| rm -f $(TEST_SUITE_LOG)
611	1163
612	1164	clean-generic:
613	1165

620	1172	@echo "it deletes files that may require special tools to rebuild."
621	1173	clean: clean-am
622	1174
623		clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
	1175	clean-am: clean-checkPROGRAMS clean-generic mostlyclean-am
624	1176
625	1177	distclean: distclean-am
626	1178	-rm -rf ./$(DEPDIR)

687	1239
688	1240	uninstall-am:
689	1241
690		.MAKE: install-am install-strip
691
692		.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
693		clean-noinstPROGRAMS ctags distclean distclean-compile \
694		distclean-generic distclean-tags distdir dvi dvi-am html \
695		html-am info info-am install install-am install-data \
696		install-data-am install-dvi install-dvi-am install-exec \
697		install-exec-am install-html install-html-am install-info \
698		install-info-am install-man install-pdf install-pdf-am \
699		install-ps install-ps-am install-strip installcheck \
700		installcheck-am installdirs maintainer-clean \
701		maintainer-clean-generic mostlyclean mostlyclean-compile \
702		mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
703		uninstall-am
	1242	.MAKE: check-am install-am install-strip
	1243
	1244	.PHONY: CTAGS GTAGS TAGS all all-am check check-TESTS check-am clean \
	1245	clean-checkPROGRAMS clean-generic cscopelist-am ctags ctags-am \
	1246	distclean distclean-compile distclean-generic distclean-tags \
	1247	distdir dvi dvi-am html html-am info info-am install \
	1248	install-am install-data install-data-am install-dvi \
	1249	install-dvi-am install-exec install-exec-am install-html \
	1250	install-html-am install-info install-info-am install-man \
	1251	install-pdf install-pdf-am install-ps install-ps-am \
	1252	install-strip installcheck installcheck-am installdirs \
	1253	maintainer-clean maintainer-clean-generic mostlyclean \
	1254	mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
	1255	recheck tags tags-am uninstall uninstall-am
704	1256
705	1257
706	1258	# Tell versions [3.59,3.63) of GNU make to not export all variables.

+139

-0

test-driver less more

	0	#! /bin/sh
	1	# test-driver - basic testsuite driver script.
	2
	3	scriptversion=2013-07-13.22; # UTC
	4
	5	# Copyright (C) 2011-2013 Free Software Foundation, Inc.
	6	#
	7	# This program is free software; you can redistribute it and/or modify
	8	# it under the terms of the GNU General Public License as published by
	9	# the Free Software Foundation; either version 2, or (at your option)
	10	# any later version.
	11	#
	12	# This program is distributed in the hope that it will be useful,
	13	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	14	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	15	# GNU General Public License for more details.
	16	#
	17	# You should have received a copy of the GNU General Public License
	18	# along with this program. If not, see <http://www.gnu.org/licenses/>.
	19
	20	# As a special exception to the GNU General Public License, if you
	21	# distribute this file as part of a program that contains a
	22	# configuration script generated by Autoconf, you may include it under
	23	# the same distribution terms that you use for the rest of that program.
	24
	25	# This file is maintained in Automake, please report
	26	# bugs to <bug-automake@gnu.org> or send patches to
	27	# <automake-patches@gnu.org>.
	28
	29	# Make unconditional expansion of undefined variables an error. This
	30	# helps a lot in preventing typo-related bugs.
	31	set -u
	32
	33	usage_error ()
	34	{
	35	echo "$0: $*" >&2
	36	print_usage >&2
	37	exit 2
	38	}
	39
	40	print_usage ()
	41	{
	42	cat <<END
	43	Usage:
	44	test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
	45	[--expect-failure={yes\|no}] [--color-tests={yes\|no}]
	46	[--enable-hard-errors={yes\|no}] [--]
	47	TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
	48	The '--test-name', '--log-file' and '--trs-file' options are mandatory.
	49	END
	50	}
	51
	52	test_name= # Used for reporting.
	53	log_file= # Where to save the output of the test script.
	54	trs_file= # Where to save the metadata of the test run.
	55	expect_failure=no
	56	color_tests=no
	57	enable_hard_errors=yes
	58	while test $# -gt 0; do
	59	case $1 in
	60	--help) print_usage; exit $?;;
	61	--version) echo "test-driver $scriptversion"; exit $?;;
	62	--test-name) test_name=$2; shift;;
	63	--log-file) log_file=$2; shift;;
	64	--trs-file) trs_file=$2; shift;;
	65	--color-tests) color_tests=$2; shift;;
	66	--expect-failure) expect_failure=$2; shift;;
	67	--enable-hard-errors) enable_hard_errors=$2; shift;;
	68	--) shift; break;;
	69	-*) usage_error "invalid option: '$1'";;
	70	*) break;;
	71	esac
	72	shift
	73	done
	74
	75	missing_opts=
	76	test x"$test_name" = x && missing_opts="$missing_opts --test-name"
	77	test x"$log_file" = x && missing_opts="$missing_opts --log-file"
	78	test x"$trs_file" = x && missing_opts="$missing_opts --trs-file"
	79	if test x"$missing_opts" != x; then
	80	usage_error "the following mandatory options are missing:$missing_opts"
	81	fi
	82
	83	if test $# -eq 0; then
	84	usage_error "missing argument"
	85	fi
	86
	87	if test $color_tests = yes; then
	88	# Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
	89	red='[0;31m' # Red.
	90	grn='[0;32m' # Green.
	91	lgn='[1;32m' # Light green.
	92	blu='[1;34m' # Blue.
	93	mgn='[0;35m' # Magenta.
	94	std='[m' # No color.
	95	else
	96	red= grn= lgn= blu= mgn= std=
	97	fi
	98
	99	do_exit='rm -f $log_file $trs_file; (exit $st); exit $st'
	100	trap "st=129; $do_exit" 1
	101	trap "st=130; $do_exit" 2
	102	trap "st=141; $do_exit" 13
	103	trap "st=143; $do_exit" 15
	104
	105	# Test script is run here.
	106	"$@" >$log_file 2>&1
	107	estatus=$?
	108	if test $enable_hard_errors = no && test $estatus -eq 99; then
	109	estatus=1
	110	fi
	111
	112	case $estatus:$expect_failure in
	113	0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
	114	0:*) col=$grn res=PASS recheck=no gcopy=no;;
	115	77:*) col=$blu res=SKIP recheck=no gcopy=yes;;
	116	99:*) col=$mgn res=ERROR recheck=yes gcopy=yes;;
	117	*:yes) col=$lgn res=XFAIL recheck=no gcopy=yes;;
	118	:) col=$red res=FAIL recheck=yes gcopy=yes;;
	119	esac
	120
	121	# Report outcome to console.
	122	echo "${col}${res}${std}: $test_name"
	123
	124	# Register the test result, and other relevant metadata.
	125	echo ":test-result: $res" > $trs_file
	126	echo ":global-test-result: $res" >> $trs_file
	127	echo ":recheck: $recheck" >> $trs_file
	128	echo ":copy-in-global-log: $gcopy" >> $trs_file
	129
	130	# Local Variables:
	131	# mode: shell-script
	132	# sh-indentation: 2
	133	# eval: (add-hook 'write-file-hooks 'time-stamp)
	134	# time-stamp-start: "scriptversion="
	135	# time-stamp-format: "%:y-%02m-%02d.%02H"
	136	# time-stamp-time-zone: "UTC"
	137	# time-stamp-end: "; # UTC"
	138	# End: