[med-svn] [abyss] 07/14: Imported Upstream version 1.3.6
Charles Plessy
plessy at alioth.debian.org
Sun Sep 8 05:30:20 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository abyss.
commit b391f1fbcc7182c01bd33ad628b1fc400c208fa6
Author: Charles Plessy <plessy at debian.org>
Date: Sun Sep 8 11:22:26 2013 +0900
Imported Upstream version 1.3.6
---
._depcomp | Bin 368 -> 0 bytes
ABYSS/Makefile.in | 223 ++++++++++++-------
AdjList/Makefile.in | 223 ++++++++++++-------
Align/Makefile.in | 341 +++++++++++++++++------------
Align/mergepairs.cc | 2 +-
Assembly/Makefile.in | 290 +++++++++++++++----------
ChangeLog | 37 ++++
Common/BitUtil.h | 42 ++--
Common/Histogram.h | 45 ++--
Common/Makefile.in | 402 +++++++++++++++++++---------------
Common/Sequence.cpp | 47 +++-
Consensus/Makefile.in | 223 ++++++++++++-------
DAssembler/Makefile.in | 247 +++++++++++++--------
DataLayer/FastaReader.cpp | 8 +-
DataLayer/Makefile.in | 309 +++++++++++++++++----------
DataLayer/fac.cc | 40 +++-
DistanceEst/Makefile.in | 247 +++++++++++++--------
FMIndex/Makefile.in | 254 ++++++++++++++--------
FMIndex/abyss-dawg.cc | 2 -
FMIndex/count.cc | 2 -
FilterGraph/FilterGraph.cpp | 39 +++-
FilterGraph/Makefile.in | 223 ++++++++++++-------
Graph/AdjIO.h | 7 +-
Graph/Makefile.in | 293 +++++++++++++++----------
KAligner/Makefile.in | 247 +++++++++++++--------
Layout/Makefile.in | 223 ++++++++++++-------
Makefile.am | 2 +-
Makefile.in | 288 +++++++++++++------------
Map/Makefile.in | 261 ++++++++++++++---------
Map/index.cc | 2 -
Map/map.cc | 39 +++-
Map/overlap.cc | 2 -
MergePaths/Makefile.in | 261 ++++++++++++++---------
Misc/Makefile.in | 182 +++++++++++++---
Overlap/Makefile.in | 223 ++++++++++++-------
Parallel/Makefile.in | 295 +++++++++++++++----------
ParseAligns/Makefile.in | 258 +++++++++++++---------
ParseAligns/abyss-fixmate.cc | 95 ++++++++-
PathOverlap/Makefile.in | 223 ++++++++++++-------
PopBubbles/Makefile.in | 223 ++++++++++++-------
PopBubbles/PopBubbles.cpp | 15 +-
README.html | 26 ++-
README.md | 18 +-
Scaffold/Makefile.in | 261 ++++++++++++++---------
SimpleGraph/Makefile.in | 223 ++++++++++++-------
aclocal.m4 | 485 ++++++++++++++++++++++++++++--------------
bin/Makefile.in | 109 +++++++---
bin/abyss-pe | 2 +-
compile | 347 ++++++++++++++++++++++++++++++
config.h.in | 9 +-
configure | 275 +++++++++++++++++++++---
configure.ac | 17 +-
depcomp | 454 +++++++++++++++++++++++----------------
dialign/Makefile.in | 191 +++++++++++------
doc/ABYSS.1 | 2 +-
doc/Makefile.in | 123 ++++++-----
doc/abyss-pe.1 | 2 +-
doc/abyss-tofastq.1 | 2 +-
doxygen.conf | 16 +-
kmerprint/Makefile.in | 194 +++++++++++------
missing | 405 +++++++++++++----------------------
61 files changed, 6136 insertions(+), 3410 deletions(-)
diff --git a/._depcomp b/._depcomp
deleted file mode 100755
index 407412f..0000000
Binary files a/._depcomp and /dev/null differ
diff --git a/ABYSS/Makefile.in b/ABYSS/Makefile.in
index e09e003..f15189a 100644
--- a/ABYSS/Makefile.in
+++ b/ABYSS/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = ABYSS$(EXEEXT)
subdir = ABYSS
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -68,15 +95,39 @@ ABYSS_OBJECTS = $(am_ABYSS_OBJECTS)
ABYSS_DEPENDENCIES = $(top_builddir)/Assembly/libassembly.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(ABYSS_SOURCES)
DIST_SOURCES = $(ABYSS_SOURCES)
am__can_run_installinfo = \
@@ -84,12 +135,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -237,10 +306,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -261,16 +331,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
ABYSS$(EXEEXT): $(ABYSS_OBJECTS) $(ABYSS_DEPENDENCIES) $(EXTRA_ABYSS_DEPENDENCIES)
@rm -f ABYSS$(EXEEXT)
- $(CXXLINK) $(ABYSS_OBJECTS) $(ABYSS_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(ABYSS_OBJECTS) $(ABYSS_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -281,53 +353,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ABYSS-Abyss.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
ABYSS-Abyss.o: Abyss.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS-Abyss.o -MD -MP -MF $(DEPDIR)/ABYSS-Abyss.Tpo -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo '$(srcdir)/'`Abyss.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS-Abyss.Tpo $(DEPDIR)/ABYSS-Abyss.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Abyss.cpp' object='ABYSS-Abyss.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS-Abyss.o -MD -MP -MF $(DEPDIR)/ABYSS-Abyss.Tpo -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo '$(srcdir)/'`Abyss.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS-Abyss.Tpo $(DEPDIR)/ABYSS-Abyss.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Abyss.cpp' object='ABYSS-Abyss.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo '$(srcdir)/'`Abyss.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo '$(srcdir)/'`Abyss.cpp
ABYSS-Abyss.obj: Abyss.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS-Abyss.obj -MD -MP -MF $(DEPDIR)/ABYSS-Abyss.Tpo -c -o ABYSS-Abyss.obj `if test -f 'Abyss.cpp'; then $(CYGPATH_W) 'Abyss.cpp'; else $(CYGPATH_W) '$(srcdir)/Abyss.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS-Abyss.Tpo $(DEPDIR)/ABYSS-Abyss.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Abyss.cpp' object='ABYSS-Abyss.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS-Abyss.obj -MD -MP -MF $(DEPDIR)/ABYSS-Abyss.Tpo -c -o ABYSS-Abyss.obj `if test -f 'Abyss.cpp'; then $(CYGPATH_W) 'Abyss.cpp'; else $(CYGPATH_W) '$(srcdir)/Abyss.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS-Abyss.Tpo $(DEPDIR)/ABYSS-Abyss.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Abyss.cpp' object='ABYSS-Abyss.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS-Abyss.obj `if test -f 'Abyss.cpp'; then $(CYGPATH_W) 'Abyss.cpp'; else $(CYGPATH_W) '$(srcdir)/Abyss.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS-Abyss.obj `if test -f 'Abyss.cpp'; then $(CYGPATH_W) 'Abyss.cpp'; else $(CYGPATH_W) '$(srcdir)/Abyss.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -339,15 +400,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -356,9 +413,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -512,18 +570,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/AdjList/Makefile.in b/AdjList/Makefile.in
index d083670..dac3840 100644
--- a/AdjList/Makefile.in
+++ b/AdjList/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = AdjList$(EXEEXT)
subdir = AdjList
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -68,15 +95,39 @@ AdjList_OBJECTS = $(am_AdjList_OBJECTS)
AdjList_DEPENDENCIES = $(top_builddir)/Graph/libgraph.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(AdjList_SOURCES)
DIST_SOURCES = $(AdjList_SOURCES)
am__can_run_installinfo = \
@@ -84,12 +135,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -238,10 +307,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -262,16 +332,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
AdjList$(EXEEXT): $(AdjList_OBJECTS) $(AdjList_DEPENDENCIES) $(EXTRA_AdjList_DEPENDENCIES)
@rm -f AdjList$(EXEEXT)
- $(CXXLINK) $(AdjList_OBJECTS) $(AdjList_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(AdjList_OBJECTS) $(AdjList_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -282,53 +354,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/AdjList-AdjList.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
AdjList-AdjList.o: AdjList.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AdjList-AdjList.o -MD -MP -MF $(DEPDIR)/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo '$(srcdir)/'`AdjList.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/AdjList-AdjList.Tpo $(DEPDIR)/AdjList-AdjList.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='AdjList.cpp' object='AdjList-AdjList.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AdjList-AdjList.o -MD -MP -MF $(DEPDIR)/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo '$(srcdir)/'`AdjList.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/AdjList-AdjList.Tpo $(DEPDIR)/AdjList-AdjList.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='AdjList.cpp' object='AdjList-AdjList.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo '$(srcdir)/'`AdjList.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo '$(srcdir)/'`AdjList.cpp
AdjList-AdjList.obj: AdjList.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AdjList-AdjList.obj -MD -MP -MF $(DEPDIR)/AdjList-AdjList.Tpo -c -o AdjList-AdjList.obj `if test -f 'AdjList.cpp'; then $(CYGPATH_W) 'AdjList.cpp'; else $(CYGPATH_W) '$(srcdir)/AdjList.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/AdjList-AdjList.Tpo $(DEPDIR)/AdjList-AdjList.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='AdjList.cpp' object='AdjList-AdjList.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AdjList-AdjList.obj -MD -MP -MF $(DEPDIR)/AdjList-AdjList.Tpo -c -o AdjList-AdjList.obj `if test -f 'AdjList.cpp'; then $(CYGPATH_W) 'AdjList.cpp'; else $(CYGPATH_W) '$(srcdir)/AdjList.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/AdjList-AdjList.Tpo $(DEPDIR)/AdjList-AdjList.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='AdjList.cpp' object='AdjList-AdjList.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AdjList-AdjList.obj `if test -f 'AdjList.cpp'; then $(CYGPATH_W) 'AdjList.cpp'; else $(CYGPATH_W) '$(srcdir)/AdjList.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AdjList_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AdjList-AdjList.obj `if test -f 'AdjList.cpp'; then $(CYGPATH_W) 'AdjList.cpp'; else $(CYGPATH_W) '$(srcdir)/AdjList.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -340,15 +401,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -357,9 +414,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -513,18 +571,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Align/Makefile.in b/Align/Makefile.in
index d638430..7b8e3cd 100644
--- a/Align/Makefile.in
+++ b/Align/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,23 +16,51 @@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-align$(EXEEXT) abyss-mergepairs$(EXEEXT)
subdir = Align
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -65,6 +92,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libalign_a_AR = $(AR) $(ARFLAGS)
libalign_a_LIBADD =
am_libalign_a_OBJECTS = libalign_a-alignGlobal.$(OBJEXT) \
@@ -90,19 +121,51 @@ abyss_mergepairs_DEPENDENCIES = $(builddir)/libalign.a \
$(top_builddir)/Common/libcommon.a
abyss_mergepairs_LINK = $(CXXLD) $(abyss_mergepairs_CXXFLAGS) \
$(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libalign_a_SOURCES) $(abyss_align_SOURCES) \
$(abyss_mergepairs_SOURCES)
DIST_SOURCES = $(libalign_a_SOURCES) $(abyss_align_SOURCES) \
@@ -112,12 +175,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -277,10 +358,11 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libalign.a: $(libalign_a_OBJECTS) $(libalign_a_DEPENDENCIES) $(EXTRA_libalign_a_DEPENDENCIES)
- -rm -f libalign.a
- $(libalign_a_AR) libalign.a $(libalign_a_OBJECTS) $(libalign_a_LIBADD)
- $(RANLIB) libalign.a
+ $(AM_V_at)-rm -f libalign.a
+ $(AM_V_AR)$(libalign_a_AR) libalign.a $(libalign_a_OBJECTS) $(libalign_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libalign.a
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -290,10 +372,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -314,19 +397,22 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-align$(EXEEXT): $(abyss_align_OBJECTS) $(abyss_align_DEPENDENCIES) $(EXTRA_abyss_align_DEPENDENCIES)
@rm -f abyss-align$(EXEEXT)
- $(abyss_align_LINK) $(abyss_align_OBJECTS) $(abyss_align_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_align_LINK) $(abyss_align_OBJECTS) $(abyss_align_LDADD) $(LIBS)
+
abyss-mergepairs$(EXEEXT): $(abyss_mergepairs_OBJECTS) $(abyss_mergepairs_DEPENDENCIES) $(EXTRA_abyss_mergepairs_DEPENDENCIES)
@rm -f abyss-mergepairs$(EXEEXT)
- $(abyss_mergepairs_LINK) $(abyss_mergepairs_OBJECTS) $(abyss_mergepairs_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_mergepairs_LINK) $(abyss_mergepairs_OBJECTS) $(abyss_mergepairs_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -342,137 +428,126 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libalign_a-smith_waterman.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
libalign_a-alignGlobal.o: alignGlobal.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-alignGlobal.o -MD -MP -MF $(DEPDIR)/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo '$(srcdir)/'`alignGlobal.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-alignGlobal.Tpo $(DEPDIR)/libalign_a-alignGlobal.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='alignGlobal.cc' object='libalign_a-alignGlobal.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-alignGlobal.o -MD -MP -MF $(DEPDIR)/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo '$(srcdir)/'`alignGlobal.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-alignGlobal.Tpo $(DEPDIR)/libalign_a-alignGlobal.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='alignGlobal.cc' object='libalign_a-alignGlobal.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo '$(srcdir)/'`alignGlobal.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo '$(srcdir)/'`alignGlobal.cc
libalign_a-alignGlobal.obj: alignGlobal.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-alignGlobal.obj -MD -MP -MF $(DEPDIR)/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.obj `if test -f 'alignGlobal.cc'; then $(CYGPATH_W) 'alignGlobal.cc'; else $(CYGPATH_W) '$(srcdir)/alignGlobal.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-alignGlobal.Tpo $(DEPDIR)/libalign_a-alignGlobal.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='alignGlobal.cc' object='libalign_a-alignGlobal.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-alignGlobal.obj -MD -MP -MF $(DEPDIR)/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.obj `if test -f 'alignGlobal.cc'; then $(CYGPATH_W) 'alignGlobal.cc'; else $(CYGPATH_W) '$(srcdir)/alignGlobal.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-alignGlobal.Tpo $(DEPDIR)/libalign_a-alignGlobal.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='alignGlobal.cc' object='libalign_a-alignGlobal.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-alignGlobal.obj `if test -f 'alignGlobal.cc'; then $(CYGPATH_W) 'alignGlobal.cc'; else $(CYGPATH_W) '$(srcdir)/alignGlobal.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-alignGlobal.obj `if test -f 'alignGlobal.cc'; then $(CYGPATH_W) 'alignGlobal.cc'; else $(CYGPATH_W) '$(srcdir)/alignGlobal.cc'; fi`
libalign_a-dialign.o: dialign.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dialign.o -MD -MP -MF $(DEPDIR)/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo '$(srcdir)/'`dialign.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-dialign.Tpo $(DEPDIR)/libalign_a-dialign.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='dialign.cpp' object='libalign_a-dialign.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dialign.o -MD -MP -MF $(DEPDIR)/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo '$(srcdir)/'`dialign.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-dialign.Tpo $(DEPDIR)/libalign_a-dialign.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='dialign.cpp' object='libalign_a-dialign.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo '$(srcdir)/'`dialign.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo '$(srcdir)/'`dialign.cpp
libalign_a-dialign.obj: dialign.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dialign.obj -MD -MP -MF $(DEPDIR)/libalign_a-dialign.Tpo -c -o libalign_a-dialign.obj `if test -f 'dialign.cpp'; then $(CYGPATH_W) 'dialign.cpp'; else $(CYGPATH_W) '$(srcdir)/dialign.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-dialign.Tpo $(DEPDIR)/libalign_a-dialign.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='dialign.cpp' object='libalign_a-dialign.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dialign.obj -MD -MP -MF $(DEPDIR)/libalign_a-dialign.Tpo -c -o libalign_a-dialign.obj `if test -f 'dialign.cpp'; then $(CYGPATH_W) 'dialign.cpp'; else $(CYGPATH_W) '$(srcdir)/dialign.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-dialign.Tpo $(DEPDIR)/libalign_a-dialign.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='dialign.cpp' object='libalign_a-dialign.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dialign.obj `if test -f 'dialign.cpp'; then $(CYGPATH_W) 'dialign.cpp'; else $(CYGPATH_W) '$(srcdir)/dialign.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dialign.obj `if test -f 'dialign.cpp'; then $(CYGPATH_W) 'dialign.cpp'; else $(CYGPATH_W) '$(srcdir)/dialign.cpp'; fi`
libalign_a-dna_diag_prob.o: dna_diag_prob.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dna_diag_prob.o -MD -MP -MF $(DEPDIR)/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo '$(srcdir)/'`dna_diag_prob.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-dna_diag_prob.Tpo $(DEPDIR)/libalign_a-dna_diag_prob.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='dna_diag_prob.cc' object='libalign_a-dna_diag_prob.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dna_diag_prob.o -MD -MP -MF $(DEPDIR)/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo '$(srcdir)/'`dna_diag_prob.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-dna_diag_prob.Tpo $(DEPDIR)/libalign_a-dna_diag_prob.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='dna_diag_prob.cc' object='libalign_a-dna_diag_prob.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo '$(srcdir)/'`dna_diag_prob.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo '$(srcdir)/'`dna_diag_prob.cc
libalign_a-dna_diag_prob.obj: dna_diag_prob.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dna_diag_prob.obj -MD -MP -MF $(DEPDIR)/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.obj `if test -f 'dna_diag_prob.cc'; then $(CYGPATH_W) 'dna_diag_prob.cc'; else $(CYGPATH_W) '$(srcdir)/dna_diag_prob.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libalign_a-dna_diag_prob.Tpo $(DEPDIR)/libalign_a-dna_diag_prob.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='dna_diag_prob.cc' object='libalign_a-dna_diag_prob.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-dna_diag_prob.obj -MD -MP -MF $(DEPDIR)/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.obj `if test -f 'dna_diag_prob.cc'; then $(CYGPATH_W) 'dna_diag_prob.cc'; else $(CYGPATH_W) '$(srcdir)/dna_diag_prob.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-dna_diag_prob.Tpo $(DEPDIR)/libalign_a-dna_diag_prob.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='dna_diag_prob.cc' object='libalign_a-dna_diag_prob.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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libalign_a-smith_waterman.o: smith_waterman.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-smith_waterman.o -MD -MP -MF $(DEPDIR)/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo '$(srcdir)/'`smith_waterman.cpp
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='smith_waterman.cpp' object='libalign_a-smith_waterman.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-smith_waterman.Tpo $(DEPDIR)/libalign_a-smith_waterman.Po
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libalign_a-smith_waterman.obj: smith_waterman.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-smith_waterman.obj -MD -MP -MF $(DEPDIR)/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.obj `if test -f 'smith_waterman.cpp'; then $(CYGPATH_W) 'smith_waterman.cpp'; else $(CYGPATH_W) '$(srcdir)/smith_waterman.cpp'; fi`
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libalign_a-smith_waterman.obj -MD -MP -MF $(DEPDIR)/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.obj `if test -f 'smith_waterman.cpp'; then $(CYGPATH_W) 'smith_waterman.cpp'; else $(CYGPATH_W) '$(srcdir)/smith_waterman.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libalign_a-smith_waterman.Tpo $(DEPDIR)/libalign_a-smith_waterman.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='smith_waterman.cpp' object='libalign_a-smith_waterman.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libalign_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libalign_a-smith_waterman.obj `if test -f 'smith_waterman.cpp'; then $(CYGPATH_W) 'smith_waterman.cpp'; else $(CYGPATH_W) '$(srcdir)/smith_waterman.cpp'; fi`
abyss_align-align.o: align.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -MT abyss_align-align.o -MD -MP -MF $(DEPDIR)/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo '$(srcdir)/'`align.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_align-align.Tpo $(DEPDIR)/abyss_align-align.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='align.cc' object='abyss_align-align.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -MT abyss_align-align.o -MD -MP -MF $(DEPDIR)/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo '$(srcdir)/'`align.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_align-align.Tpo $(DEPDIR)/abyss_align-align.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='align.cc' object='abyss_align-align.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -c -o abyss_align-align.o `test -f 'align.cc' || echo '$(srcdir)/'`align.cc
abyss_align-align.obj: align.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -MT abyss_align-align.obj -MD -MP -MF $(DEPDIR)/abyss_align-align.Tpo -c -o abyss_align-align.obj `if test -f 'align.cc'; then $(CYGPATH_W) 'align.cc'; else $(CYGPATH_W) '$(srcdir)/align.cc'; fi`
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='align.cc' object='abyss_align-align.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -MT abyss_align-align.obj -MD -MP -MF $(DEPDIR)/abyss_align-align.Tpo -c -o abyss_align-align.obj `if test -f 'align.cc'; then $(CYGPATH_W) 'align.cc'; else $(CYGPATH_W) '$(srcdir)/align.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_align-align.Tpo $(DEPDIR)/abyss_align-align.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='align.cc' object='abyss_align-align.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -c -o abyss_align-align.obj `if test -f 'align.cc'; then $(CYGPATH_W) 'align.cc'; else $(CYGPATH_W) '$(srcdir)/align.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_align_CPPFLAGS) $(CPPFLAGS) $(abyss_align_CXXFLAGS) $(CXXFLAGS) -c -o abyss_align-align.obj `if test -f 'align.cc'; then $(CYGPATH_W) 'align.cc'; else $(CYGPATH_W) '$(srcdir)/align.cc'; fi`
abyss_mergepairs-mergepairs.o: mergepairs.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -MT abyss_mergepairs-mergepairs.o -MD -MP -MF $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo '$(srcdir)/'`mergepairs.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo $(DEPDIR)/abyss_mergepairs-mergepairs.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='mergepairs.cc' object='abyss_mergepairs-mergepairs.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -MT abyss_mergepairs-mergepairs.o -MD -MP -MF $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo '$(srcdir)/'`mergepairs.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo $(DEPDIR)/abyss_mergepairs-mergepairs.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='mergepairs.cc' object='abyss_mergepairs-mergepairs.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo '$(srcdir)/'`mergepairs.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo '$(srcdir)/'`mergepairs.cc
abyss_mergepairs-mergepairs.obj: mergepairs.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -MT abyss_mergepairs-mergepairs.obj -MD -MP -MF $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.obj `if test -f 'mergepairs.cc'; then $(CYGPATH_W) 'mergepairs.cc'; else $(CYGPATH_W) '$(srcdir)/mergepairs.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo $(DEPDIR)/abyss_mergepairs-mergepairs.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='mergepairs.cc' object='abyss_mergepairs-mergepairs.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -MT abyss_mergepairs-mergepairs.obj -MD -MP -MF $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.obj `if test -f 'mergepairs.cc'; then $(CYGPATH_W) 'mergepairs.cc'; else $(CYGPATH_W) '$(srcdir)/mergepairs.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_mergepairs-mergepairs.Tpo $(DEPDIR)/abyss_mergepairs-mergepairs.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='mergepairs.cc' object='abyss_mergepairs-mergepairs.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -c -o abyss_mergepairs-mergepairs.obj `if test -f 'mergepairs.cc'; then $(CYGPATH_W) 'mergepairs.cc'; else $(CYGPATH_W) '$(srcdir)/mergepairs.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_mergepairs_CPPFLAGS) $(CPPFLAGS) $(abyss_mergepairs_CXXFLAGS) $(CXXFLAGS) -c -o abyss_mergepairs-mergepairs.obj `if test -f 'mergepairs.cc'; then $(CYGPATH_W) 'mergepairs.cc'; else $(CYGPATH_W) '$(srcdir)/mergepairs.cc'; fi`
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -484,15 +559,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -501,9 +572,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -658,18 +730,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstLIBRARIES cscopelist ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Align/mergepairs.cc b/Align/mergepairs.cc
index 971a37c..52af592 100644
--- a/Align/mergepairs.cc
+++ b/Align/mergepairs.cc
@@ -18,7 +18,7 @@
using namespace std;
-#define PROGRAM "abyss-align"
+#define PROGRAM "abyss-mergepairs"
static const char VERSION_MESSAGE[] =
PROGRAM " (" PACKAGE_NAME ") " VERSION "\n"
diff --git a/Assembly/Makefile.in b/Assembly/Makefile.in
index af0de0d..99f0533 100644
--- a/Assembly/Makefile.in
+++ b/Assembly/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -50,7 +77,7 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = Assembly
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -63,6 +90,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libassembly_a_AR = $(AR) $(ARFLAGS)
libassembly_a_LIBADD =
am_libassembly_a_OBJECTS = libassembly_a-AssemblyAlgorithms.$(OBJEXT) \
@@ -72,19 +103,51 @@ am_libassembly_a_OBJECTS = libassembly_a-AssemblyAlgorithms.$(OBJEXT) \
libassembly_a-Options.$(OBJEXT) \
libassembly_a-SequenceCollection.$(OBJEXT)
libassembly_a_OBJECTS = $(am_libassembly_a_OBJECTS)
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libassembly_a_SOURCES)
DIST_SOURCES = $(libassembly_a_SOURCES)
am__can_run_installinfo = \
@@ -92,12 +155,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -243,10 +324,11 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libassembly.a: $(libassembly_a_OBJECTS) $(libassembly_a_DEPENDENCIES) $(EXTRA_libassembly_a_DEPENDENCIES)
- -rm -f libassembly.a
- $(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
- $(RANLIB) libassembly.a
+ $(AM_V_at)-rm -f libassembly.a
+ $(AM_V_AR)$(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libassembly.a
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -262,123 +344,112 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libassembly_a-SequenceCollection.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
libassembly_a-AssemblyAlgorithms.o: AssemblyAlgorithms.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo '$(srcdir)/'`AssemblyAlgorithms.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='AssemblyAlgorithms.cpp' object='libassembly_a-AssemblyAlgorithms.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo '$(srcdir)/'`AssemblyAlgorithms.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='AssemblyAlgorithms.cpp' object='libassembly_a-AssemblyAlgorithms.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo '$(srcdir)/'`AssemblyAlgorithms.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo '$(srcdir)/'`AssemblyAlgorithms.cpp
libassembly_a-AssemblyAlgorithms.obj: AssemblyAlgorithms.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-AssemblyAlgorithms.obj -MD -MP -MF $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.obj `if test -f 'AssemblyAlgorithms.cpp'; then $(CYGPATH_W) 'AssemblyAlgorithms.cpp'; else $(CYGPATH_W) '$(srcdir)/AssemblyAlgorithms.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='AssemblyAlgorithms.cpp' object='libassembly_a-AssemblyAlgorithms.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-AssemblyAlgorithms.obj -MD -MP -MF $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.obj `if test -f 'AssemblyAlgorithms.cpp'; then $(CYGPATH_W) 'AssemblyAlgorithms.cpp'; else $(CYGPATH_W) '$(srcdir)/AssemblyAlgorithms.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Tpo $(DEPDIR)/libassembly_a-AssemblyAlgorithms.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='AssemblyAlgorithms.cpp' object='libassembly_a-AssemblyAlgorithms.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-AssemblyAlgorithms.obj `if test -f 'AssemblyAlgorithms.cpp'; then $(CYGPATH_W) 'AssemblyAlgorithms.cpp'; else $(CYGPATH_W) '$(srcdir)/AssemblyAlgorithms.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-AssemblyAlgorithms.obj `if test -f 'AssemblyAlgorithms.cpp'; then $(CYGPATH_W) 'AssemblyAlgorithms.cpp'; else $(CYGPATH_W) '$(srcdir)/AssemblyAlgorithms.cpp'; fi`
libassembly_a-BranchGroup.o: BranchGroup.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchGroup.o -MD -MP -MF $(DEPDIR)/libassembly_a-BranchGroup.Tpo -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo '$(srcdir)/'`BranchGroup.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-BranchGroup.Tpo $(DEPDIR)/libassembly_a-BranchGroup.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='BranchGroup.cpp' object='libassembly_a-BranchGroup.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchGroup.o -MD -MP -MF $(DEPDIR)/libassembly_a-BranchGroup.Tpo -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo '$(srcdir)/'`BranchGroup.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-BranchGroup.Tpo $(DEPDIR)/libassembly_a-BranchGroup.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='BranchGroup.cpp' object='libassembly_a-BranchGroup.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo '$(srcdir)/'`BranchGroup.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo '$(srcdir)/'`BranchGroup.cpp
libassembly_a-BranchGroup.obj: BranchGroup.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchGroup.obj -MD -MP -MF $(DEPDIR)/libassembly_a-BranchGroup.Tpo -c -o libassembly_a-BranchGroup.obj `if test -f 'BranchGroup.cpp'; then $(CYGPATH_W) 'BranchGroup.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchGroup.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-BranchGroup.Tpo $(DEPDIR)/libassembly_a-BranchGroup.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='BranchGroup.cpp' object='libassembly_a-BranchGroup.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchGroup.obj -MD -MP -MF $(DEPDIR)/libassembly_a-BranchGroup.Tpo -c -o libassembly_a-BranchGroup.obj `if test -f 'BranchGroup.cpp'; then $(CYGPATH_W) 'BranchGroup.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchGroup.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-BranchGroup.Tpo $(DEPDIR)/libassembly_a-BranchGroup.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='BranchGroup.cpp' object='libassembly_a-BranchGroup.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchGroup.obj `if test -f 'BranchGroup.cpp'; then $(CYGPATH_W) 'BranchGroup.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchGroup.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchGroup.obj `if test -f 'BranchGroup.cpp'; then $(CYGPATH_W) 'BranchGroup.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchGroup.cpp'; fi`
libassembly_a-BranchRecord.o: BranchRecord.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchRecord.o -MD -MP -MF $(DEPDIR)/libassembly_a-BranchRecord.Tpo -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo '$(srcdir)/'`BranchRecord.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-BranchRecord.Tpo $(DEPDIR)/libassembly_a-BranchRecord.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='BranchRecord.cpp' object='libassembly_a-BranchRecord.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchRecord.o -MD -MP -MF $(DEPDIR)/libassembly_a-BranchRecord.Tpo -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo '$(srcdir)/'`BranchRecord.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-BranchRecord.Tpo $(DEPDIR)/libassembly_a-BranchRecord.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='BranchRecord.cpp' object='libassembly_a-BranchRecord.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo '$(srcdir)/'`BranchRecord.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo '$(srcdir)/'`BranchRecord.cpp
libassembly_a-BranchRecord.obj: BranchRecord.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchRecord.obj -MD -MP -MF $(DEPDIR)/libassembly_a-BranchRecord.Tpo -c -o libassembly_a-BranchRecord.obj `if test -f 'BranchRecord.cpp'; then $(CYGPATH_W) 'BranchRecord.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchRecord.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-BranchRecord.Tpo $(DEPDIR)/libassembly_a-BranchRecord.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='BranchRecord.cpp' object='libassembly_a-BranchRecord.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-BranchRecord.obj -MD -MP -MF $(DEPDIR)/libassembly_a-BranchRecord.Tpo -c -o libassembly_a-BranchRecord.obj `if test -f 'BranchRecord.cpp'; then $(CYGPATH_W) 'BranchRecord.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchRecord.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-BranchRecord.Tpo $(DEPDIR)/libassembly_a-BranchRecord.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='BranchRecord.cpp' object='libassembly_a-BranchRecord.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchRecord.obj `if test -f 'BranchRecord.cpp'; then $(CYGPATH_W) 'BranchRecord.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchRecord.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-BranchRecord.obj `if test -f 'BranchRecord.cpp'; then $(CYGPATH_W) 'BranchRecord.cpp'; else $(CYGPATH_W) '$(srcdir)/BranchRecord.cpp'; fi`
libassembly_a-DotWriter.o: DotWriter.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-DotWriter.o -MD -MP -MF $(DEPDIR)/libassembly_a-DotWriter.Tpo -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo '$(srcdir)/'`DotWriter.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-DotWriter.Tpo $(DEPDIR)/libassembly_a-DotWriter.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DotWriter.cpp' object='libassembly_a-DotWriter.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-DotWriter.o -MD -MP -MF $(DEPDIR)/libassembly_a-DotWriter.Tpo -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo '$(srcdir)/'`DotWriter.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-DotWriter.Tpo $(DEPDIR)/libassembly_a-DotWriter.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DotWriter.cpp' object='libassembly_a-DotWriter.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo '$(srcdir)/'`DotWriter.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo '$(srcdir)/'`DotWriter.cpp
libassembly_a-DotWriter.obj: DotWriter.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-DotWriter.obj -MD -MP -MF $(DEPDIR)/libassembly_a-DotWriter.Tpo -c -o libassembly_a-DotWriter.obj `if test -f 'DotWriter.cpp'; then $(CYGPATH_W) 'DotWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/DotWriter.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-DotWriter.Tpo $(DEPDIR)/libassembly_a-DotWriter.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DotWriter.cpp' object='libassembly_a-DotWriter.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-DotWriter.obj -MD -MP -MF $(DEPDIR)/libassembly_a-DotWriter.Tpo -c -o libassembly_a-DotWriter.obj `if test -f 'DotWriter.cpp'; then $(CYGPATH_W) 'DotWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/DotWriter.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-DotWriter.Tpo $(DEPDIR)/libassembly_a-DotWriter.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DotWriter.cpp' object='libassembly_a-DotWriter.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-DotWriter.obj `if test -f 'DotWriter.cpp'; then $(CYGPATH_W) 'DotWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/DotWriter.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-DotWriter.obj `if test -f 'DotWriter.cpp'; then $(CYGPATH_W) 'DotWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/DotWriter.cpp'; fi`
libassembly_a-Options.o: Options.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-Options.o -MD -MP -MF $(DEPDIR)/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo '$(srcdir)/'`Options.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-Options.Tpo $(DEPDIR)/libassembly_a-Options.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Options.cpp' object='libassembly_a-Options.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-Options.o -MD -MP -MF $(DEPDIR)/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo '$(srcdir)/'`Options.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-Options.Tpo $(DEPDIR)/libassembly_a-Options.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Options.cpp' object='libassembly_a-Options.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo '$(srcdir)/'`Options.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo '$(srcdir)/'`Options.cpp
libassembly_a-Options.obj: Options.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-Options.obj -MD -MP -MF $(DEPDIR)/libassembly_a-Options.Tpo -c -o libassembly_a-Options.obj `if test -f 'Options.cpp'; then $(CYGPATH_W) 'Options.cpp'; else $(CYGPATH_W) '$(srcdir)/Options.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-Options.Tpo $(DEPDIR)/libassembly_a-Options.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Options.cpp' object='libassembly_a-Options.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-Options.obj -MD -MP -MF $(DEPDIR)/libassembly_a-Options.Tpo -c -o libassembly_a-Options.obj `if test -f 'Options.cpp'; then $(CYGPATH_W) 'Options.cpp'; else $(CYGPATH_W) '$(srcdir)/Options.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-Options.Tpo $(DEPDIR)/libassembly_a-Options.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Options.cpp' object='libassembly_a-Options.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-Options.obj `if test -f 'Options.cpp'; then $(CYGPATH_W) 'Options.cpp'; else $(CYGPATH_W) '$(srcdir)/Options.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-Options.obj `if test -f 'Options.cpp'; then $(CYGPATH_W) 'Options.cpp'; else $(CYGPATH_W) '$(srcdir)/Options.cpp'; fi`
libassembly_a-SequenceCollection.o: SequenceCollection.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-SequenceCollection.o -MD -MP -MF $(DEPDIR)/libassembly_a-SequenceCollection.Tpo -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo '$(srcdir)/'`SequenceCollection.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-SequenceCollection.Tpo $(DEPDIR)/libassembly_a-SequenceCollection.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SequenceCollection.cpp' object='libassembly_a-SequenceCollection.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-SequenceCollection.o -MD -MP -MF $(DEPDIR)/libassembly_a-SequenceCollection.Tpo -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo '$(srcdir)/'`SequenceCollection.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-SequenceCollection.Tpo $(DEPDIR)/libassembly_a-SequenceCollection.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='SequenceCollection.cpp' object='libassembly_a-SequenceCollection.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo '$(srcdir)/'`SequenceCollection.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo '$(srcdir)/'`SequenceCollection.cpp
libassembly_a-SequenceCollection.obj: SequenceCollection.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-SequenceCollection.obj -MD -MP -MF $(DEPDIR)/libassembly_a-SequenceCollection.Tpo -c -o libassembly_a-SequenceCollection.obj `if test -f 'SequenceCollection.cpp'; then $(CYGPATH_W) 'SequenceCollection.cpp'; else $(CYGPATH_W) '$(srcdir)/SequenceCollection.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libassembly_a-SequenceCollection.Tpo $(DEPDIR)/libassembly_a-SequenceCollection.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SequenceCollection.cpp' object='libassembly_a-SequenceCollection.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libassembly_a-SequenceCollection.obj -MD -MP -MF $(DEPDIR)/libassembly_a-SequenceCollection.Tpo -c -o libassembly_a-SequenceCollection.obj `if test -f 'SequenceCollection.cpp'; then $(CYGPATH_W) 'SequenceCollection.cpp'; else $(CYGPATH_W) '$(srcdir)/SequenceCollection.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libassembly_a-SequenceCollection.Tpo $(DEPDIR)/libassembly_a-SequenceCollection.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='SequenceCollection.cpp' object='libassembly_a-SequenceCollection.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-SequenceCollection.obj `if test -f 'SequenceCollection.cpp'; then $(CYGPATH_W) 'SequenceCollection.cpp'; else $(CYGPATH_W) '$(srcdir)/SequenceCollection.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libassembly_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libassembly_a-SequenceCollection.obj `if test -f 'SequenceCollection.cpp'; then $(CYGPATH_W) 'SequenceCollection.cpp'; else $(CYGPATH_W) '$(srcdir)/SequenceCollection.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -390,15 +461,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -407,9 +474,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -560,8 +628,8 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstLIBRARIES cscopelist ctags distclean \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-tags distdir dvi \
dvi-am html html-am info info-am install install-am \
install-data install-data-am install-dvi install-dvi-am \
@@ -570,7 +638,7 @@ uninstall-am:
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
diff --git a/ChangeLog b/ChangeLog
index 27be8e0..7a602bc 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,40 @@
+2013-07-15 Anthony Raymond <traymond at bcgsc.ca>
+
+ * Release version 1.3.6
+ * Improved documentation for GitHub devs.
+ * ABYSS-P performance improvement.
+ * Various portability and bug fixes.
+
+ abyss-mergepairs:
+ * Fix program name.
+
+ abyss-fac:
+ * New option --exp-size to give the expected genome size needed
+ for NG50 calculation.
+ * New option --count-ambig include ambiguities in calculations.
+
+ ABYSS/ABYSS-P:
+ * Performance improvement. Runtime reduced by ~20%.
+ * Fix support for MPICH.
+
+ abyss-map:
+ * No longer require POPCNT instruction.
+ * New option --order to force output order the same as input.
+
+ abyss-filtergraph:
+ * New option --remove to remove specified contigs from graph.
+
+ PopBubbles:
+ * Bug fix. Setting branches > 2 will now work.
+
+ abyss-fixmate:
+ * Improved error when first and second read IDs do not match.
+ * New option --cov to compute and store the physical coverage in
+ a Wiggle file.
+
+ AdjIO:
+ * Bug fix for non-GCC compilers.
+
2013-03-04 Anthony Raymond <traymond at bcgsc.ca>
* Release version 1.3.5
diff --git a/Common/BitUtil.h b/Common/BitUtil.h
index 40be67d..3839297 100644
--- a/Common/BitUtil.h
+++ b/Common/BitUtil.h
@@ -3,7 +3,6 @@
#include "config.h"
#include <cstdlib> // for exit
-#include <iostream>
#include <stdint.h>
/** The return value of the CPUID instruction. */
@@ -29,37 +28,26 @@ static inline CPUID cpuid(unsigned op)
/** Return whether this processor has the POPCNT instruction. */
static inline bool havePopcnt() { return cpuid(1).c & (1 << 23); }
-/** Ensure that this machine has the popcount instruction. */
-static inline void checkPopcnt()
-{
-#if ENABLE_POPCNT
- if (!havePopcnt()) {
- std::cerr <<
-"error: " PACKAGE " has been compiled to use the POPCNT\n"
-"instruction, which this machine lacks. Recompile using\n"
-"configure --disable-popcnt to disable this feature.\n";
- exit(EXIT_FAILURE);
- }
-#endif
-}
+static const bool hasPopcnt = havePopcnt();
/** Return the Hamming weight of x. */
static inline uint64_t popcount(uint64_t x)
{
-#if ENABLE_POPCNT && __GNUC__ && __x86_64__
- __asm__("popcnt %1,%0" : "=r" (x) : "r" (x));
- return x;
-#else
- x = (x & 0x5555555555555555ULL) +
- ((x >> 1) & 0x5555555555555555ULL);
- x = (x & 0x3333333333333333ULL) +
- ((x >> 2) & 0x3333333333333333ULL);
- x = (x + (x >> 4)) & 0x0f0f0f0f0f0f0f0fULL;
- x = x + (x >> 8);
- x = x + (x >> 16);
- x = x + (x >> 32);
- return x & 0x7FLLU;
+#if HAVE_POPCNT && __GNUC__ && __x86_64__
+ if (hasPopcnt) {
+ __asm__("popcnt %1,%0" : "=r" (x) : "r" (x));
+ return x;
+ }
#endif
+ x = (x & 0x5555555555555555ULL) +
+ ((x >> 1) & 0x5555555555555555ULL);
+ x = (x & 0x3333333333333333ULL) +
+ ((x >> 2) & 0x3333333333333333ULL);
+ x = (x + (x >> 4)) & 0x0f0f0f0f0f0f0f0fULL;
+ x = x + (x >> 8);
+ x = x + (x >> 16);
+ x = x + (x >> 32);
+ return x & 0x7FLLU;
}
#endif
diff --git a/Common/Histogram.h b/Common/Histogram.h
index da61a6f..2a8e5e8 100644
--- a/Common/Histogram.h
+++ b/Common/Histogram.h
@@ -149,10 +149,10 @@ class Histogram
return percentile(0.5);
}
- /** Return the specified weighted percentile. */
- T weightedPercentile(float p) const
+ /** Return the largest weight in the arg min of partial sum of
+ * weights. */
+ T argMin(accumulator x) const
{
- accumulator x = (accumulator)ceil(p * sum());
accumulator total = 0;
for (Map::const_iterator it = m_map.begin();
it != m_map.end(); ++it) {
@@ -163,6 +163,12 @@ class Histogram
return maximum();
}
+ /** Return the specified weighted percentile. */
+ T weightedPercentile(float p) const
+ {
+ return argMin((accumulator)ceil(p * sum()));
+ }
+
/** Return the N50. */
T n50() const { return weightedPercentile(0.5); }
@@ -298,30 +304,45 @@ namespace std {
static inline std::ostream& printContiguityStats(
std::ostream& out, const Histogram& h0,
unsigned minSize, bool printHeader = true,
- const std::string& sep = "\t")
+ const std::string& sep = "\t",
+ const long long unsigned expSize = 0)
{
Histogram h = h0.trimLow(minSize);
- unsigned n50 = h.n50();
- if (printHeader)
+ if (printHeader) {
out << "n" << sep
<< "n:" << minSize << sep
- << "n:N50" << sep
- << "min" << sep
+ << "n:N50" << sep;
+ if (expSize > 0)
+ out << "n:NG50" << sep
+ << "NG50" << sep;
+ out << "min" << sep
<< "N80" << sep
<< "N50" << sep
<< "N20" << sep
<< "max" << sep
<< "sum\n";
- return out
- << toEng(h0.size()) << sep
+ }
+ unsigned n50 = h.n50();
+ out << toEng(h0.size()) << sep
<< toEng(h.size()) << sep
- << toEng(h.count(n50, INT_MAX)) << sep
+ << toEng(h.count(n50, INT_MAX)) << sep;
+ long long unsigned sum = h.sum();
+ if (expSize > 0) {
+ unsigned ng50;
+ if (sum < expSize/2)
+ ng50 = h.minimum();
+ else
+ ng50 = h.argMin(sum - expSize/2);
+ out << toEng(h.count(ng50, INT_MAX)) << sep
+ << toEng(ng50) << sep;
+ }
+ return out
<< toEng(h.minimum()) << sep
<< toEng(h.weightedPercentile(1 - 0.8)) << sep
<< toEng(n50) << sep
<< toEng(h.weightedPercentile(1 - 0.2)) << sep
<< toEng(h.maximum()) << sep
- << toEng(h.sum());
+ << toEng(sum);
}
#endif
diff --git a/Common/Makefile.in b/Common/Makefile.in
index d6b9c98..d8aa9e9 100644
--- a/Common/Makefile.in
+++ b/Common/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -50,7 +77,7 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = Common
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -63,6 +90,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libcommon_a_AR = $(AR) $(ARFLAGS)
libcommon_a_LIBADD =
am_libcommon_a_OBJECTS = libcommon_a-ContigID.$(OBJEXT) \
@@ -74,19 +105,51 @@ am_libcommon_a_OBJECTS = libcommon_a-ContigID.$(OBJEXT) \
libcommon_a-Timer.$(OBJEXT) libcommon_a-Uncompress.$(OBJEXT) \
libcommon_a-city.$(OBJEXT)
libcommon_a_OBJECTS = $(am_libcommon_a_OBJECTS)
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libcommon_a_SOURCES)
DIST_SOURCES = $(libcommon_a_SOURCES)
am__can_run_installinfo = \
@@ -94,12 +157,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -267,10 +348,11 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libcommon.a: $(libcommon_a_OBJECTS) $(libcommon_a_DEPENDENCIES) $(EXTRA_libcommon_a_DEPENDENCIES)
- -rm -f libcommon.a
- $(libcommon_a_AR) libcommon.a $(libcommon_a_OBJECTS) $(libcommon_a_LIBADD)
- $(RANLIB) libcommon.a
+ $(AM_V_at)-rm -f libcommon.a
+ $(AM_V_AR)$(libcommon_a_AR) libcommon.a $(libcommon_a_OBJECTS) $(libcommon_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libcommon.a
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -292,221 +374,210 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libcommon_a-city.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
libcommon_a-ContigID.o: ContigID.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-ContigID.o -MD -MP -MF $(DEPDIR)/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo '$(srcdir)/'`ContigID.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-ContigID.Tpo $(DEPDIR)/libcommon_a-ContigID.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='ContigID.cpp' object='libcommon_a-ContigID.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-ContigID.o -MD -MP -MF $(DEPDIR)/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo '$(srcdir)/'`ContigID.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-ContigID.Tpo $(DEPDIR)/libcommon_a-ContigID.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='ContigID.cpp' object='libcommon_a-ContigID.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo '$(srcdir)/'`ContigID.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo '$(srcdir)/'`ContigID.cpp
libcommon_a-ContigID.obj: ContigID.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-ContigID.obj -MD -MP -MF $(DEPDIR)/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.obj `if test -f 'ContigID.cpp'; then $(CYGPATH_W) 'ContigID.cpp'; else $(CYGPATH_W) '$(srcdir)/ContigID.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-ContigID.Tpo $(DEPDIR)/libcommon_a-ContigID.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='ContigID.cpp' object='libcommon_a-ContigID.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-ContigID.obj -MD -MP -MF $(DEPDIR)/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.obj `if test -f 'ContigID.cpp'; then $(CYGPATH_W) 'ContigID.cpp'; else $(CYGPATH_W) '$(srcdir)/ContigID.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-ContigID.Tpo $(DEPDIR)/libcommon_a-ContigID.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='ContigID.cpp' object='libcommon_a-ContigID.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-ContigID.obj `if test -f 'ContigID.cpp'; then $(CYGPATH_W) 'ContigID.cpp'; else $(CYGPATH_W) '$(srcdir)/ContigID.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-ContigID.obj `if test -f 'ContigID.cpp'; then $(CYGPATH_W) 'ContigID.cpp'; else $(CYGPATH_W) '$(srcdir)/ContigID.cpp'; fi`
libcommon_a-Fcontrol.o: Fcontrol.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Fcontrol.o -MD -MP -MF $(DEPDIR)/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo '$(srcdir)/'`Fcontrol.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Fcontrol.Tpo $(DEPDIR)/libcommon_a-Fcontrol.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Fcontrol.cpp' object='libcommon_a-Fcontrol.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Fcontrol.o -MD -MP -MF $(DEPDIR)/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo '$(srcdir)/'`Fcontrol.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Fcontrol.Tpo $(DEPDIR)/libcommon_a-Fcontrol.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Fcontrol.cpp' object='libcommon_a-Fcontrol.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo '$(srcdir)/'`Fcontrol.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo '$(srcdir)/'`Fcontrol.cpp
libcommon_a-Fcontrol.obj: Fcontrol.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Fcontrol.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.obj `if test -f 'Fcontrol.cpp'; then $(CYGPATH_W) 'Fcontrol.cpp'; else $(CYGPATH_W) '$(srcdir)/Fcontrol.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Fcontrol.Tpo $(DEPDIR)/libcommon_a-Fcontrol.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Fcontrol.cpp' object='libcommon_a-Fcontrol.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Fcontrol.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.obj `if test -f 'Fcontrol.cpp'; then $(CYGPATH_W) 'Fcontrol.cpp'; else $(CYGPATH_W) '$(srcdir)/Fcontrol.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Fcontrol.Tpo $(DEPDIR)/libcommon_a-Fcontrol.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Fcontrol.cpp' object='libcommon_a-Fcontrol.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Fcontrol.obj `if test -f 'Fcontrol.cpp'; then $(CYGPATH_W) 'Fcontrol.cpp'; else $(CYGPATH_W) '$(srcdir)/Fcontrol.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Fcontrol.obj `if test -f 'Fcontrol.cpp'; then $(CYGPATH_W) 'Fcontrol.cpp'; else $(CYGPATH_W) '$(srcdir)/Fcontrol.cpp'; fi`
libcommon_a-Histogram.o: Histogram.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Histogram.o -MD -MP -MF $(DEPDIR)/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo '$(srcdir)/'`Histogram.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Histogram.Tpo $(DEPDIR)/libcommon_a-Histogram.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Histogram.cpp' object='libcommon_a-Histogram.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Histogram.o -MD -MP -MF $(DEPDIR)/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo '$(srcdir)/'`Histogram.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Histogram.Tpo $(DEPDIR)/libcommon_a-Histogram.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Histogram.cpp' object='libcommon_a-Histogram.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo '$(srcdir)/'`Histogram.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo '$(srcdir)/'`Histogram.cpp
libcommon_a-Histogram.obj: Histogram.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Histogram.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.obj `if test -f 'Histogram.cpp'; then $(CYGPATH_W) 'Histogram.cpp'; else $(CYGPATH_W) '$(srcdir)/Histogram.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Histogram.Tpo $(DEPDIR)/libcommon_a-Histogram.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Histogram.cpp' object='libcommon_a-Histogram.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Histogram.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.obj `if test -f 'Histogram.cpp'; then $(CYGPATH_W) 'Histogram.cpp'; else $(CYGPATH_W) '$(srcdir)/Histogram.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Histogram.Tpo $(DEPDIR)/libcommon_a-Histogram.Po
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libcommon_a-SignalHandler.obj: SignalHandler.cpp
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+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-SignalHandler.Tpo $(DEPDIR)/libcommon_a-SignalHandler.Po
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-SignalHandler.obj `if test -f 'SignalHandler.cpp'; then $(CYGPATH_W) 'SignalHandler.cpp'; else $(CYGPATH_W) '$(srcdir)/SignalHandler.cpp'; fi`
libcommon_a-Timer.o: Timer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Timer.o -MD -MP -MF $(DEPDIR)/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo '$(srcdir)/'`Timer.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Timer.Tpo $(DEPDIR)/libcommon_a-Timer.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Timer.cpp' object='libcommon_a-Timer.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Timer.o -MD -MP -MF $(DEPDIR)/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo '$(srcdir)/'`Timer.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Timer.Tpo $(DEPDIR)/libcommon_a-Timer.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Timer.cpp' object='libcommon_a-Timer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo '$(srcdir)/'`Timer.cpp
libcommon_a-Timer.obj: Timer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Timer.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.obj `if test -f 'Timer.cpp'; then $(CYGPATH_W) 'Timer.cpp'; else $(CYGPATH_W) '$(srcdir)/Timer.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Timer.Tpo $(DEPDIR)/libcommon_a-Timer.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Timer.cpp' object='libcommon_a-Timer.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Timer.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.obj `if test -f 'Timer.cpp'; then $(CYGPATH_W) 'Timer.cpp'; else $(CYGPATH_W) '$(srcdir)/Timer.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Timer.Tpo $(DEPDIR)/libcommon_a-Timer.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Timer.cpp' object='libcommon_a-Timer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Timer.obj `if test -f 'Timer.cpp'; then $(CYGPATH_W) 'Timer.cpp'; else $(CYGPATH_W) '$(srcdir)/Timer.cpp'; fi`
libcommon_a-Uncompress.o: Uncompress.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Uncompress.o -MD -MP -MF $(DEPDIR)/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo '$(srcdir)/'`Uncompress.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Uncompress.Tpo $(DEPDIR)/libcommon_a-Uncompress.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Uncompress.cpp' object='libcommon_a-Uncompress.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Uncompress.o -MD -MP -MF $(DEPDIR)/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo '$(srcdir)/'`Uncompress.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Uncompress.Tpo $(DEPDIR)/libcommon_a-Uncompress.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Uncompress.cpp' object='libcommon_a-Uncompress.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo '$(srcdir)/'`Uncompress.cpp
libcommon_a-Uncompress.obj: Uncompress.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Uncompress.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.obj `if test -f 'Uncompress.cpp'; then $(CYGPATH_W) 'Uncompress.cpp'; else $(CYGPATH_W) '$(srcdir)/Uncompress.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-Uncompress.Tpo $(DEPDIR)/libcommon_a-Uncompress.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Uncompress.cpp' object='libcommon_a-Uncompress.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-Uncompress.obj -MD -MP -MF $(DEPDIR)/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.obj `if test -f 'Uncompress.cpp'; then $(CYGPATH_W) 'Uncompress.cpp'; else $(CYGPATH_W) '$(srcdir)/Uncompress.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-Uncompress.Tpo $(DEPDIR)/libcommon_a-Uncompress.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Uncompress.cpp' object='libcommon_a-Uncompress.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-Uncompress.obj `if test -f 'Uncompress.cpp'; then $(CYGPATH_W) 'Uncompress.cpp'; else $(CYGPATH_W) '$(srcdir)/Uncompress.cpp'; fi`
libcommon_a-city.o: city.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-city.o -MD -MP -MF $(DEPDIR)/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo '$(srcdir)/'`city.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-city.Tpo $(DEPDIR)/libcommon_a-city.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='city.cc' object='libcommon_a-city.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-city.o -MD -MP -MF $(DEPDIR)/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo '$(srcdir)/'`city.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-city.Tpo $(DEPDIR)/libcommon_a-city.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='city.cc' object='libcommon_a-city.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-city.o `test -f 'city.cc' || echo '$(srcdir)/'`city.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-city.o `test -f 'city.cc' || echo '$(srcdir)/'`city.cc
libcommon_a-city.obj: city.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-city.obj -MD -MP -MF $(DEPDIR)/libcommon_a-city.Tpo -c -o libcommon_a-city.obj `if test -f 'city.cc'; then $(CYGPATH_W) 'city.cc'; else $(CYGPATH_W) '$(srcdir)/city.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libcommon_a-city.Tpo $(DEPDIR)/libcommon_a-city.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='city.cc' object='libcommon_a-city.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libcommon_a-city.obj -MD -MP -MF $(DEPDIR)/libcommon_a-city.Tpo -c -o libcommon_a-city.obj `if test -f 'city.cc'; then $(CYGPATH_W) 'city.cc'; else $(CYGPATH_W) '$(srcdir)/city.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libcommon_a-city.Tpo $(DEPDIR)/libcommon_a-city.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='city.cc' object='libcommon_a-city.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-city.obj `if test -f 'city.cc'; then $(CYGPATH_W) 'city.cc'; else $(CYGPATH_W) '$(srcdir)/city.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcommon_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libcommon_a-city.obj `if test -f 'city.cc'; then $(CYGPATH_W) 'city.cc'; else $(CYGPATH_W) '$(srcdir)/city.cc'; fi`
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -518,15 +589,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -535,9 +602,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -688,8 +756,8 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstLIBRARIES cscopelist ctags distclean \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-tags distdir dvi \
dvi-am html html-am info info-am install install-am \
install-data install-data-am install-dvi install-dvi-am \
@@ -698,7 +766,7 @@ uninstall-am:
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
diff --git a/Common/Sequence.cpp b/Common/Sequence.cpp
index 6b19824..01ff305 100644
--- a/Common/Sequence.cpp
+++ b/Common/Sequence.cpp
@@ -57,16 +57,49 @@ Sequence reverseComplement(const Sequence& s)
return rc;
}
+static const uint8_t b2C[256] = {
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0x00, 0x01, 0x02, 0x03, 0xFF, 0xFF, 0xFF, 0xFF, //3 0 1 2 3
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //4 A C G
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //5 T
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //6
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //7
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
+ 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
+};
+
/** Return the base enumeration for the specified character. */
uint8_t baseToCode(char base)
{
- switch (base) {
- case 'A': case '0': return 0;
- case 'C': case '1': return 1;
- case 'G': case '2': return 2;
- case 'T': case '3': return 3;
- }
- cerr << "error: unexpected character: `" << base << "'\n";
+ uint8_t r = b2C[unsigned(base)];
+ if (r != 0xFF) return r;
+
+ cerr << "error: unexpected character: '"
+ << base << "'\n";
assert(false);
abort();
}
diff --git a/Consensus/Makefile.in b/Consensus/Makefile.in
index 0d2558c..f15027b 100644
--- a/Consensus/Makefile.in
+++ b/Consensus/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = Consensus$(EXEEXT)
subdir = Consensus
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -67,15 +94,39 @@ am_Consensus_OBJECTS = Consensus-Consensus.$(OBJEXT)
Consensus_OBJECTS = $(am_Consensus_OBJECTS)
Consensus_DEPENDENCIES = $(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(Consensus_SOURCES)
DIST_SOURCES = $(Consensus_SOURCES)
am__can_run_installinfo = \
@@ -83,12 +134,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -236,10 +305,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -260,16 +330,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
Consensus$(EXEEXT): $(Consensus_OBJECTS) $(Consensus_DEPENDENCIES) $(EXTRA_Consensus_DEPENDENCIES)
@rm -f Consensus$(EXEEXT)
- $(CXXLINK) $(Consensus_OBJECTS) $(Consensus_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(Consensus_OBJECTS) $(Consensus_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -280,53 +352,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Consensus-Consensus.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
Consensus-Consensus.o: Consensus.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Consensus-Consensus.o -MD -MP -MF $(DEPDIR)/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo '$(srcdir)/'`Consensus.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/Consensus-Consensus.Tpo $(DEPDIR)/Consensus-Consensus.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Consensus.cpp' object='Consensus-Consensus.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Consensus-Consensus.o -MD -MP -MF $(DEPDIR)/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo '$(srcdir)/'`Consensus.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/Consensus-Consensus.Tpo $(DEPDIR)/Consensus-Consensus.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Consensus.cpp' object='Consensus-Consensus.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo '$(srcdir)/'`Consensus.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo '$(srcdir)/'`Consensus.cpp
Consensus-Consensus.obj: Consensus.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Consensus-Consensus.obj -MD -MP -MF $(DEPDIR)/Consensus-Consensus.Tpo -c -o Consensus-Consensus.obj `if test -f 'Consensus.cpp'; then $(CYGPATH_W) 'Consensus.cpp'; else $(CYGPATH_W) '$(srcdir)/Consensus.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/Consensus-Consensus.Tpo $(DEPDIR)/Consensus-Consensus.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Consensus.cpp' object='Consensus-Consensus.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Consensus-Consensus.obj -MD -MP -MF $(DEPDIR)/Consensus-Consensus.Tpo -c -o Consensus-Consensus.obj `if test -f 'Consensus.cpp'; then $(CYGPATH_W) 'Consensus.cpp'; else $(CYGPATH_W) '$(srcdir)/Consensus.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/Consensus-Consensus.Tpo $(DEPDIR)/Consensus-Consensus.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Consensus.cpp' object='Consensus-Consensus.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Consensus-Consensus.obj `if test -f 'Consensus.cpp'; then $(CYGPATH_W) 'Consensus.cpp'; else $(CYGPATH_W) '$(srcdir)/Consensus.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Consensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Consensus-Consensus.obj `if test -f 'Consensus.cpp'; then $(CYGPATH_W) 'Consensus.cpp'; else $(CYGPATH_W) '$(srcdir)/Consensus.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -338,15 +399,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -355,9 +412,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -511,18 +569,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/DAssembler/Makefile.in b/DAssembler/Makefile.in
index 99f6d40..f510a3d 100644
--- a/DAssembler/Makefile.in
+++ b/DAssembler/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = DAssembler$(EXEEXT)
subdir = DAssembler
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -68,19 +95,51 @@ am_DAssembler_OBJECTS = DAssembler-DAssembler.$(OBJEXT) \
DAssembler_OBJECTS = $(am_DAssembler_OBJECTS)
DAssembler_DEPENDENCIES = $(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(DAssembler_SOURCES)
DIST_SOURCES = $(DAssembler_SOURCES)
am__can_run_installinfo = \
@@ -88,12 +147,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -242,10 +319,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -266,16 +344,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
DAssembler$(EXEEXT): $(DAssembler_OBJECTS) $(DAssembler_DEPENDENCIES) $(EXTRA_DAssembler_DEPENDENCIES)
@rm -f DAssembler$(EXEEXT)
- $(CXXLINK) $(DAssembler_OBJECTS) $(DAssembler_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(DAssembler_OBJECTS) $(DAssembler_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -287,67 +367,56 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/DAssembler-RotatedRead.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
DAssembler-DAssembler.o: DAssembler.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-DAssembler.o -MD -MP -MF $(DEPDIR)/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo '$(srcdir)/'`DAssembler.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DAssembler-DAssembler.Tpo $(DEPDIR)/DAssembler-DAssembler.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DAssembler.cpp' object='DAssembler-DAssembler.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-DAssembler.o -MD -MP -MF $(DEPDIR)/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo '$(srcdir)/'`DAssembler.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DAssembler-DAssembler.Tpo $(DEPDIR)/DAssembler-DAssembler.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DAssembler.cpp' object='DAssembler-DAssembler.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo '$(srcdir)/'`DAssembler.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo '$(srcdir)/'`DAssembler.cpp
DAssembler-DAssembler.obj: DAssembler.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-DAssembler.obj -MD -MP -MF $(DEPDIR)/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.obj `if test -f 'DAssembler.cpp'; then $(CYGPATH_W) 'DAssembler.cpp'; else $(CYGPATH_W) '$(srcdir)/DAssembler.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DAssembler-DAssembler.Tpo $(DEPDIR)/DAssembler-DAssembler.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DAssembler.cpp' object='DAssembler-DAssembler.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-DAssembler.obj -MD -MP -MF $(DEPDIR)/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.obj `if test -f 'DAssembler.cpp'; then $(CYGPATH_W) 'DAssembler.cpp'; else $(CYGPATH_W) '$(srcdir)/DAssembler.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DAssembler-DAssembler.Tpo $(DEPDIR)/DAssembler-DAssembler.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DAssembler.cpp' object='DAssembler-DAssembler.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-DAssembler.obj `if test -f 'DAssembler.cpp'; then $(CYGPATH_W) 'DAssembler.cpp'; else $(CYGPATH_W) '$(srcdir)/DAssembler.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-DAssembler.obj `if test -f 'DAssembler.cpp'; then $(CYGPATH_W) 'DAssembler.cpp'; else $(CYGPATH_W) '$(srcdir)/DAssembler.cpp'; fi`
DAssembler-RotatedRead.o: RotatedRead.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-RotatedRead.o -MD -MP -MF $(DEPDIR)/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo '$(srcdir)/'`RotatedRead.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DAssembler-RotatedRead.Tpo $(DEPDIR)/DAssembler-RotatedRead.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='RotatedRead.cpp' object='DAssembler-RotatedRead.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-RotatedRead.o -MD -MP -MF $(DEPDIR)/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo '$(srcdir)/'`RotatedRead.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DAssembler-RotatedRead.Tpo $(DEPDIR)/DAssembler-RotatedRead.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='RotatedRead.cpp' object='DAssembler-RotatedRead.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo '$(srcdir)/'`RotatedRead.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo '$(srcdir)/'`RotatedRead.cpp
DAssembler-RotatedRead.obj: RotatedRead.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-RotatedRead.obj -MD -MP -MF $(DEPDIR)/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.obj `if test -f 'RotatedRead.cpp'; then $(CYGPATH_W) 'RotatedRead.cpp'; else $(CYGPATH_W) '$(srcdir)/RotatedRead.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DAssembler-RotatedRead.Tpo $(DEPDIR)/DAssembler-RotatedRead.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='RotatedRead.cpp' object='DAssembler-RotatedRead.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DAssembler-RotatedRead.obj -MD -MP -MF $(DEPDIR)/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.obj `if test -f 'RotatedRead.cpp'; then $(CYGPATH_W) 'RotatedRead.cpp'; else $(CYGPATH_W) '$(srcdir)/RotatedRead.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DAssembler-RotatedRead.Tpo $(DEPDIR)/DAssembler-RotatedRead.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='RotatedRead.cpp' object='DAssembler-RotatedRead.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-RotatedRead.obj `if test -f 'RotatedRead.cpp'; then $(CYGPATH_W) 'RotatedRead.cpp'; else $(CYGPATH_W) '$(srcdir)/RotatedRead.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DAssembler_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DAssembler-RotatedRead.obj `if test -f 'RotatedRead.cpp'; then $(CYGPATH_W) 'RotatedRead.cpp'; else $(CYGPATH_W) '$(srcdir)/RotatedRead.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -359,15 +428,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -376,9 +441,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -532,18 +598,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/DataLayer/FastaReader.cpp b/DataLayer/FastaReader.cpp
index 1138145..655be43 100644
--- a/DataLayer/FastaReader.cpp
+++ b/DataLayer/FastaReader.cpp
@@ -224,8 +224,12 @@ next_record:
if (opt::trimMasked && !colourSpace) {
// Removed masked (lower case) sequence at the beginning
// and end of the read.
- size_t trimFront = s.find_first_not_of("acgtn");
- size_t trimBack = s.find_last_not_of("acgtn") + 1;
+ size_t trimFront = 0;
+ while (trimFront <= s.length() && islower(s[trimFront]))
+ trimFront++;
+ size_t trimBack = s.length();
+ while (trimBack > 0 && islower(s[trimBack - 1]))
+ trimBack--;
s.erase(trimBack);
s.erase(0, trimFront);
if (!q.empty()) {
diff --git a/DataLayer/Makefile.in b/DataLayer/Makefile.in
index 1fe4fd3..dd61834 100644
--- a/DataLayer/Makefile.in
+++ b/DataLayer/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,23 +16,51 @@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-fac$(EXEEXT) abyss-tofastq$(EXEEXT)
subdir = DataLayer
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -65,6 +92,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libdatalayer_a_AR = $(AR) $(ARFLAGS)
libdatalayer_a_LIBADD =
am_libdatalayer_a_OBJECTS = libdatalayer_a-FastaReader.$(OBJEXT) \
@@ -80,19 +111,51 @@ am_abyss_tofastq_OBJECTS = abyss_tofastq-abyss-tofastq.$(OBJEXT)
abyss_tofastq_OBJECTS = $(am_abyss_tofastq_OBJECTS)
abyss_tofastq_DEPENDENCIES = libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libdatalayer_a_SOURCES) $(abyss_fac_SOURCES) \
$(abyss_tofastq_SOURCES)
DIST_SOURCES = $(libdatalayer_a_SOURCES) $(abyss_fac_SOURCES) \
@@ -102,12 +165,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -263,10 +344,11 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libdatalayer.a: $(libdatalayer_a_OBJECTS) $(libdatalayer_a_DEPENDENCIES) $(EXTRA_libdatalayer_a_DEPENDENCIES)
- -rm -f libdatalayer.a
- $(libdatalayer_a_AR) libdatalayer.a $(libdatalayer_a_OBJECTS) $(libdatalayer_a_LIBADD)
- $(RANLIB) libdatalayer.a
+ $(AM_V_at)-rm -f libdatalayer.a
+ $(AM_V_AR)$(libdatalayer_a_AR) libdatalayer.a $(libdatalayer_a_OBJECTS) $(libdatalayer_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libdatalayer.a
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -276,10 +358,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -300,19 +383,22 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-fac$(EXEEXT): $(abyss_fac_OBJECTS) $(abyss_fac_DEPENDENCIES) $(EXTRA_abyss_fac_DEPENDENCIES)
@rm -f abyss-fac$(EXEEXT)
- $(CXXLINK) $(abyss_fac_OBJECTS) $(abyss_fac_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_fac_OBJECTS) $(abyss_fac_LDADD) $(LIBS)
+
abyss-tofastq$(EXEEXT): $(abyss_tofastq_OBJECTS) $(abyss_tofastq_DEPENDENCIES) $(EXTRA_abyss_tofastq_DEPENDENCIES)
@rm -f abyss-tofastq$(EXEEXT)
- $(CXXLINK) $(abyss_tofastq_OBJECTS) $(abyss_tofastq_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_tofastq_OBJECTS) $(abyss_tofastq_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -326,109 +412,98 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libdatalayer_a-FastaWriter.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
libdatalayer_a-FastaReader.o: FastaReader.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaReader.o -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo '$(srcdir)/'`FastaReader.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libdatalayer_a-FastaReader.Tpo $(DEPDIR)/libdatalayer_a-FastaReader.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FastaReader.cpp' object='libdatalayer_a-FastaReader.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaReader.o -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo '$(srcdir)/'`FastaReader.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libdatalayer_a-FastaReader.Tpo $(DEPDIR)/libdatalayer_a-FastaReader.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FastaReader.cpp' object='libdatalayer_a-FastaReader.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo '$(srcdir)/'`FastaReader.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo '$(srcdir)/'`FastaReader.cpp
libdatalayer_a-FastaReader.obj: FastaReader.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaReader.obj -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.obj `if test -f 'FastaReader.cpp'; then $(CYGPATH_W) 'FastaReader.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaReader.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libdatalayer_a-FastaReader.Tpo $(DEPDIR)/libdatalayer_a-FastaReader.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FastaReader.cpp' object='libdatalayer_a-FastaReader.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaReader.obj -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.obj `if test -f 'FastaReader.cpp'; then $(CYGPATH_W) 'FastaReader.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaReader.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libdatalayer_a-FastaReader.Tpo $(DEPDIR)/libdatalayer_a-FastaReader.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FastaReader.cpp' object='libdatalayer_a-FastaReader.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaReader.obj `if test -f 'FastaReader.cpp'; then $(CYGPATH_W) 'FastaReader.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaReader.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaReader.obj `if test -f 'FastaReader.cpp'; then $(CYGPATH_W) 'FastaReader.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaReader.cpp'; fi`
libdatalayer_a-FastaWriter.o: FastaWriter.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaWriter.o -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo '$(srcdir)/'`FastaWriter.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo $(DEPDIR)/libdatalayer_a-FastaWriter.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FastaWriter.cpp' object='libdatalayer_a-FastaWriter.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaWriter.o -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo '$(srcdir)/'`FastaWriter.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo $(DEPDIR)/libdatalayer_a-FastaWriter.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FastaWriter.cpp' object='libdatalayer_a-FastaWriter.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo '$(srcdir)/'`FastaWriter.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo '$(srcdir)/'`FastaWriter.cpp
libdatalayer_a-FastaWriter.obj: FastaWriter.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaWriter.obj -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.obj `if test -f 'FastaWriter.cpp'; then $(CYGPATH_W) 'FastaWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaWriter.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo $(DEPDIR)/libdatalayer_a-FastaWriter.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FastaWriter.cpp' object='libdatalayer_a-FastaWriter.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libdatalayer_a-FastaWriter.obj -MD -MP -MF $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.obj `if test -f 'FastaWriter.cpp'; then $(CYGPATH_W) 'FastaWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaWriter.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libdatalayer_a-FastaWriter.Tpo $(DEPDIR)/libdatalayer_a-FastaWriter.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FastaWriter.cpp' object='libdatalayer_a-FastaWriter.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaWriter.obj `if test -f 'FastaWriter.cpp'; then $(CYGPATH_W) 'FastaWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaWriter.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libdatalayer_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libdatalayer_a-FastaWriter.obj `if test -f 'FastaWriter.cpp'; then $(CYGPATH_W) 'FastaWriter.cpp'; else $(CYGPATH_W) '$(srcdir)/FastaWriter.cpp'; fi`
abyss_fac-fac.o: fac.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fac-fac.o -MD -MP -MF $(DEPDIR)/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo '$(srcdir)/'`fac.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_fac-fac.Tpo $(DEPDIR)/abyss_fac-fac.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='fac.cc' object='abyss_fac-fac.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fac-fac.o -MD -MP -MF $(DEPDIR)/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo '$(srcdir)/'`fac.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_fac-fac.Tpo $(DEPDIR)/abyss_fac-fac.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fac.cc' object='abyss_fac-fac.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo '$(srcdir)/'`fac.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo '$(srcdir)/'`fac.cc
abyss_fac-fac.obj: fac.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fac-fac.obj -MD -MP -MF $(DEPDIR)/abyss_fac-fac.Tpo -c -o abyss_fac-fac.obj `if test -f 'fac.cc'; then $(CYGPATH_W) 'fac.cc'; else $(CYGPATH_W) '$(srcdir)/fac.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_fac-fac.Tpo $(DEPDIR)/abyss_fac-fac.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='fac.cc' object='abyss_fac-fac.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fac-fac.obj -MD -MP -MF $(DEPDIR)/abyss_fac-fac.Tpo -c -o abyss_fac-fac.obj `if test -f 'fac.cc'; then $(CYGPATH_W) 'fac.cc'; else $(CYGPATH_W) '$(srcdir)/fac.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_fac-fac.Tpo $(DEPDIR)/abyss_fac-fac.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fac.cc' object='abyss_fac-fac.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fac-fac.obj `if test -f 'fac.cc'; then $(CYGPATH_W) 'fac.cc'; else $(CYGPATH_W) '$(srcdir)/fac.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fac_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fac-fac.obj `if test -f 'fac.cc'; then $(CYGPATH_W) 'fac.cc'; else $(CYGPATH_W) '$(srcdir)/fac.cc'; fi`
abyss_tofastq-abyss-tofastq.o: abyss-tofastq.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo '$(srcdir)/'`abyss-tofastq.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo $(DEPDIR)/abyss_tofastq-abyss-tofastq.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-tofastq.cc' object='abyss_tofastq-abyss-tofastq.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo '$(srcdir)/'`abyss-tofastq.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo $(DEPDIR)/abyss_tofastq-abyss-tofastq.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-tofastq.cc' object='abyss_tofastq-abyss-tofastq.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo '$(srcdir)/'`abyss-tofastq.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo '$(srcdir)/'`abyss-tofastq.cc
abyss_tofastq-abyss-tofastq.obj: abyss-tofastq.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_tofastq-abyss-tofastq.obj -MD -MP -MF $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.obj `if test -f 'abyss-tofastq.cc'; then $(CYGPATH_W) 'abyss-tofastq.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-tofastq.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo $(DEPDIR)/abyss_tofastq-abyss-tofastq.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-tofastq.cc' object='abyss_tofastq-abyss-tofastq.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_tofastq-abyss-tofastq.obj -MD -MP -MF $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.obj `if test -f 'abyss-tofastq.cc'; then $(CYGPATH_W) 'abyss-tofastq.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-tofastq.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_tofastq-abyss-tofastq.Tpo $(DEPDIR)/abyss_tofastq-abyss-tofastq.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-tofastq.cc' object='abyss_tofastq-abyss-tofastq.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_tofastq-abyss-tofastq.obj `if test -f 'abyss-tofastq.cc'; then $(CYGPATH_W) 'abyss-tofastq.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-tofastq.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_tofastq_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_tofastq-abyss-tofastq.obj `if test -f 'abyss-tofastq.cc'; then $(CYGPATH_W) 'abyss-tofastq.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-tofastq.cc'; fi`
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -440,15 +515,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -457,9 +528,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -614,18 +686,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstLIBRARIES cscopelist ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/DataLayer/fac.cc b/DataLayer/fac.cc
index 4cf6764..44f897b 100644
--- a/DataLayer/fac.cc
+++ b/DataLayer/fac.cc
@@ -29,6 +29,8 @@ static const char USAGE_MESSAGE[] =
"\n"
" Options:\n"
"\n"
+" -e, --exp-size=N expected genome size. Will calculate NG50\n"
+" and associated stats\n"
" -s, -t, --min-length=N ignore sequences shorter than N bp [500]\n"
" -d, --delimiter=S use S for the field delimiter [\\t]\n"
" -j, --jira output JIRA format\n"
@@ -38,6 +40,8 @@ static const char USAGE_MESSAGE[] =
" --trim-masked trim masked bases from the end\n"
" --no-trim-masked do not trim masked bases from the ends\n"
" of sequences [default]\n"
+" --count-ambig count ambiguity codes in sequences\n"
+" --no-count-ambig do not count ambiguity codes in sequences [default]\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
@@ -46,17 +50,20 @@ static const char USAGE_MESSAGE[] =
namespace opt {
static unsigned minLength = 500;
+ static long long unsigned expSize = 0;
static string delimiter = "\t";
static int format;
static int verbose;
+ static int countAmbig;
}
enum { TAB, JIRA, MMD };
-static const char shortopts[] = "d:jms:t:v";
+static const char shortopts[] = "d:jms:t:e:v";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
+ { "exp-size", no_argument, NULL, 'e' },
{ "min-length", no_argument, NULL, 's' },
{ "delimiter", required_argument, NULL, 'd' },
{ "jira", no_argument, NULL, 'j' },
@@ -65,6 +72,8 @@ static const struct option longopts[] = {
{ "no-chastity", no_argument, &opt::chastityFilter, 0 },
{ "trim-masked", no_argument, &opt::trimMasked, 1 },
{ "no-trim-masked", no_argument, &opt::trimMasked, 0 },
+ { "count-ambig", no_argument, &opt::countAmbig, 1 },
+ { "no-count-ambig", no_argument, &opt::countAmbig, 0 },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
@@ -88,7 +97,8 @@ static void printContiguityStatistics(const char* path)
Histogram h;
FastaReader in(path, FASTAREADER_FLAGS);
for (string s; in >> s;)
- h.insert(count_if(s.begin(), s.end(), isACGT));
+ h.insert(opt::countAmbig ? s.length() :
+ count_if(s.begin(), s.end(), isACGT));
assert(in.eof());
// Print the table header.
@@ -98,8 +108,11 @@ static void printContiguityStatistics(const char* path)
cout << "||"
<< "n" << sep
<< "n:" << opt::minLength << sep
- << "n:N50" << sep
- << "min" << sep
+ << "n:N50" << sep;
+ if (opt::expSize > 0)
+ cout << "n:NG50" << sep
+ << "NG50" << sep;
+ cout << "min" << sep
<< "N80" << sep
<< "N50" << sep
<< "N20" << sep
@@ -111,15 +124,21 @@ static void printContiguityStatistics(const char* path)
const char* sep = "\t|";
cout << "n" << sep
<< "n:" << opt::minLength << sep
- << "n:N50" << sep
- << "min" << sep
+ << "n:N50" << sep;
+ if (opt::expSize > 0)
+ cout << "n:NG50" << sep
+ << "NG50" << sep;
+ cout << "min" << sep
<< "N80" << sep
<< "N50" << sep
<< "N20" << sep
<< "max" << sep
<< "sum" << sep
- << "name" << '\n'
- << "------" << sep
+ << "name" << '\n';
+ if (opt::expSize > 0)
+ cout << "------" << sep
+ << "------" << sep;
+ cout << "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
@@ -135,7 +154,7 @@ static void printContiguityStatistics(const char* path)
if (opt::format == JIRA)
cout << '|';
printContiguityStats(cout, h, opt::minLength,
- printHeader, opt::delimiter)
+ printHeader, opt::delimiter, opt::expSize)
<< opt::delimiter << path;
if (opt::format == JIRA)
cout << opt::delimiter;
@@ -167,6 +186,9 @@ int main(int argc, char** argv)
opt::delimiter = "\t|";
opt::format = MMD;
break;
+ case 'e':
+ arg >> opt::expSize;
+ break;
case 's': case 't':
arg >> opt::minLength;
break;
diff --git a/DistanceEst/Makefile.in b/DistanceEst/Makefile.in
index a1750c7..bf4b7d4 100644
--- a/DistanceEst/Makefile.in
+++ b/DistanceEst/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = DistanceEst$(EXEEXT)
subdir = DistanceEst
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -69,19 +96,51 @@ DistanceEst_OBJECTS = $(am_DistanceEst_OBJECTS)
DistanceEst_DEPENDENCIES = $(top_builddir)/Common/libcommon.a
DistanceEst_LINK = $(CXXLD) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(DistanceEst_SOURCES)
DIST_SOURCES = $(DistanceEst_SOURCES)
am__can_run_installinfo = \
@@ -89,12 +148,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -239,10 +316,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -263,16 +341,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
DistanceEst$(EXEEXT): $(DistanceEst_OBJECTS) $(DistanceEst_DEPENDENCIES) $(EXTRA_DistanceEst_DEPENDENCIES)
@rm -f DistanceEst$(EXEEXT)
- $(DistanceEst_LINK) $(DistanceEst_OBJECTS) $(DistanceEst_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(DistanceEst_LINK) $(DistanceEst_OBJECTS) $(DistanceEst_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -284,67 +364,56 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/DistanceEst-MLE.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
DistanceEst-DistanceEst.o: DistanceEst.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-DistanceEst.o -MD -MP -MF $(DEPDIR)/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo '$(srcdir)/'`DistanceEst.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DistanceEst-DistanceEst.Tpo $(DEPDIR)/DistanceEst-DistanceEst.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DistanceEst.cpp' object='DistanceEst-DistanceEst.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-DistanceEst.o -MD -MP -MF $(DEPDIR)/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo '$(srcdir)/'`DistanceEst.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DistanceEst-DistanceEst.Tpo $(DEPDIR)/DistanceEst-DistanceEst.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DistanceEst.cpp' object='DistanceEst-DistanceEst.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo '$(srcdir)/'`DistanceEst.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo '$(srcdir)/'`DistanceEst.cpp
DistanceEst-DistanceEst.obj: DistanceEst.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-DistanceEst.obj -MD -MP -MF $(DEPDIR)/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.obj `if test -f 'DistanceEst.cpp'; then $(CYGPATH_W) 'DistanceEst.cpp'; else $(CYGPATH_W) '$(srcdir)/DistanceEst.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DistanceEst-DistanceEst.Tpo $(DEPDIR)/DistanceEst-DistanceEst.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='DistanceEst.cpp' object='DistanceEst-DistanceEst.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-DistanceEst.obj -MD -MP -MF $(DEPDIR)/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.obj `if test -f 'DistanceEst.cpp'; then $(CYGPATH_W) 'DistanceEst.cpp'; else $(CYGPATH_W) '$(srcdir)/DistanceEst.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DistanceEst-DistanceEst.Tpo $(DEPDIR)/DistanceEst-DistanceEst.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='DistanceEst.cpp' object='DistanceEst-DistanceEst.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-DistanceEst.obj `if test -f 'DistanceEst.cpp'; then $(CYGPATH_W) 'DistanceEst.cpp'; else $(CYGPATH_W) '$(srcdir)/DistanceEst.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-DistanceEst.obj `if test -f 'DistanceEst.cpp'; then $(CYGPATH_W) 'DistanceEst.cpp'; else $(CYGPATH_W) '$(srcdir)/DistanceEst.cpp'; fi`
DistanceEst-MLE.o: MLE.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-MLE.o -MD -MP -MF $(DEPDIR)/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo '$(srcdir)/'`MLE.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DistanceEst-MLE.Tpo $(DEPDIR)/DistanceEst-MLE.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MLE.cpp' object='DistanceEst-MLE.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-MLE.o -MD -MP -MF $(DEPDIR)/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo '$(srcdir)/'`MLE.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DistanceEst-MLE.Tpo $(DEPDIR)/DistanceEst-MLE.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MLE.cpp' object='DistanceEst-MLE.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo '$(srcdir)/'`MLE.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo '$(srcdir)/'`MLE.cpp
DistanceEst-MLE.obj: MLE.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-MLE.obj -MD -MP -MF $(DEPDIR)/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.obj `if test -f 'MLE.cpp'; then $(CYGPATH_W) 'MLE.cpp'; else $(CYGPATH_W) '$(srcdir)/MLE.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/DistanceEst-MLE.Tpo $(DEPDIR)/DistanceEst-MLE.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MLE.cpp' object='DistanceEst-MLE.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -MT DistanceEst-MLE.obj -MD -MP -MF $(DEPDIR)/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.obj `if test -f 'MLE.cpp'; then $(CYGPATH_W) 'MLE.cpp'; else $(CYGPATH_W) '$(srcdir)/MLE.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/DistanceEst-MLE.Tpo $(DEPDIR)/DistanceEst-MLE.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MLE.cpp' object='DistanceEst-MLE.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-MLE.obj `if test -f 'MLE.cpp'; then $(CYGPATH_W) 'MLE.cpp'; else $(CYGPATH_W) '$(srcdir)/MLE.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(DistanceEst_CPPFLAGS) $(CPPFLAGS) $(DistanceEst_CXXFLAGS) $(CXXFLAGS) -c -o DistanceEst-MLE.obj `if test -f 'MLE.cpp'; then $(CYGPATH_W) 'MLE.cpp'; else $(CYGPATH_W) '$(srcdir)/MLE.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -356,15 +425,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -373,9 +438,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -529,18 +595,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/FMIndex/Makefile.in b/FMIndex/Makefile.in
index 49c0a76..f190387 100644
--- a/FMIndex/Makefile.in
+++ b/FMIndex/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,23 +16,51 @@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
noinst_PROGRAMS = abyss-count$(EXEEXT) abyss-dawg$(EXEEXT)
subdir = FMIndex
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -65,6 +92,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libfmindex_a_AR = $(AR) $(ARFLAGS)
libfmindex_a_LIBADD =
am_libfmindex_a_OBJECTS = libfmindex_a-bit_array.$(OBJEXT)
@@ -78,19 +109,51 @@ am_abyss_dawg_OBJECTS = abyss_dawg-abyss-dawg.$(OBJEXT)
abyss_dawg_OBJECTS = $(am_abyss_dawg_OBJECTS)
abyss_dawg_DEPENDENCIES = libfmindex.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libfmindex_a_SOURCES) $(abyss_count_SOURCES) \
$(abyss_dawg_SOURCES)
DIST_SOURCES = $(libfmindex_a_SOURCES) $(abyss_count_SOURCES) \
@@ -100,12 +163,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -259,19 +340,22 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libfmindex.a: $(libfmindex_a_OBJECTS) $(libfmindex_a_DEPENDENCIES) $(EXTRA_libfmindex_a_DEPENDENCIES)
- -rm -f libfmindex.a
- $(libfmindex_a_AR) libfmindex.a $(libfmindex_a_OBJECTS) $(libfmindex_a_LIBADD)
- $(RANLIB) libfmindex.a
+ $(AM_V_at)-rm -f libfmindex.a
+ $(AM_V_AR)$(libfmindex_a_AR) libfmindex.a $(libfmindex_a_OBJECTS) $(libfmindex_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libfmindex.a
clean-noinstPROGRAMS:
-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+
abyss-count$(EXEEXT): $(abyss_count_OBJECTS) $(abyss_count_DEPENDENCIES) $(EXTRA_abyss_count_DEPENDENCIES)
@rm -f abyss-count$(EXEEXT)
- $(CXXLINK) $(abyss_count_OBJECTS) $(abyss_count_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_count_OBJECTS) $(abyss_count_LDADD) $(LIBS)
+
abyss-dawg$(EXEEXT): $(abyss_dawg_OBJECTS) $(abyss_dawg_DEPENDENCIES) $(EXTRA_abyss_dawg_DEPENDENCIES)
@rm -f abyss-dawg$(EXEEXT)
- $(CXXLINK) $(abyss_dawg_OBJECTS) $(abyss_dawg_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_dawg_OBJECTS) $(abyss_dawg_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -284,81 +368,70 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libfmindex_a-bit_array.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
libfmindex_a-bit_array.o: bit_array.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libfmindex_a-bit_array.o -MD -MP -MF $(DEPDIR)/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo '$(srcdir)/'`bit_array.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libfmindex_a-bit_array.Tpo $(DEPDIR)/libfmindex_a-bit_array.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='bit_array.cc' object='libfmindex_a-bit_array.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libfmindex_a-bit_array.o -MD -MP -MF $(DEPDIR)/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo '$(srcdir)/'`bit_array.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libfmindex_a-bit_array.Tpo $(DEPDIR)/libfmindex_a-bit_array.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='bit_array.cc' object='libfmindex_a-bit_array.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo '$(srcdir)/'`bit_array.cc
libfmindex_a-bit_array.obj: bit_array.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libfmindex_a-bit_array.obj -MD -MP -MF $(DEPDIR)/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.obj `if test -f 'bit_array.cc'; then $(CYGPATH_W) 'bit_array.cc'; else $(CYGPATH_W) '$(srcdir)/bit_array.cc'; fi`
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='bit_array.cc' object='libfmindex_a-bit_array.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libfmindex_a-bit_array.obj -MD -MP -MF $(DEPDIR)/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.obj `if test -f 'bit_array.cc'; then $(CYGPATH_W) 'bit_array.cc'; else $(CYGPATH_W) '$(srcdir)/bit_array.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libfmindex_a-bit_array.Tpo $(DEPDIR)/libfmindex_a-bit_array.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='bit_array.cc' object='libfmindex_a-bit_array.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libfmindex_a-bit_array.obj `if test -f 'bit_array.cc'; then $(CYGPATH_W) 'bit_array.cc'; else $(CYGPATH_W) '$(srcdir)/bit_array.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libfmindex_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libfmindex_a-bit_array.obj `if test -f 'bit_array.cc'; then $(CYGPATH_W) 'bit_array.cc'; else $(CYGPATH_W) '$(srcdir)/bit_array.cc'; fi`
abyss_count-count.o: count.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_count-count.o -MD -MP -MF $(DEPDIR)/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo '$(srcdir)/'`count.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_count-count.Tpo $(DEPDIR)/abyss_count-count.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='count.cc' object='abyss_count-count.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_count-count.o -MD -MP -MF $(DEPDIR)/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo '$(srcdir)/'`count.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_count-count.Tpo $(DEPDIR)/abyss_count-count.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='count.cc' object='abyss_count-count.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_count-count.o `test -f 'count.cc' || echo '$(srcdir)/'`count.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_count-count.o `test -f 'count.cc' || echo '$(srcdir)/'`count.cc
abyss_count-count.obj: count.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_count-count.obj -MD -MP -MF $(DEPDIR)/abyss_count-count.Tpo -c -o abyss_count-count.obj `if test -f 'count.cc'; then $(CYGPATH_W) 'count.cc'; else $(CYGPATH_W) '$(srcdir)/count.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_count-count.Tpo $(DEPDIR)/abyss_count-count.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='count.cc' object='abyss_count-count.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_count-count.obj -MD -MP -MF $(DEPDIR)/abyss_count-count.Tpo -c -o abyss_count-count.obj `if test -f 'count.cc'; then $(CYGPATH_W) 'count.cc'; else $(CYGPATH_W) '$(srcdir)/count.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_count-count.Tpo $(DEPDIR)/abyss_count-count.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='count.cc' object='abyss_count-count.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_count_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_count-count.obj `if test -f 'count.cc'; then $(CYGPATH_W) 'count.cc'; else $(CYGPATH_W) '$(srcdir)/count.cc'; fi`
abyss_dawg-abyss-dawg.o: abyss-dawg.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_dawg-abyss-dawg.o -MD -MP -MF $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo '$(srcdir)/'`abyss-dawg.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo $(DEPDIR)/abyss_dawg-abyss-dawg.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-dawg.cc' object='abyss_dawg-abyss-dawg.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_dawg-abyss-dawg.o -MD -MP -MF $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo '$(srcdir)/'`abyss-dawg.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo $(DEPDIR)/abyss_dawg-abyss-dawg.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-dawg.cc' object='abyss_dawg-abyss-dawg.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo '$(srcdir)/'`abyss-dawg.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo '$(srcdir)/'`abyss-dawg.cc
abyss_dawg-abyss-dawg.obj: abyss-dawg.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_dawg-abyss-dawg.obj -MD -MP -MF $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.obj `if test -f 'abyss-dawg.cc'; then $(CYGPATH_W) 'abyss-dawg.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-dawg.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo $(DEPDIR)/abyss_dawg-abyss-dawg.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-dawg.cc' object='abyss_dawg-abyss-dawg.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_dawg-abyss-dawg.obj -MD -MP -MF $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.obj `if test -f 'abyss-dawg.cc'; then $(CYGPATH_W) 'abyss-dawg.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-dawg.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_dawg-abyss-dawg.Tpo $(DEPDIR)/abyss_dawg-abyss-dawg.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-dawg.cc' object='abyss_dawg-abyss-dawg.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_dawg-abyss-dawg.obj `if test -f 'abyss-dawg.cc'; then $(CYGPATH_W) 'abyss-dawg.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-dawg.cc'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_dawg_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_dawg-abyss-dawg.obj `if test -f 'abyss-dawg.cc'; then $(CYGPATH_W) 'abyss-dawg.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-dawg.cc'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -370,15 +443,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -387,9 +456,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -541,18 +611,18 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstLIBRARIES clean-noinstPROGRAMS cscopelist ctags \
- distclean distclean-compile distclean-generic distclean-tags \
- distdir dvi dvi-am html html-am info info-am install \
- install-am install-data install-data-am install-dvi \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstLIBRARIES clean-noinstPROGRAMS cscopelist-am ctags \
+ ctags-am distclean distclean-compile distclean-generic \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
install-dvi-am install-exec install-exec-am install-html \
install-html-am install-info install-info-am install-man \
install-pdf install-pdf-am install-ps install-ps-am \
install-strip installcheck installcheck-am installdirs \
maintainer-clean maintainer-clean-generic mostlyclean \
mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am
+ tags tags-am uninstall uninstall-am
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/FMIndex/abyss-dawg.cc b/FMIndex/abyss-dawg.cc
index 2343167..451475f 100644
--- a/FMIndex/abyss-dawg.cc
+++ b/FMIndex/abyss-dawg.cc
@@ -116,8 +116,6 @@ static void readFMIndex(FMIndex& g, const string& faPath)
int main(int argc, char** argv)
{
- checkPopcnt();
-
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
diff --git a/FMIndex/count.cc b/FMIndex/count.cc
index 9985247..bc79ad5 100644
--- a/FMIndex/count.cc
+++ b/FMIndex/count.cc
@@ -160,8 +160,6 @@ static void readFMIndex(FMIndex& g, const string& faPath)
int main(int argc, char** argv)
{
- checkPopcnt();
-
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
diff --git a/FilterGraph/FilterGraph.cpp b/FilterGraph/FilterGraph.cpp
index e285366..93dcfbe 100644
--- a/FilterGraph/FilterGraph.cpp
+++ b/FilterGraph/FilterGraph.cpp
@@ -65,6 +65,7 @@ static const char USAGE_MESSAGE[] =
" --no-assemble disable assembling of paths [default]\n"
" -g, --graph=FILE write the contig adjacency graph to FILE\n"
" -i, --ignore=FILE ignore contigs seen in FILE\n"
+" -r, --remove=FILE remove contigs seen in FILE\n"
" --adj output the graph in adj format [default]\n"
" --asqg output the graph in asqg format\n"
" --dot output the graph in dot format\n"
@@ -100,6 +101,9 @@ namespace opt {
/** Contigs to ignore. */
static string ignorePath;
+ /** Contigs to remove. */
+ static string removePath;
+
/** The minimum overlap allowed between two contigs. */
static int minOverlap = 10;
@@ -107,7 +111,7 @@ namespace opt {
int format = ADJ; // used by ContigProperties
}
-static const char shortopts[] = "g:i:k:l:m:t:T:v";
+static const char shortopts[] = "g:i:r:k:l:m:t:T:v";
enum { OPT_HELP = 1, OPT_VERSION };
@@ -119,6 +123,7 @@ static const struct option longopts[] = {
{ "sam", no_argument, &opt::format, SAM },
{ "graph", required_argument, NULL, 'g' },
{ "ignore", required_argument, NULL, 'i' },
+ { "remove", required_argument, NULL, 'r' },
{ "kmer", required_argument, NULL, 'k' },
{ "island", required_argument, NULL, 'T' },
{ "tip", required_argument, NULL, 't' },
@@ -279,6 +284,14 @@ static void addNewEdges(Graph& g, const vector<EdgeInfo>& eds)
}
}
+static void removeContig(vertex_descriptor v, Graph& g)
+{
+ clear_vertex(v, g);
+ remove_vertex(v, g);
+ g_removed.push_back(get(vertex_contig_index, g, v));
+ g_count.removed++;
+}
+
/** Remove the specified contig from the adjacency graph. */
static void removeContigs(Graph& g, vector<vertex_descriptor>& sc)
{
@@ -313,10 +326,7 @@ static void removeContigs(Graph& g, vector<vertex_descriptor>& sc)
else
continue;
- clear_vertex(v, g);
- remove_vertex(v, g);
- g_removed.push_back(get(vertex_contig_index, g, v));
- g_count.removed++;
+ removeContig(v, g);
}
sc.swap(out);
}
@@ -457,6 +467,9 @@ int main(int argc, char** argv)
case 'i':
arg >> opt::ignorePath;
break;
+ case 'r':
+ arg >> opt::removePath;
+ break;
case 'k':
arg >> opt::k;
break;
@@ -536,6 +549,22 @@ int main(int argc, char** argv)
printGraphStats(cerr, g);
}
+ // Remove list of contigs
+ if (!opt::removePath.empty()) {
+ ifstream in(opt::removePath.c_str());
+ assert(in.good());
+ string s;
+ size_t b = g_removed.size();
+ while (in >> s) {
+ size_t i = get(g_contigNames, s);
+ removeContig(ContigNode(i,0), g);
+ }
+ assert(in.eof());
+ if (opt::verbose)
+ cerr << "Removed " << g_removed.size() - b
+ << " contigs.\n";
+ }
+
// Remove shims.
if (opt::shim)
removeShims(g, seen);
diff --git a/FilterGraph/Makefile.in b/FilterGraph/Makefile.in
index 97d0ea9..5663710 100644
--- a/FilterGraph/Makefile.in
+++ b/FilterGraph/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-filtergraph$(EXEEXT)
subdir = FilterGraph
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -71,15 +98,39 @@ abyss_filtergraph_DEPENDENCIES = $(top_builddir)/Graph/libgraph.a \
$(top_builddir)/Common/libcommon.a
abyss_filtergraph_LINK = $(CXXLD) $(abyss_filtergraph_CXXFLAGS) \
$(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(abyss_filtergraph_SOURCES)
DIST_SOURCES = $(abyss_filtergraph_SOURCES)
am__can_run_installinfo = \
@@ -87,12 +138,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -240,10 +309,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -264,16 +334,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-filtergraph$(EXEEXT): $(abyss_filtergraph_OBJECTS) $(abyss_filtergraph_DEPENDENCIES) $(EXTRA_abyss_filtergraph_DEPENDENCIES)
@rm -f abyss-filtergraph$(EXEEXT)
- $(abyss_filtergraph_LINK) $(abyss_filtergraph_OBJECTS) $(abyss_filtergraph_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_filtergraph_LINK) $(abyss_filtergraph_OBJECTS) $(abyss_filtergraph_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -284,53 +356,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/abyss_filtergraph-FilterGraph.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
abyss_filtergraph-FilterGraph.o: FilterGraph.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo '$(srcdir)/'`FilterGraph.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo $(DEPDIR)/abyss_filtergraph-FilterGraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FilterGraph.cpp' object='abyss_filtergraph-FilterGraph.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo '$(srcdir)/'`FilterGraph.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo $(DEPDIR)/abyss_filtergraph-FilterGraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FilterGraph.cpp' object='abyss_filtergraph-FilterGraph.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo '$(srcdir)/'`FilterGraph.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo '$(srcdir)/'`FilterGraph.cpp
abyss_filtergraph-FilterGraph.obj: FilterGraph.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -MT abyss_filtergraph-FilterGraph.obj -MD -MP -MF $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.obj `if test -f 'FilterGraph.cpp'; then $(CYGPATH_W) 'FilterGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/FilterGraph.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo $(DEPDIR)/abyss_filtergraph-FilterGraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='FilterGraph.cpp' object='abyss_filtergraph-FilterGraph.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -MT abyss_filtergraph-FilterGraph.obj -MD -MP -MF $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.obj `if test -f 'FilterGraph.cpp'; then $(CYGPATH_W) 'FilterGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/FilterGraph.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_filtergraph-FilterGraph.Tpo $(DEPDIR)/abyss_filtergraph-FilterGraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='FilterGraph.cpp' object='abyss_filtergraph-FilterGraph.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -c -o abyss_filtergraph-FilterGraph.obj `if test -f 'FilterGraph.cpp'; then $(CYGPATH_W) 'FilterGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/FilterGraph.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_filtergraph_CPPFLAGS) $(CPPFLAGS) $(abyss_filtergraph_CXXFLAGS) $(CXXFLAGS) -c -o abyss_filtergraph-FilterGraph.obj `if test -f 'FilterGraph.cpp'; then $(CYGPATH_W) 'FilterGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/FilterGraph.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -342,15 +403,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -359,9 +416,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -515,18 +573,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Graph/AdjIO.h b/Graph/AdjIO.h
index 3e98f50..8f1c342 100644
--- a/Graph/AdjIO.h
+++ b/Graph/AdjIO.h
@@ -130,7 +130,7 @@ std::istream& read_adj(std::istream& in, ContigGraph<Graph>& g,
if (adjFormat || faiFormat) {
assert(num_vertices(g) == 0);
in.clear();
- in.seekg(std::ios_base::beg);
+ in.seekg(0, std::ios::beg);
assert(in);
for (std::string uname; in >> uname;) {
vertex_property_type vp;
@@ -155,7 +155,7 @@ std::istream& read_adj(std::istream& in, ContigGraph<Graph>& g,
// Read the edges.
in.clear();
- in.seekg(std::ios_base::beg);
+ in.seekg(0, std::ios::beg);
assert(in);
for (std::string name; in >> name;) {
if (adjFormat)
@@ -169,7 +169,8 @@ std::istream& read_adj(std::istream& in, ContigGraph<Graph>& g,
if (!adjFormat) {
readDistEdges(ss, g, u ^ sense, betterEP);
} else
- for (std::string vname; ss >> vname >> std::ws;) {
+ for (std::string vname; ss >> vname;) {
+ ss >> std::ws;
vertex_descriptor v = find_vertex(vname, g);
assert(!edge(u ^ sense, v ^ sense, g).second);
if (ss.peek() == '[') {
diff --git a/Graph/Makefile.in b/Graph/Makefile.in
index 16c083c..34c5517 100644
--- a/Graph/Makefile.in
+++ b/Graph/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,23 +16,51 @@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-gc$(EXEEXT) abyss-todot$(EXEEXT)
subdir = Graph
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -65,6 +92,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libgraph_a_AR = $(AR) $(ARFLAGS)
libgraph_a_LIBADD =
am_libgraph_a_OBJECTS = libgraph_a-ConstrainedSearch.$(OBJEXT)
@@ -80,19 +111,51 @@ abyss_todot_DEPENDENCIES = libgraph.a \
$(top_builddir)/Common/libcommon.a
abyss_todot_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) \
$(abyss_todot_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libgraph_a_SOURCES) $(abyss_gc_SOURCES) \
$(abyss_todot_SOURCES)
DIST_SOURCES = $(libgraph_a_SOURCES) $(abyss_gc_SOURCES) \
@@ -102,12 +165,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -269,10 +350,11 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libgraph.a: $(libgraph_a_OBJECTS) $(libgraph_a_DEPENDENCIES) $(EXTRA_libgraph_a_DEPENDENCIES)
- -rm -f libgraph.a
- $(libgraph_a_AR) libgraph.a $(libgraph_a_OBJECTS) $(libgraph_a_LIBADD)
- $(RANLIB) libgraph.a
+ $(AM_V_at)-rm -f libgraph.a
+ $(AM_V_AR)$(libgraph_a_AR) libgraph.a $(libgraph_a_OBJECTS) $(libgraph_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libgraph.a
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -282,10 +364,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -306,19 +389,22 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-gc$(EXEEXT): $(abyss_gc_OBJECTS) $(abyss_gc_DEPENDENCIES) $(EXTRA_abyss_gc_DEPENDENCIES)
@rm -f abyss-gc$(EXEEXT)
- $(CXXLINK) $(abyss_gc_OBJECTS) $(abyss_gc_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_gc_OBJECTS) $(abyss_gc_LDADD) $(LIBS)
+
abyss-todot$(EXEEXT): $(abyss_todot_OBJECTS) $(abyss_todot_DEPENDENCIES) $(EXTRA_abyss_todot_DEPENDENCIES)
@rm -f abyss-todot$(EXEEXT)
- $(abyss_todot_LINK) $(abyss_todot_OBJECTS) $(abyss_todot_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_todot_LINK) $(abyss_todot_OBJECTS) $(abyss_todot_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -331,95 +417,84 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/libgraph_a-ConstrainedSearch.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
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libgraph_a-ConstrainedSearch.o: ConstrainedSearch.cpp
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libgraph_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libgraph_a-ConstrainedSearch.o -MD -MP -MF $(DEPDIR)/libgraph_a-ConstrainedSearch.Tpo -c -o libgraph_a-ConstrainedSearch.o `test -f 'ConstrainedSearch.cpp' || echo '$(srcdir)/'`ConstrainedSearch.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libgraph_a-ConstrainedSearch.Tpo $(DEPDIR)/libgraph_a-ConstrainedSearch.Po
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libgraph_a-ConstrainedSearch.obj: ConstrainedSearch.cpp
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libgraph_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libgraph_a-ConstrainedSearch.obj -MD -MP -MF $(DEPDIR)/libgraph_a-ConstrainedSearch.Tpo -c -o libgraph_a-ConstrainedSearch.obj `if test -f 'ConstrainedSearch.cpp'; then $(CYGPATH_W) 'ConstrainedSearch.cpp'; else $(CYGPATH_W) '$(srcdir)/ConstrainedSearch.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/libgraph_a-ConstrainedSearch.Tpo $(DEPDIR)/libgraph_a-ConstrainedSearch.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libgraph_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libgraph_a-ConstrainedSearch.obj `if test -f 'ConstrainedSearch.cpp'; then $(CYGPATH_W) 'ConstrainedSearch.cpp'; else $(CYGPATH_W) '$(srcdir)/ConstrainedSearch.cpp'; fi`
abyss_gc-gc.o: gc.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_gc_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_gc-gc.o -MD -MP -MF $(DEPDIR)/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo '$(srcdir)/'`gc.cc
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='gc.cc' object='abyss_gc-gc.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_gc_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_gc-gc.o -MD -MP -MF $(DEPDIR)/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo '$(srcdir)/'`gc.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_gc-gc.Tpo $(DEPDIR)/abyss_gc-gc.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='gc.cc' object='abyss_gc-gc.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_gc_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo '$(srcdir)/'`gc.cc
abyss_gc-gc.obj: gc.cc
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_gc_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_gc-gc.obj -MD -MP -MF $(DEPDIR)/abyss_gc-gc.Tpo -c -o abyss_gc-gc.obj `if test -f 'gc.cc'; then $(CYGPATH_W) 'gc.cc'; else $(CYGPATH_W) '$(srcdir)/gc.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_gc-gc.Tpo $(DEPDIR)/abyss_gc-gc.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_gc_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_gc-gc.obj `if test -f 'gc.cc'; then $(CYGPATH_W) 'gc.cc'; else $(CYGPATH_W) '$(srcdir)/gc.cc'; fi`
abyss_todot-todot.o: todot.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_todot_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_todot-todot.o -MD -MP -MF $(DEPDIR)/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo '$(srcdir)/'`todot.cc
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='todot.cc' object='abyss_todot-todot.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_todot_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_todot-todot.o -MD -MP -MF $(DEPDIR)/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo '$(srcdir)/'`todot.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_todot-todot.Tpo $(DEPDIR)/abyss_todot-todot.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='todot.cc' object='abyss_todot-todot.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_todot_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo '$(srcdir)/'`todot.cc
abyss_todot-todot.obj: todot.cc
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_todot_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_todot-todot.obj -MD -MP -MF $(DEPDIR)/abyss_todot-todot.Tpo -c -o abyss_todot-todot.obj `if test -f 'todot.cc'; then $(CYGPATH_W) 'todot.cc'; else $(CYGPATH_W) '$(srcdir)/todot.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_todot-todot.Tpo $(DEPDIR)/abyss_todot-todot.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_todot_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_todot-todot.obj `if test -f 'todot.cc'; then $(CYGPATH_W) 'todot.cc'; else $(CYGPATH_W) '$(srcdir)/todot.cc'; fi`
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -431,15 +506,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -448,9 +519,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -605,18 +677,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstLIBRARIES cscopelist ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/KAligner/Makefile.in b/KAligner/Makefile.in
index be84430..42bcb6b 100644
--- a/KAligner/Makefile.in
+++ b/KAligner/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = KAligner$(EXEEXT)
subdir = KAligner
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -70,19 +97,51 @@ KAligner_DEPENDENCIES = $(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
KAligner_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) \
$(KAligner_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(KAligner_SOURCES)
DIST_SOURCES = $(KAligner_SOURCES)
am__can_run_installinfo = \
@@ -90,12 +149,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -244,10 +321,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -268,16 +346,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
KAligner$(EXEEXT): $(KAligner_OBJECTS) $(KAligner_DEPENDENCIES) $(EXTRA_KAligner_DEPENDENCIES)
@rm -f KAligner$(EXEEXT)
- $(KAligner_LINK) $(KAligner_OBJECTS) $(KAligner_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(KAligner_LINK) $(KAligner_OBJECTS) $(KAligner_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -289,67 +369,56 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/KAligner-KAligner.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
KAligner-KAligner.o: KAligner.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-KAligner.o -MD -MP -MF $(DEPDIR)/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo '$(srcdir)/'`KAligner.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/KAligner-KAligner.Tpo $(DEPDIR)/KAligner-KAligner.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='KAligner.cpp' object='KAligner-KAligner.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-KAligner.o -MD -MP -MF $(DEPDIR)/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo '$(srcdir)/'`KAligner.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/KAligner-KAligner.Tpo $(DEPDIR)/KAligner-KAligner.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='KAligner.cpp' object='KAligner-KAligner.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo '$(srcdir)/'`KAligner.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo '$(srcdir)/'`KAligner.cpp
KAligner-KAligner.obj: KAligner.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-KAligner.obj -MD -MP -MF $(DEPDIR)/KAligner-KAligner.Tpo -c -o KAligner-KAligner.obj `if test -f 'KAligner.cpp'; then $(CYGPATH_W) 'KAligner.cpp'; else $(CYGPATH_W) '$(srcdir)/KAligner.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/KAligner-KAligner.Tpo $(DEPDIR)/KAligner-KAligner.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='KAligner.cpp' object='KAligner-KAligner.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-KAligner.obj -MD -MP -MF $(DEPDIR)/KAligner-KAligner.Tpo -c -o KAligner-KAligner.obj `if test -f 'KAligner.cpp'; then $(CYGPATH_W) 'KAligner.cpp'; else $(CYGPATH_W) '$(srcdir)/KAligner.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/KAligner-KAligner.Tpo $(DEPDIR)/KAligner-KAligner.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='KAligner.cpp' object='KAligner-KAligner.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-KAligner.obj `if test -f 'KAligner.cpp'; then $(CYGPATH_W) 'KAligner.cpp'; else $(CYGPATH_W) '$(srcdir)/KAligner.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-KAligner.obj `if test -f 'KAligner.cpp'; then $(CYGPATH_W) 'KAligner.cpp'; else $(CYGPATH_W) '$(srcdir)/KAligner.cpp'; fi`
KAligner-Aligner.o: Aligner.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-Aligner.o -MD -MP -MF $(DEPDIR)/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo '$(srcdir)/'`Aligner.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/KAligner-Aligner.Tpo $(DEPDIR)/KAligner-Aligner.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Aligner.cpp' object='KAligner-Aligner.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-Aligner.o -MD -MP -MF $(DEPDIR)/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo '$(srcdir)/'`Aligner.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/KAligner-Aligner.Tpo $(DEPDIR)/KAligner-Aligner.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Aligner.cpp' object='KAligner-Aligner.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo '$(srcdir)/'`Aligner.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo '$(srcdir)/'`Aligner.cpp
KAligner-Aligner.obj: Aligner.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-Aligner.obj -MD -MP -MF $(DEPDIR)/KAligner-Aligner.Tpo -c -o KAligner-Aligner.obj `if test -f 'Aligner.cpp'; then $(CYGPATH_W) 'Aligner.cpp'; else $(CYGPATH_W) '$(srcdir)/Aligner.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/KAligner-Aligner.Tpo $(DEPDIR)/KAligner-Aligner.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Aligner.cpp' object='KAligner-Aligner.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT KAligner-Aligner.obj -MD -MP -MF $(DEPDIR)/KAligner-Aligner.Tpo -c -o KAligner-Aligner.obj `if test -f 'Aligner.cpp'; then $(CYGPATH_W) 'Aligner.cpp'; else $(CYGPATH_W) '$(srcdir)/Aligner.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/KAligner-Aligner.Tpo $(DEPDIR)/KAligner-Aligner.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Aligner.cpp' object='KAligner-Aligner.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-Aligner.obj `if test -f 'Aligner.cpp'; then $(CYGPATH_W) 'Aligner.cpp'; else $(CYGPATH_W) '$(srcdir)/Aligner.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(KAligner_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o KAligner-Aligner.obj `if test -f 'Aligner.cpp'; then $(CYGPATH_W) 'Aligner.cpp'; else $(CYGPATH_W) '$(srcdir)/Aligner.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -361,15 +430,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -378,9 +443,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -534,18 +600,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Layout/Makefile.in b/Layout/Makefile.in
index a51de8a..4504628 100644
--- a/Layout/Makefile.in
+++ b/Layout/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-layout$(EXEEXT)
subdir = Layout
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -66,15 +93,39 @@ PROGRAMS = $(bin_PROGRAMS)
am_abyss_layout_OBJECTS = abyss_layout-layout.$(OBJEXT)
abyss_layout_OBJECTS = $(am_abyss_layout_OBJECTS)
abyss_layout_DEPENDENCIES = $(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(abyss_layout_SOURCES)
DIST_SOURCES = $(abyss_layout_SOURCES)
am__can_run_installinfo = \
@@ -82,12 +133,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -227,10 +296,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -251,16 +321,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-layout$(EXEEXT): $(abyss_layout_OBJECTS) $(abyss_layout_DEPENDENCIES) $(EXTRA_abyss_layout_DEPENDENCIES)
@rm -f abyss-layout$(EXEEXT)
- $(CXXLINK) $(abyss_layout_OBJECTS) $(abyss_layout_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_layout_OBJECTS) $(abyss_layout_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -271,53 +343,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/abyss_layout-layout.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
abyss_layout-layout.o: layout.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_layout-layout.o -MD -MP -MF $(DEPDIR)/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo '$(srcdir)/'`layout.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_layout-layout.Tpo $(DEPDIR)/abyss_layout-layout.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='layout.cc' object='abyss_layout-layout.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_layout-layout.o -MD -MP -MF $(DEPDIR)/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo '$(srcdir)/'`layout.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_layout-layout.Tpo $(DEPDIR)/abyss_layout-layout.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='layout.cc' object='abyss_layout-layout.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo '$(srcdir)/'`layout.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo '$(srcdir)/'`layout.cc
abyss_layout-layout.obj: layout.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_layout-layout.obj -MD -MP -MF $(DEPDIR)/abyss_layout-layout.Tpo -c -o abyss_layout-layout.obj `if test -f 'layout.cc'; then $(CYGPATH_W) 'layout.cc'; else $(CYGPATH_W) '$(srcdir)/layout.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_layout-layout.Tpo $(DEPDIR)/abyss_layout-layout.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='layout.cc' object='abyss_layout-layout.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_layout-layout.obj -MD -MP -MF $(DEPDIR)/abyss_layout-layout.Tpo -c -o abyss_layout-layout.obj `if test -f 'layout.cc'; then $(CYGPATH_W) 'layout.cc'; else $(CYGPATH_W) '$(srcdir)/layout.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_layout-layout.Tpo $(DEPDIR)/abyss_layout-layout.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='layout.cc' object='abyss_layout-layout.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_layout-layout.obj `if test -f 'layout.cc'; then $(CYGPATH_W) 'layout.cc'; else $(CYGPATH_W) '$(srcdir)/layout.cc'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_layout_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_layout-layout.obj `if test -f 'layout.cc'; then $(CYGPATH_W) 'layout.cc'; else $(CYGPATH_W) '$(srcdir)/layout.cc'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -329,15 +390,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -346,9 +403,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -502,18 +560,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Makefile.am b/Makefile.am
index 6620981..14d63a8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -37,4 +37,4 @@ SUBDIRS = \
FilterGraph
%.html: %.md
- multimarkdown $< >$@
+ -multimarkdown $< >$@
diff --git a/Makefile.in b/Makefile.in
index 0e23a00..1bd58f7 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
esac; \
- test $$am__dry = yes; \
- }
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -50,9 +77,9 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = .
-DIST_COMMON = $(am__configure_deps) $(dist_doc_DATA) \
- $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
- $(srcdir)/config.h.in $(top_srcdir)/configure ChangeLog \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(top_srcdir)/configure $(am__configure_deps) \
+ $(srcdir)/config.h.in $(dist_doc_DATA) ChangeLog compile \
depcomp install-sh missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -64,15 +91,28 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
SOURCES =
DIST_SOURCES =
-RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
- html-recursive info-recursive install-data-recursive \
- install-dvi-recursive install-exec-recursive \
- install-html-recursive install-info-recursive \
- install-pdf-recursive install-ps-recursive install-recursive \
- installcheck-recursive installdirs-recursive pdf-recursive \
- ps-recursive uninstall-recursive
+RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
+ ctags-recursive dvi-recursive html-recursive info-recursive \
+ install-data-recursive install-dvi-recursive \
+ install-exec-recursive install-html-recursive \
+ install-info-recursive install-pdf-recursive \
+ install-ps-recursive install-recursive installcheck-recursive \
+ installdirs-recursive pdf-recursive ps-recursive \
+ tags-recursive uninstall-recursive
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -109,9 +149,30 @@ am__installdirs = "$(DESTDIR)$(docdir)"
DATA = $(dist_doc_DATA)
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
- $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+am__recursive_targets = \
+ $(RECURSIVE_TARGETS) \
+ $(RECURSIVE_CLEAN_TARGETS) \
+ $(am__extra_recursive_targets)
+AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
cscope distdir dist dist-all distcheck
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
+ $(LISP)config.h.in
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
CSCOPE = cscope
@@ -165,6 +226,7 @@ distcleancheck_listfiles = find . -type f -print
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -332,8 +394,8 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @if test ! -f $@; then rm -f stamp-h1; else :; fi
- @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+ @test -f $@ || rm -f stamp-h1
+ @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -373,17 +435,20 @@ uninstall-dist_docDATA:
# (1) if the variable is set in 'config.status', edit 'config.status'
# (which will cause the Makefiles to be regenerated when you run 'make');
# (2) otherwise, pass the desired values on the 'make' command line.
-$(RECURSIVE_TARGETS):
- @fail= failcom='exit 1'; \
- for f in x $$MAKEFLAGS; do \
- case $$f in \
- *=* | --[!k]*);; \
- *k*) failcom='fail=yes';; \
- esac; \
- done; \
+$(am__recursive_targets):
+ @fail=; \
+ if $(am__make_keepgoing); then \
+ failcom='fail=yes'; \
+ else \
+ failcom='exit 1'; \
+ fi; \
dot_seen=no; \
target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
+ case "$@" in \
+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+ *) list='$(SUBDIRS)' ;; \
+ esac; \
+ for subdir in $$list; do \
echo "Making $$target in $$subdir"; \
if test "$$subdir" = "."; then \
dot_seen=yes; \
@@ -398,61 +463,12 @@ $(RECURSIVE_TARGETS):
$(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
fi; test -z "$$fail"
-$(RECURSIVE_CLEAN_TARGETS):
- @fail= failcom='exit 1'; \
- for f in x $$MAKEFLAGS; do \
- case $$f in \
- *=* | --[!k]*);; \
- *k*) failcom='fail=yes';; \
- esac; \
- done; \
- dot_seen=no; \
- case "$@" in \
- distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
- *) list='$(SUBDIRS)' ;; \
- esac; \
- rev=''; for subdir in $$list; do \
- if test "$$subdir" = "."; then :; else \
- rev="$$subdir $$rev"; \
- fi; \
- done; \
- rev="$$rev ."; \
- target=`echo $@ | sed s/-recursive//`; \
- for subdir in $$rev; do \
- echo "Making $$target in $$subdir"; \
- if test "$$subdir" = "."; then \
- local_target="$$target-am"; \
- else \
- local_target="$$target"; \
- fi; \
- ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
- || eval $$failcom; \
- done && test -z "$$fail"
-tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
- done
-ctags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
-cscopelist-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) cscopelist); \
- done
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-recursive
+TAGS: tags
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
@@ -468,12 +484,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
fi; \
done; \
- list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -485,15 +496,11 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-recursive
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -502,18 +509,16 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
-
cscope: cscope.files
test ! -s cscope.files \
|| $(CSCOPE) -b -q $(AM_CSCOPEFLAGS) $(CSCOPEFLAGS) -i cscope.files $(CSCOPE_ARGS)
-
clean-cscope:
-rm -f cscope.files
+cscope.files: clean-cscope cscopelist
+cscopelist: cscopelist-recursive
-cscope.files: clean-cscope cscopelist-recursive cscopelist
-
-cscopelist: cscopelist-recursive $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -611,10 +616,16 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
$(am__post_remove_distdir)
@@ -647,9 +658,9 @@ distcheck: dist
*.zip*) \
unzip $(distdir).zip ;;\
esac
- chmod -R a-w $(distdir); chmod a+w $(distdir)
- mkdir $(distdir)/_build
- mkdir $(distdir)/_inst
+ chmod -R a-w $(distdir)
+ chmod u+w $(distdir)
+ mkdir $(distdir)/_build $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
@@ -818,30 +829,27 @@ ps-am:
uninstall-am: uninstall-dist_docDATA
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
- cscopelist-recursive ctags-recursive install-am install-strip \
- tags-recursive
-
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
- all all-am am--refresh check check-am clean clean-cscope \
- clean-generic cscope cscopelist cscopelist-recursive ctags \
- ctags-recursive dist dist-all dist-bzip2 dist-gzip dist-lzip \
- dist-shar dist-tarZ dist-xz dist-zip distcheck distclean \
- distclean-generic distclean-hdr distclean-tags distcleancheck \
- distdir distuninstallcheck dvi dvi-am html html-am info \
- info-am install install-am install-data install-data-am \
- install-dist_docDATA install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
- uninstall-dist_docDATA
+.MAKE: $(am__recursive_targets) all install-am install-strip
+
+.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
+ am--refresh check check-am clean clean-cscope clean-generic \
+ cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
+ dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
+ distcheck distclean distclean-generic distclean-hdr \
+ distclean-tags distcleancheck distdir distuninstallcheck dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dist_docDATA install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ installdirs-am maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
+ tags-am uninstall uninstall-am uninstall-dist_docDATA
%.html: %.md
- multimarkdown $< >$@
+ -multimarkdown $< >$@
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
diff --git a/Map/Makefile.in b/Map/Makefile.in
index ba5dd10..1f7ec91 100644
--- a/Map/Makefile.in
+++ b/Map/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ POST_UNINSTALL = :
bin_PROGRAMS = abyss-index$(EXEEXT) abyss-map$(EXEEXT) \
abyss-overlap$(EXEEXT)
subdir = Map
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -83,15 +110,39 @@ abyss_overlap_DEPENDENCIES = $(top_builddir)/FMIndex/libfmindex.a \
$(top_builddir)/Common/libcommon.a
abyss_overlap_LINK = $(CXXLD) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(abyss_index_SOURCES) $(abyss_map_SOURCES) \
$(abyss_overlap_SOURCES)
DIST_SOURCES = $(abyss_index_SOURCES) $(abyss_map_SOURCES) \
@@ -101,12 +152,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -278,10 +347,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -302,22 +372,26 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
abyss-index$(EXEEXT): $(abyss_index_OBJECTS) $(abyss_index_DEPENDENCIES) $(EXTRA_abyss_index_DEPENDENCIES)
@rm -f abyss-index$(EXEEXT)
- $(CXXLINK) $(abyss_index_OBJECTS) $(abyss_index_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_index_OBJECTS) $(abyss_index_LDADD) $(LIBS)
+
abyss-map$(EXEEXT): $(abyss_map_OBJECTS) $(abyss_map_DEPENDENCIES) $(EXTRA_abyss_map_DEPENDENCIES)
@rm -f abyss-map$(EXEEXT)
- $(abyss_map_LINK) $(abyss_map_OBJECTS) $(abyss_map_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_map_LINK) $(abyss_map_OBJECTS) $(abyss_map_LDADD) $(LIBS)
+
abyss-overlap$(EXEEXT): $(abyss_overlap_OBJECTS) $(abyss_overlap_DEPENDENCIES) $(EXTRA_abyss_overlap_DEPENDENCIES)
@rm -f abyss-overlap$(EXEEXT)
- $(abyss_overlap_LINK) $(abyss_overlap_OBJECTS) $(abyss_overlap_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_overlap_LINK) $(abyss_overlap_OBJECTS) $(abyss_overlap_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -330,81 +404,70 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/abyss_overlap-overlap.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
abyss_index-index.o: index.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_index-index.o -MD -MP -MF $(DEPDIR)/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo '$(srcdir)/'`index.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_index-index.Tpo $(DEPDIR)/abyss_index-index.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='index.cc' object='abyss_index-index.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_index-index.o -MD -MP -MF $(DEPDIR)/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo '$(srcdir)/'`index.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_index-index.Tpo $(DEPDIR)/abyss_index-index.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='index.cc' object='abyss_index-index.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_index-index.o `test -f 'index.cc' || echo '$(srcdir)/'`index.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_index-index.o `test -f 'index.cc' || echo '$(srcdir)/'`index.cc
abyss_index-index.obj: index.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_index-index.obj -MD -MP -MF $(DEPDIR)/abyss_index-index.Tpo -c -o abyss_index-index.obj `if test -f 'index.cc'; then $(CYGPATH_W) 'index.cc'; else $(CYGPATH_W) '$(srcdir)/index.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_index-index.Tpo $(DEPDIR)/abyss_index-index.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='index.cc' object='abyss_index-index.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_index-index.obj -MD -MP -MF $(DEPDIR)/abyss_index-index.Tpo -c -o abyss_index-index.obj `if test -f 'index.cc'; then $(CYGPATH_W) 'index.cc'; else $(CYGPATH_W) '$(srcdir)/index.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_index-index.Tpo $(DEPDIR)/abyss_index-index.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='index.cc' object='abyss_index-index.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_index-index.obj `if test -f 'index.cc'; then $(CYGPATH_W) 'index.cc'; else $(CYGPATH_W) '$(srcdir)/index.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_index_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_index-index.obj `if test -f 'index.cc'; then $(CYGPATH_W) 'index.cc'; else $(CYGPATH_W) '$(srcdir)/index.cc'; fi`
abyss_map-map.o: map.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -MT abyss_map-map.o -MD -MP -MF $(DEPDIR)/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo '$(srcdir)/'`map.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_map-map.Tpo $(DEPDIR)/abyss_map-map.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='map.cc' object='abyss_map-map.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -MT abyss_map-map.o -MD -MP -MF $(DEPDIR)/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo '$(srcdir)/'`map.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_map-map.Tpo $(DEPDIR)/abyss_map-map.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='map.cc' object='abyss_map-map.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -c -o abyss_map-map.o `test -f 'map.cc' || echo '$(srcdir)/'`map.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -c -o abyss_map-map.o `test -f 'map.cc' || echo '$(srcdir)/'`map.cc
abyss_map-map.obj: map.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -MT abyss_map-map.obj -MD -MP -MF $(DEPDIR)/abyss_map-map.Tpo -c -o abyss_map-map.obj `if test -f 'map.cc'; then $(CYGPATH_W) 'map.cc'; else $(CYGPATH_W) '$(srcdir)/map.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_map-map.Tpo $(DEPDIR)/abyss_map-map.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='map.cc' object='abyss_map-map.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -MT abyss_map-map.obj -MD -MP -MF $(DEPDIR)/abyss_map-map.Tpo -c -o abyss_map-map.obj `if test -f 'map.cc'; then $(CYGPATH_W) 'map.cc'; else $(CYGPATH_W) '$(srcdir)/map.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_map-map.Tpo $(DEPDIR)/abyss_map-map.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='map.cc' object='abyss_map-map.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -c -o abyss_map-map.obj `if test -f 'map.cc'; then $(CYGPATH_W) 'map.cc'; else $(CYGPATH_W) '$(srcdir)/map.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_map_CPPFLAGS) $(CPPFLAGS) $(abyss_map_CXXFLAGS) $(CXXFLAGS) -c -o abyss_map-map.obj `if test -f 'map.cc'; then $(CYGPATH_W) 'map.cc'; else $(CYGPATH_W) '$(srcdir)/map.cc'; fi`
abyss_overlap-overlap.o: overlap.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -MT abyss_overlap-overlap.o -MD -MP -MF $(DEPDIR)/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo '$(srcdir)/'`overlap.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_overlap-overlap.Tpo $(DEPDIR)/abyss_overlap-overlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='overlap.cc' object='abyss_overlap-overlap.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -MT abyss_overlap-overlap.o -MD -MP -MF $(DEPDIR)/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo '$(srcdir)/'`overlap.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_overlap-overlap.Tpo $(DEPDIR)/abyss_overlap-overlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='overlap.cc' object='abyss_overlap-overlap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo '$(srcdir)/'`overlap.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo '$(srcdir)/'`overlap.cc
abyss_overlap-overlap.obj: overlap.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -MT abyss_overlap-overlap.obj -MD -MP -MF $(DEPDIR)/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.obj `if test -f 'overlap.cc'; then $(CYGPATH_W) 'overlap.cc'; else $(CYGPATH_W) '$(srcdir)/overlap.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_overlap-overlap.Tpo $(DEPDIR)/abyss_overlap-overlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='overlap.cc' object='abyss_overlap-overlap.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -MT abyss_overlap-overlap.obj -MD -MP -MF $(DEPDIR)/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.obj `if test -f 'overlap.cc'; then $(CYGPATH_W) 'overlap.cc'; else $(CYGPATH_W) '$(srcdir)/overlap.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_overlap-overlap.Tpo $(DEPDIR)/abyss_overlap-overlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='overlap.cc' object='abyss_overlap-overlap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -c -o abyss_overlap-overlap.obj `if test -f 'overlap.cc'; then $(CYGPATH_W) 'overlap.cc'; else $(CYGPATH_W) '$(srcdir)/overlap.cc'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_overlap_CPPFLAGS) $(CPPFLAGS) $(abyss_overlap_CXXFLAGS) $(CXXFLAGS) -c -o abyss_overlap-overlap.obj `if test -f 'overlap.cc'; then $(CYGPATH_W) 'overlap.cc'; else $(CYGPATH_W) '$(srcdir)/overlap.cc'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -416,15 +479,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -433,9 +492,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -589,18 +649,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Map/index.cc b/Map/index.cc
index 66a3e11..33dfbd8 100644
--- a/Map/index.cc
+++ b/Map/index.cc
@@ -172,8 +172,6 @@ static void buildFMIndex(FMIndex& fm, const string& path)
int main(int argc, char **argv)
{
- checkPopcnt();
-
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
diff --git a/Map/map.cc b/Map/map.cc
index ed67733..183405f 100644
--- a/Map/map.cc
+++ b/Map/map.cc
@@ -19,6 +19,7 @@
#include <stdint.h>
#include <string>
#include <utility>
+#include <queue>
#if _OPENMP
# include <omp.h>
#endif
@@ -45,6 +46,9 @@ static const char USAGE_MESSAGE[] =
" -s, --sample=N sample the suffix array [1]\n"
" -d, --dup identify and print duplicate sequence\n"
" IDs between QUERY and TARGET\n"
+" --order print alignments in the same order as\n"
+" read from QUERY\n"
+" --no-order print alignments ASAP [default]\n"
" --chastity discard unchaste reads\n"
" --no-chastity do not discard unchaste reads [default]\n"
" -v, --verbose display verbose output\n"
@@ -66,6 +70,8 @@ namespace opt {
/** Identify duplicate and subsumed sequences. */
static bool dup = false;
+ static int order;
+
/** Verbose output. */
static int verbose;
}
@@ -79,6 +85,8 @@ static const struct option longopts[] = {
{ "min-align", required_argument, NULL, 'l' },
{ "dup", no_argument, NULL, 'd' },
{ "threads", required_argument, NULL, 'j' },
+ { "order", no_argument, &opt::order, 1 },
+ { "no-order", no_argument, &opt::order, 0 },
{ "verbose", no_argument, NULL, 'v' },
{ "chastity", no_argument, &opt::chastityFilter, 1 },
{ "no-chastity", no_argument, &opt::chastityFilter, 0 },
@@ -208,6 +216,8 @@ static void printDuplicates(const Match& m, const Match& rcm,
}
+static queue<string> g_pq;
+
/** Return the mapping of the specified sequence. */
static void find(const FastaIndex& faIndex, const FMIndex& fmIndex,
const FastqRecord& rec)
@@ -255,11 +265,22 @@ static void find(const FastaIndex& faIndex, const FMIndex& fmIndex,
sam.mapq = 0;
}
+ bool print = opt::order == 0;
+ do {
#pragma omp critical(cout)
- {
- cout << sam << '\n';
- assert_good(cout, "stdout");
- }
+ {
+#pragma omp critical(g_pq)
+ if (!print) {
+ print = g_pq.front() == rec.id;
+ if (print)
+ g_pq.pop();
+ }
+ if (print) {
+ cout << sam << '\n';
+ assert_good(cout, "stdout");
+ }
+ }
+ } while (!print); // spinlock :(
if (sam.isUnmapped())
#pragma omp atomic
@@ -280,7 +301,13 @@ static void find(const FastaIndex& faIndex, const FMIndex& fmIndex,
for (FastqRecord rec;;) {
bool good;
#pragma omp critical(in)
- good = in >> rec;
+ {
+ good = in >> rec;
+ if (opt::order) {
+#pragma omp critical(g_pq)
+ g_pq.push(rec.id);
+ }
+ }
if (good)
find(faIndex, fmIndex, rec);
else
@@ -346,8 +373,6 @@ static void checkIndexes(const string& path,
int main(int argc, char** argv)
{
- checkPopcnt();
-
string commandLine;
{
ostringstream ss;
diff --git a/Map/overlap.cc b/Map/overlap.cc
index 5148356..02a63a2 100644
--- a/Map/overlap.cc
+++ b/Map/overlap.cc
@@ -346,8 +346,6 @@ static void checkIndexes(const string& path,
int main(int argc, char** argv)
{
- checkPopcnt();
-
string commandLine;
{
ostringstream ss;
diff --git a/MergePaths/Makefile.in b/MergePaths/Makefile.in
index 783e2f6..4b85d98 100644
--- a/MergePaths/Makefile.in
+++ b/MergePaths/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ POST_UNINSTALL = :
bin_PROGRAMS = MergePaths$(EXEEXT) MergeContigs$(EXEEXT) \
PathConsensus$(EXEEXT)
subdir = MergePaths
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -84,15 +111,39 @@ PathConsensus_DEPENDENCIES = $(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Align/libalign.a \
$(top_builddir)/Common/libcommon.a \
$(top_builddir)/dialign/libdialign.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(MergeContigs_SOURCES) $(MergePaths_SOURCES) \
$(PathConsensus_SOURCES)
DIST_SOURCES = $(MergeContigs_SOURCES) $(MergePaths_SOURCES) \
@@ -102,12 +153,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -285,10 +354,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -309,22 +379,26 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
MergeContigs$(EXEEXT): $(MergeContigs_OBJECTS) $(MergeContigs_DEPENDENCIES) $(EXTRA_MergeContigs_DEPENDENCIES)
@rm -f MergeContigs$(EXEEXT)
- $(CXXLINK) $(MergeContigs_OBJECTS) $(MergeContigs_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(MergeContigs_OBJECTS) $(MergeContigs_LDADD) $(LIBS)
+
MergePaths$(EXEEXT): $(MergePaths_OBJECTS) $(MergePaths_DEPENDENCIES) $(EXTRA_MergePaths_DEPENDENCIES)
@rm -f MergePaths$(EXEEXT)
- $(MergePaths_LINK) $(MergePaths_OBJECTS) $(MergePaths_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(MergePaths_LINK) $(MergePaths_OBJECTS) $(MergePaths_LDADD) $(LIBS)
+
PathConsensus$(EXEEXT): $(PathConsensus_OBJECTS) $(PathConsensus_DEPENDENCIES) $(EXTRA_PathConsensus_DEPENDENCIES)
@rm -f PathConsensus$(EXEEXT)
- $(CXXLINK) $(PathConsensus_OBJECTS) $(PathConsensus_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(PathConsensus_OBJECTS) $(PathConsensus_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -337,81 +411,70 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/PathConsensus-PathConsensus.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
MergeContigs-MergeContigs.o: MergeContigs.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MergeContigs-MergeContigs.o -MD -MP -MF $(DEPDIR)/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo '$(srcdir)/'`MergeContigs.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/MergeContigs-MergeContigs.Tpo $(DEPDIR)/MergeContigs-MergeContigs.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MergeContigs.cpp' object='MergeContigs-MergeContigs.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MergeContigs-MergeContigs.o -MD -MP -MF $(DEPDIR)/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo '$(srcdir)/'`MergeContigs.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/MergeContigs-MergeContigs.Tpo $(DEPDIR)/MergeContigs-MergeContigs.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MergeContigs.cpp' object='MergeContigs-MergeContigs.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo '$(srcdir)/'`MergeContigs.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo '$(srcdir)/'`MergeContigs.cpp
MergeContigs-MergeContigs.obj: MergeContigs.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MergeContigs-MergeContigs.obj -MD -MP -MF $(DEPDIR)/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.obj `if test -f 'MergeContigs.cpp'; then $(CYGPATH_W) 'MergeContigs.cpp'; else $(CYGPATH_W) '$(srcdir)/MergeContigs.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/MergeContigs-MergeContigs.Tpo $(DEPDIR)/MergeContigs-MergeContigs.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MergeContigs.cpp' object='MergeContigs-MergeContigs.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MergeContigs-MergeContigs.obj -MD -MP -MF $(DEPDIR)/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.obj `if test -f 'MergeContigs.cpp'; then $(CYGPATH_W) 'MergeContigs.cpp'; else $(CYGPATH_W) '$(srcdir)/MergeContigs.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/MergeContigs-MergeContigs.Tpo $(DEPDIR)/MergeContigs-MergeContigs.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MergeContigs.cpp' object='MergeContigs-MergeContigs.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MergeContigs-MergeContigs.obj `if test -f 'MergeContigs.cpp'; then $(CYGPATH_W) 'MergeContigs.cpp'; else $(CYGPATH_W) '$(srcdir)/MergeContigs.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergeContigs_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MergeContigs-MergeContigs.obj `if test -f 'MergeContigs.cpp'; then $(CYGPATH_W) 'MergeContigs.cpp'; else $(CYGPATH_W) '$(srcdir)/MergeContigs.cpp'; fi`
MergePaths-MergePaths.o: MergePaths.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -MT MergePaths-MergePaths.o -MD -MP -MF $(DEPDIR)/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo '$(srcdir)/'`MergePaths.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/MergePaths-MergePaths.Tpo $(DEPDIR)/MergePaths-MergePaths.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MergePaths.cpp' object='MergePaths-MergePaths.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -MT MergePaths-MergePaths.o -MD -MP -MF $(DEPDIR)/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo '$(srcdir)/'`MergePaths.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/MergePaths-MergePaths.Tpo $(DEPDIR)/MergePaths-MergePaths.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MergePaths.cpp' object='MergePaths-MergePaths.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo '$(srcdir)/'`MergePaths.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo '$(srcdir)/'`MergePaths.cpp
MergePaths-MergePaths.obj: MergePaths.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -MT MergePaths-MergePaths.obj -MD -MP -MF $(DEPDIR)/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.obj `if test -f 'MergePaths.cpp'; then $(CYGPATH_W) 'MergePaths.cpp'; else $(CYGPATH_W) '$(srcdir)/MergePaths.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/MergePaths-MergePaths.Tpo $(DEPDIR)/MergePaths-MergePaths.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='MergePaths.cpp' object='MergePaths-MergePaths.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -MT MergePaths-MergePaths.obj -MD -MP -MF $(DEPDIR)/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.obj `if test -f 'MergePaths.cpp'; then $(CYGPATH_W) 'MergePaths.cpp'; else $(CYGPATH_W) '$(srcdir)/MergePaths.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/MergePaths-MergePaths.Tpo $(DEPDIR)/MergePaths-MergePaths.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='MergePaths.cpp' object='MergePaths-MergePaths.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -c -o MergePaths-MergePaths.obj `if test -f 'MergePaths.cpp'; then $(CYGPATH_W) 'MergePaths.cpp'; else $(CYGPATH_W) '$(srcdir)/MergePaths.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(MergePaths_CPPFLAGS) $(CPPFLAGS) $(MergePaths_CXXFLAGS) $(CXXFLAGS) -c -o MergePaths-MergePaths.obj `if test -f 'MergePaths.cpp'; then $(CYGPATH_W) 'MergePaths.cpp'; else $(CYGPATH_W) '$(srcdir)/MergePaths.cpp'; fi`
PathConsensus-PathConsensus.o: PathConsensus.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathConsensus-PathConsensus.o -MD -MP -MF $(DEPDIR)/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo '$(srcdir)/'`PathConsensus.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PathConsensus-PathConsensus.Tpo $(DEPDIR)/PathConsensus-PathConsensus.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PathConsensus.cpp' object='PathConsensus-PathConsensus.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathConsensus-PathConsensus.o -MD -MP -MF $(DEPDIR)/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo '$(srcdir)/'`PathConsensus.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PathConsensus-PathConsensus.Tpo $(DEPDIR)/PathConsensus-PathConsensus.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PathConsensus.cpp' object='PathConsensus-PathConsensus.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo '$(srcdir)/'`PathConsensus.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo '$(srcdir)/'`PathConsensus.cpp
PathConsensus-PathConsensus.obj: PathConsensus.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathConsensus-PathConsensus.obj -MD -MP -MF $(DEPDIR)/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.obj `if test -f 'PathConsensus.cpp'; then $(CYGPATH_W) 'PathConsensus.cpp'; else $(CYGPATH_W) '$(srcdir)/PathConsensus.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PathConsensus-PathConsensus.Tpo $(DEPDIR)/PathConsensus-PathConsensus.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PathConsensus.cpp' object='PathConsensus-PathConsensus.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathConsensus-PathConsensus.obj -MD -MP -MF $(DEPDIR)/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.obj `if test -f 'PathConsensus.cpp'; then $(CYGPATH_W) 'PathConsensus.cpp'; else $(CYGPATH_W) '$(srcdir)/PathConsensus.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PathConsensus-PathConsensus.Tpo $(DEPDIR)/PathConsensus-PathConsensus.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PathConsensus.cpp' object='PathConsensus-PathConsensus.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathConsensus-PathConsensus.obj `if test -f 'PathConsensus.cpp'; then $(CYGPATH_W) 'PathConsensus.cpp'; else $(CYGPATH_W) '$(srcdir)/PathConsensus.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathConsensus_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathConsensus-PathConsensus.obj `if test -f 'PathConsensus.cpp'; then $(CYGPATH_W) 'PathConsensus.cpp'; else $(CYGPATH_W) '$(srcdir)/PathConsensus.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -423,15 +486,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -440,9 +499,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -596,18 +656,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Misc/Makefile.in b/Misc/Makefile.in
index ed34c2c..575213c 100644
--- a/Misc/Makefile.in
+++ b/Misc/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
@HAVE_GHC_TRUE at bin_PROGRAMS = abyss-samtobreak$(EXEEXT)
subdir = Misc
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -65,11 +92,31 @@ PROGRAMS = $(bin_PROGRAMS)
am_abyss_samtobreak_OBJECTS =
abyss_samtobreak_OBJECTS = $(am_abyss_samtobreak_OBJECTS)
abyss_samtobreak_LDADD = $(LDADD)
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(abyss_samtobreak_SOURCES)
DIST_SOURCES = $(abyss_samtobreak_SOURCES)
am__can_run_installinfo = \
@@ -77,10 +124,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
+ETAGS = etags
+CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -219,10 +286,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -243,7 +311,8 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
@@ -256,14 +325,58 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-cscope cscopelist:
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ set x; \
+ here=`pwd`; \
+ $(am__define_uniq_tagged_files); \
+ shift; \
+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ if test $$# -gt 0; then \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ "$$@" $$unique; \
+ else \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$unique; \
+ fi; \
+ fi
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
+ test -z "$(CTAGS_ARGS)$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
+
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
+ case "$(srcdir)" in \
+ [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+ *) sdir=$(subdir)/$(srcdir) ;; \
+ esac; \
+ for i in $$list; do \
+ if test -f "$$i"; then \
+ echo "$(subdir)/$$i"; \
+ else \
+ echo "$$sdir/$$i"; \
+ fi; \
+ done >> $(top_builddir)/cscope.files
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
distdir: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -339,7 +452,8 @@ clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
distclean: distclean-am
-rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic
+distclean-am: clean-am distclean-compile distclean-generic \
+ distclean-tags
dvi: dvi-am
@@ -401,8 +515,9 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: all all-am check check-am clean clean-binPROGRAMS \
- clean-generic distclean distclean-compile distclean-generic \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
distdir dvi dvi-am html html-am info info-am install \
install-am install-binPROGRAMS install-data install-data-am \
install-dvi install-dvi-am install-exec install-exec-am \
@@ -411,7 +526,8 @@ uninstall-am: uninstall-binPROGRAMS
install-ps-am install-strip installcheck installcheck-am \
installdirs maintainer-clean maintainer-clean-generic \
mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
- ps ps-am uninstall uninstall-am uninstall-binPROGRAMS
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
abyss-samtobreak$(EXEEXT): $(abyss_samtobreak_SOURCES)
diff --git a/Overlap/Makefile.in b/Overlap/Makefile.in
index 0199f6b..b807ba5 100644
--- a/Overlap/Makefile.in
+++ b/Overlap/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = Overlap$(EXEEXT)
subdir = Overlap
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -68,15 +95,39 @@ Overlap_OBJECTS = $(am_Overlap_OBJECTS)
Overlap_DEPENDENCIES = $(top_builddir)/Graph/libgraph.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(Overlap_SOURCES)
DIST_SOURCES = $(Overlap_SOURCES)
am__can_run_installinfo = \
@@ -84,12 +135,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -238,10 +307,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -262,16 +332,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
Overlap$(EXEEXT): $(Overlap_OBJECTS) $(Overlap_DEPENDENCIES) $(EXTRA_Overlap_DEPENDENCIES)
@rm -f Overlap$(EXEEXT)
- $(CXXLINK) $(Overlap_OBJECTS) $(Overlap_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(Overlap_OBJECTS) $(Overlap_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -282,53 +354,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Overlap-Overlap.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
Overlap-Overlap.o: Overlap.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Overlap-Overlap.o -MD -MP -MF $(DEPDIR)/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo '$(srcdir)/'`Overlap.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/Overlap-Overlap.Tpo $(DEPDIR)/Overlap-Overlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Overlap.cpp' object='Overlap-Overlap.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Overlap-Overlap.o -MD -MP -MF $(DEPDIR)/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo '$(srcdir)/'`Overlap.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/Overlap-Overlap.Tpo $(DEPDIR)/Overlap-Overlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Overlap.cpp' object='Overlap-Overlap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo '$(srcdir)/'`Overlap.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo '$(srcdir)/'`Overlap.cpp
Overlap-Overlap.obj: Overlap.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Overlap-Overlap.obj -MD -MP -MF $(DEPDIR)/Overlap-Overlap.Tpo -c -o Overlap-Overlap.obj `if test -f 'Overlap.cpp'; then $(CYGPATH_W) 'Overlap.cpp'; else $(CYGPATH_W) '$(srcdir)/Overlap.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/Overlap-Overlap.Tpo $(DEPDIR)/Overlap-Overlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Overlap.cpp' object='Overlap-Overlap.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Overlap-Overlap.obj -MD -MP -MF $(DEPDIR)/Overlap-Overlap.Tpo -c -o Overlap-Overlap.obj `if test -f 'Overlap.cpp'; then $(CYGPATH_W) 'Overlap.cpp'; else $(CYGPATH_W) '$(srcdir)/Overlap.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/Overlap-Overlap.Tpo $(DEPDIR)/Overlap-Overlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Overlap.cpp' object='Overlap-Overlap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Overlap-Overlap.obj `if test -f 'Overlap.cpp'; then $(CYGPATH_W) 'Overlap.cpp'; else $(CYGPATH_W) '$(srcdir)/Overlap.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(Overlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Overlap-Overlap.obj `if test -f 'Overlap.cpp'; then $(CYGPATH_W) 'Overlap.cpp'; else $(CYGPATH_W) '$(srcdir)/Overlap.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -340,15 +401,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -357,9 +414,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -513,18 +571,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/Parallel/Makefile.in b/Parallel/Makefile.in
index fc1c2f9..0fc127f 100644
--- a/Parallel/Makefile.in
+++ b/Parallel/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = ABYSS-P$(EXEEXT)
subdir = Parallel
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -72,19 +99,51 @@ am__DEPENDENCIES_1 =
ABYSS_P_DEPENDENCIES = $(top_builddir)/Assembly/libassembly.a \
$(top_builddir)/Common/libcommon.a \
$(top_builddir)/DataLayer/libdatalayer.a $(am__DEPENDENCIES_1)
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(ABYSS_P_SOURCES)
DIST_SOURCES = $(ABYSS_P_SOURCES)
am__can_run_installinfo = \
@@ -92,12 +151,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -252,10 +329,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -276,16 +354,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
ABYSS-P$(EXEEXT): $(ABYSS_P_OBJECTS) $(ABYSS_P_DEPENDENCIES) $(EXTRA_ABYSS_P_DEPENDENCIES)
@rm -f ABYSS-P$(EXEEXT)
- $(CXXLINK) $(ABYSS_P_OBJECTS) $(ABYSS_P_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(ABYSS_P_OBJECTS) $(ABYSS_P_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -300,109 +380,98 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ABYSS_P-parallelAbyss.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
ABYSS_P-parallelAbyss.o: parallelAbyss.cpp
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- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo $(DEPDIR)/ABYSS_P-parallelAbyss.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='parallelAbyss.cpp' object='ABYSS_P-parallelAbyss.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-parallelAbyss.o -MD -MP -MF $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo '$(srcdir)/'`parallelAbyss.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo $(DEPDIR)/ABYSS_P-parallelAbyss.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='parallelAbyss.cpp' object='ABYSS_P-parallelAbyss.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo '$(srcdir)/'`parallelAbyss.cpp
ABYSS_P-parallelAbyss.obj: parallelAbyss.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-parallelAbyss.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-parallelAbyss.obj `if test -f 'parallelAbyss.cpp'; then $(CYGPATH_W) 'parallelAbyss.cpp'; else $(CYGPATH_W) '$(srcdir)/parallelAbyss.cpp'; fi`
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='parallelAbyss.cpp' object='ABYSS_P-parallelAbyss.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-parallelAbyss.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-parallelAbyss.obj `if test -f 'parallelAbyss.cpp'; then $(CYGPATH_W) 'parallelAbyss.cpp'; else $(CYGPATH_W) '$(srcdir)/parallelAbyss.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-parallelAbyss.Tpo $(DEPDIR)/ABYSS_P-parallelAbyss.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='parallelAbyss.cpp' object='ABYSS_P-parallelAbyss.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-parallelAbyss.obj `if test -f 'parallelAbyss.cpp'; then $(CYGPATH_W) 'parallelAbyss.cpp'; else $(CYGPATH_W) '$(srcdir)/parallelAbyss.cpp'; fi`
ABYSS_P-CommLayer.o: CommLayer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-CommLayer.o -MD -MP -MF $(DEPDIR)/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo '$(srcdir)/'`CommLayer.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-CommLayer.Tpo $(DEPDIR)/ABYSS_P-CommLayer.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='CommLayer.cpp' object='ABYSS_P-CommLayer.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-CommLayer.o -MD -MP -MF $(DEPDIR)/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo '$(srcdir)/'`CommLayer.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-CommLayer.Tpo $(DEPDIR)/ABYSS_P-CommLayer.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='CommLayer.cpp' object='ABYSS_P-CommLayer.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo '$(srcdir)/'`CommLayer.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo '$(srcdir)/'`CommLayer.cpp
ABYSS_P-CommLayer.obj: CommLayer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-CommLayer.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.obj `if test -f 'CommLayer.cpp'; then $(CYGPATH_W) 'CommLayer.cpp'; else $(CYGPATH_W) '$(srcdir)/CommLayer.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-CommLayer.Tpo $(DEPDIR)/ABYSS_P-CommLayer.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='CommLayer.cpp' object='ABYSS_P-CommLayer.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-CommLayer.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-CommLayer.Tpo -c -o ABYSS_P-CommLayer.obj `if test -f 'CommLayer.cpp'; then $(CYGPATH_W) 'CommLayer.cpp'; else $(CYGPATH_W) '$(srcdir)/CommLayer.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-CommLayer.Tpo $(DEPDIR)/ABYSS_P-CommLayer.Po
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-CommLayer.obj `if test -f 'CommLayer.cpp'; then $(CYGPATH_W) 'CommLayer.cpp'; else $(CYGPATH_W) '$(srcdir)/CommLayer.cpp'; fi`
ABYSS_P-NetworkSequenceCollection.o: NetworkSequenceCollection.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-NetworkSequenceCollection.o -MD -MP -MF $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Tpo -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo '$(srcdir)/'`NetworkSequenceCollection.cpp
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='NetworkSequenceCollection.cpp' object='ABYSS_P-NetworkSequenceCollection.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-NetworkSequenceCollection.o -MD -MP -MF $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Tpo -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo '$(srcdir)/'`NetworkSequenceCollection.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Tpo $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Po
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ABYSS_P-NetworkSequenceCollection.obj: NetworkSequenceCollection.cpp
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='NetworkSequenceCollection.cpp' object='ABYSS_P-NetworkSequenceCollection.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-NetworkSequenceCollection.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Tpo -c -o ABYSS_P-NetworkSequenceCollection.obj `if test -f 'NetworkSequenceCollection.cpp'; then $(CYGPATH_W) 'NetworkSequenceCollection.cpp'; else $(CYGPATH_W) '$(srcdir)/NetworkSequenceCollection.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Tpo $(DEPDIR)/ABYSS_P-NetworkSequenceCollection.Po
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ABYSS_P-MessageBuffer.o: MessageBuffer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-MessageBuffer.o -MD -MP -MF $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo '$(srcdir)/'`MessageBuffer.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo $(DEPDIR)/ABYSS_P-MessageBuffer.Po
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+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-MessageBuffer.o -MD -MP -MF $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo '$(srcdir)/'`MessageBuffer.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo $(DEPDIR)/ABYSS_P-MessageBuffer.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo '$(srcdir)/'`MessageBuffer.cpp
ABYSS_P-MessageBuffer.obj: MessageBuffer.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-MessageBuffer.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo -c -o ABYSS_P-MessageBuffer.obj `if test -f 'MessageBuffer.cpp'; then $(CYGPATH_W) 'MessageBuffer.cpp'; else $(CYGPATH_W) '$(srcdir)/MessageBuffer.cpp'; fi`
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+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-MessageBuffer.Tpo $(DEPDIR)/ABYSS_P-MessageBuffer.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-MessageBuffer.obj `if test -f 'MessageBuffer.cpp'; then $(CYGPATH_W) 'MessageBuffer.cpp'; else $(CYGPATH_W) '$(srcdir)/MessageBuffer.cpp'; fi`
ABYSS_P-Messages.o: Messages.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-Messages.o -MD -MP -MF $(DEPDIR)/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo '$(srcdir)/'`Messages.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-Messages.Tpo $(DEPDIR)/ABYSS_P-Messages.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Messages.cpp' object='ABYSS_P-Messages.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-Messages.o -MD -MP -MF $(DEPDIR)/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo '$(srcdir)/'`Messages.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-Messages.Tpo $(DEPDIR)/ABYSS_P-Messages.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Messages.cpp' object='ABYSS_P-Messages.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo '$(srcdir)/'`Messages.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo '$(srcdir)/'`Messages.cpp
ABYSS_P-Messages.obj: Messages.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-Messages.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.obj `if test -f 'Messages.cpp'; then $(CYGPATH_W) 'Messages.cpp'; else $(CYGPATH_W) '$(srcdir)/Messages.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ABYSS_P-Messages.Tpo $(DEPDIR)/ABYSS_P-Messages.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='Messages.cpp' object='ABYSS_P-Messages.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ABYSS_P-Messages.obj -MD -MP -MF $(DEPDIR)/ABYSS_P-Messages.Tpo -c -o ABYSS_P-Messages.obj `if test -f 'Messages.cpp'; then $(CYGPATH_W) 'Messages.cpp'; else $(CYGPATH_W) '$(srcdir)/Messages.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ABYSS_P-Messages.Tpo $(DEPDIR)/ABYSS_P-Messages.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='Messages.cpp' object='ABYSS_P-Messages.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-Messages.obj `if test -f 'Messages.cpp'; then $(CYGPATH_W) 'Messages.cpp'; else $(CYGPATH_W) '$(srcdir)/Messages.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ABYSS_P_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ABYSS_P-Messages.obj `if test -f 'Messages.cpp'; then $(CYGPATH_W) 'Messages.cpp'; else $(CYGPATH_W) '$(srcdir)/Messages.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -414,15 +483,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -431,9 +496,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -587,18 +653,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/ParseAligns/Makefile.in b/ParseAligns/Makefile.in
index f566614..1f80d62 100644
--- a/ParseAligns/Makefile.in
+++ b/ParseAligns/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = abyss-fixmate$(EXEEXT) ParseAligns$(EXEEXT)
subdir = ParseAligns
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -69,15 +96,39 @@ ParseAligns_DEPENDENCIES = $(top_builddir)/Common/libcommon.a
am_abyss_fixmate_OBJECTS = abyss_fixmate-abyss-fixmate.$(OBJEXT)
abyss_fixmate_OBJECTS = $(am_abyss_fixmate_OBJECTS)
abyss_fixmate_DEPENDENCIES = $(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(ParseAligns_SOURCES) $(abyss_fixmate_SOURCES)
DIST_SOURCES = $(ParseAligns_SOURCES) $(abyss_fixmate_SOURCES)
am__can_run_installinfo = \
@@ -85,12 +136,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -243,10 +312,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -267,19 +337,22 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
ParseAligns$(EXEEXT): $(ParseAligns_OBJECTS) $(ParseAligns_DEPENDENCIES) $(EXTRA_ParseAligns_DEPENDENCIES)
@rm -f ParseAligns$(EXEEXT)
- $(CXXLINK) $(ParseAligns_OBJECTS) $(ParseAligns_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(ParseAligns_OBJECTS) $(ParseAligns_LDADD) $(LIBS)
+
abyss-fixmate$(EXEEXT): $(abyss_fixmate_OBJECTS) $(abyss_fixmate_DEPENDENCIES) $(EXTRA_abyss_fixmate_DEPENDENCIES)
@rm -f abyss-fixmate$(EXEEXT)
- $(CXXLINK) $(abyss_fixmate_OBJECTS) $(abyss_fixmate_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_fixmate_OBJECTS) $(abyss_fixmate_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -291,81 +364,70 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/abyss_fixmate-abyss-fixmate.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
ParseAligns-ParseAligns.o: ParseAligns.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ParseAligns-ParseAligns.o -MD -MP -MF $(DEPDIR)/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo '$(srcdir)/'`ParseAligns.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ParseAligns-ParseAligns.Tpo $(DEPDIR)/ParseAligns-ParseAligns.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='ParseAligns.cpp' object='ParseAligns-ParseAligns.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ParseAligns-ParseAligns.o -MD -MP -MF $(DEPDIR)/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo '$(srcdir)/'`ParseAligns.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ParseAligns-ParseAligns.Tpo $(DEPDIR)/ParseAligns-ParseAligns.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='ParseAligns.cpp' object='ParseAligns-ParseAligns.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo '$(srcdir)/'`ParseAligns.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo '$(srcdir)/'`ParseAligns.cpp
ParseAligns-ParseAligns.obj: ParseAligns.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ParseAligns-ParseAligns.obj -MD -MP -MF $(DEPDIR)/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.obj `if test -f 'ParseAligns.cpp'; then $(CYGPATH_W) 'ParseAligns.cpp'; else $(CYGPATH_W) '$(srcdir)/ParseAligns.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/ParseAligns-ParseAligns.Tpo $(DEPDIR)/ParseAligns-ParseAligns.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='ParseAligns.cpp' object='ParseAligns-ParseAligns.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ParseAligns-ParseAligns.obj -MD -MP -MF $(DEPDIR)/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.obj `if test -f 'ParseAligns.cpp'; then $(CYGPATH_W) 'ParseAligns.cpp'; else $(CYGPATH_W) '$(srcdir)/ParseAligns.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/ParseAligns-ParseAligns.Tpo $(DEPDIR)/ParseAligns-ParseAligns.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='ParseAligns.cpp' object='ParseAligns-ParseAligns.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ParseAligns-ParseAligns.obj `if test -f 'ParseAligns.cpp'; then $(CYGPATH_W) 'ParseAligns.cpp'; else $(CYGPATH_W) '$(srcdir)/ParseAligns.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(ParseAligns_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ParseAligns-ParseAligns.obj `if test -f 'ParseAligns.cpp'; then $(CYGPATH_W) 'ParseAligns.cpp'; else $(CYGPATH_W) '$(srcdir)/ParseAligns.cpp'; fi`
abyss_fixmate-abyss-fixmate.o: abyss-fixmate.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo '$(srcdir)/'`abyss-fixmate.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo $(DEPDIR)/abyss_fixmate-abyss-fixmate.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-fixmate.cc' object='abyss_fixmate-abyss-fixmate.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo '$(srcdir)/'`abyss-fixmate.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo $(DEPDIR)/abyss_fixmate-abyss-fixmate.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-fixmate.cc' object='abyss_fixmate-abyss-fixmate.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo '$(srcdir)/'`abyss-fixmate.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo '$(srcdir)/'`abyss-fixmate.cc
abyss_fixmate-abyss-fixmate.obj: abyss-fixmate.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fixmate-abyss-fixmate.obj -MD -MP -MF $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.obj `if test -f 'abyss-fixmate.cc'; then $(CYGPATH_W) 'abyss-fixmate.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-fixmate.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo $(DEPDIR)/abyss_fixmate-abyss-fixmate.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='abyss-fixmate.cc' object='abyss_fixmate-abyss-fixmate.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_fixmate-abyss-fixmate.obj -MD -MP -MF $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.obj `if test -f 'abyss-fixmate.cc'; then $(CYGPATH_W) 'abyss-fixmate.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-fixmate.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_fixmate-abyss-fixmate.Tpo $(DEPDIR)/abyss_fixmate-abyss-fixmate.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='abyss-fixmate.cc' object='abyss_fixmate-abyss-fixmate.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fixmate-abyss-fixmate.obj `if test -f 'abyss-fixmate.cc'; then $(CYGPATH_W) 'abyss-fixmate.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-fixmate.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_fixmate_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_fixmate-abyss-fixmate.obj `if test -f 'abyss-fixmate.cc'; then $(CYGPATH_W) 'abyss-fixmate.cc'; else $(CYGPATH_W) '$(srcdir)/abyss-fixmate.cc'; fi`
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -377,15 +439,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -394,9 +452,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -550,18 +609,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
index c019065..52112c7 100644
--- a/ParseAligns/abyss-fixmate.cc
+++ b/ParseAligns/abyss-fixmate.cc
@@ -5,6 +5,7 @@
#include "StringUtil.h"
#include "Uncompress.h"
#include "UnorderedMap.h"
+#include "ContigID.h"
#include <algorithm>
#include <climits>
#include <cstdlib>
@@ -40,6 +41,7 @@ static const char USAGE_MESSAGE[] =
" -l, --min-align=N the minimal alignment size [1]\n"
" -s, --same=SAME write properly-paired reads to this file\n"
" -h, --hist=FILE write the fragment size histogram to FILE\n"
+" -c, --cov=FILE write the physical coverage to FILE\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
@@ -49,23 +51,25 @@ static const char USAGE_MESSAGE[] =
namespace opt {
static string fragPath;
static string histPath;
+ static string covPath;
static int qname;
static int verbose;
}
-static const char shortopts[] = "h:l:s:v";
+static const char shortopts[] = "h:c:l:s:v";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
- { "qname", no_argument, &opt::qname, 1 },
- { "no-qname", no_argument, &opt::qname, 0 },
+ { "qname", no_argument, &opt::qname, 1 },
+ { "no-qname", no_argument, &opt::qname, 0 },
{ "min-align", required_argument, NULL, 'l' },
- { "hist", required_argument, NULL, 'h' },
- { "same", required_argument, NULL, 's' },
- { "verbose", no_argument, NULL, 'v' },
- { "help", no_argument, NULL, OPT_HELP },
- { "version", no_argument, NULL, OPT_VERSION },
+ { "hist", required_argument, NULL, 'h' },
+ { "cov", required_argument, NULL, 'c' },
+ { "same", required_argument, NULL, 's' },
+ { "verbose", no_argument, NULL, 'v' },
+ { "help", no_argument, NULL, OPT_HELP },
+ { "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
};
@@ -79,6 +83,19 @@ static struct {
static ofstream g_fragFile;
static Histogram g_histogram;
+static ofstream g_covFile;
+static vector< vector<int> > g_contigCov;
+
+static void incrementRange(SAMRecord& a)
+{
+ unsigned inx = get(g_contigNames, a.rname);
+ g_contigCov[inx][a.pos]++;
+ assert(a.isize >= 0);
+ unsigned end = a.pos + a.isize;
+ if (end >= g_contigCov[inx].size())
+ end = g_contigCov[inx].size() - 1;
+ g_contigCov[inx][end]--;
+}
static void handlePair(SAMRecord& a0, SAMRecord& a1)
{
@@ -113,6 +130,10 @@ static void handlePair(SAMRecord& a0, SAMRecord& a1)
stats.numFF++;
} else {
// Same target, FR or RF orientation.
+ if (!opt::covPath.empty()) {
+ SAMRecord a = a0.isize >= 0 ? a0 : a1;
+ incrementRange(a);
+ }
g_histogram.insert(a0.isReverse() ? a1.isize : a0.isize);
if (!opt::fragPath.empty()) {
g_fragFile << a0 << '\n' << a1 << '\n';
@@ -180,6 +201,45 @@ static void assert_eof(istream& in)
exit(EXIT_FAILURE);
}
+/** Print physical coverage in wiggle format. */
+static void printCov(string file)
+{
+ ofstream out(file.c_str());
+ for (unsigned i = 0; i < g_contigCov.size(); i++) {
+ out << "variableStep\tchrom=" << get(g_contigNames, i) << '\n';
+ int prev = g_contigCov[i][0];
+ if (prev != 0) out << "0\t" << prev << '\n';
+ for (unsigned j = 1; j < g_contigCov[i].size(); j++) {
+ prev += g_contigCov[i][j];
+ if (prev != 0) out << j << "\t" << prev << '\n';
+ }
+ }
+}
+
+void parseTag(string line) {
+ stringstream ss(line);
+ string tag;
+ char type[2];
+ string id;
+ char delim;
+ unsigned length;
+ ss >> tag;
+ if (tag != "@SQ")
+ return;
+ while (ss >> type[0] >> type[1] >> delim) {
+ assert(delim == ':');
+ if (type[0] == 'S' && type[1] == 'N')
+ ss >> id;
+ else if (type[0] == 'L' && type[1] == 'N')
+ ss >> length;
+ }
+
+ assert(length > 0);
+ assert(id.size() > 0);
+ put(g_contigNames, g_contigCov.size(), id);
+ g_contigCov.push_back(vector<int>(length));
+}
+
static void readAlignments(istream& in, Alignments* pMap)
{
for (SAMRecord sam; in >> ws;) {
@@ -187,12 +247,18 @@ static void readAlignments(istream& in, Alignments* pMap)
string line;
getline(in, line);
assert(in);
+
+ if (!opt::covPath.empty())
+ parseTag(line);
+
cout << line << '\n';
if (!opt::fragPath.empty())
g_fragFile << line << '\n';
} else if (in >> sam)
handleAlignment(sam, *pMap);
}
+ if (!opt::covPath.empty())
+ printCov(opt::covPath);
assert_eof(in);
}
@@ -241,6 +307,7 @@ int main(int argc, char* const* argv)
break;
case 's': arg >> opt::fragPath; break;
case 'h': arg >> opt::histPath; break;
+ case 'c': arg >> opt::covPath; break;
case 'v': opt::verbose++; break;
case OPT_HELP:
cout << USAGE_MESSAGE;
@@ -308,6 +375,13 @@ int main(int argc, char* const* argv)
"FF " << percent(stats.numFF, sum) << "\n"
"Different " << percent(stats.numDifferent, sum) << "\n"
"Total " << sum << endl;
+
+ if (alignments.size() == sum) {
+ cerr << PROGRAM ": error: All reads are mateless. This "
+ "can happen when first and second read IDs do not match."
+ << endl;
+ exit(EXIT_FAILURE);
+ }
if (!opt::fragPath.empty())
g_fragFile.close();
@@ -345,8 +419,9 @@ int main(int argc, char* const* argv)
}
if (stats.numFF > numFR && stats.numFF > numRF) {
- cerr << "error: The mate pairs of this library are oriented "
- "forward-forward (FF), which is not supported by ABySS."
+ cerr << PROGRAM ": error: The mate pairs of this library are "
+ "oriented forward-forward (FF), which is not supported "
+ "by ABySS."
<< endl;
exit(EXIT_FAILURE);
}
diff --git a/PathOverlap/Makefile.in b/PathOverlap/Makefile.in
index a82b9c1..b2d93eb 100644
--- a/PathOverlap/Makefile.in
+++ b/PathOverlap/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = PathOverlap$(EXEEXT)
subdir = PathOverlap
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -68,15 +95,39 @@ PathOverlap_OBJECTS = $(am_PathOverlap_OBJECTS)
PathOverlap_DEPENDENCIES = $(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Graph/libgraph.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(PathOverlap_SOURCES)
DIST_SOURCES = $(PathOverlap_SOURCES)
am__can_run_installinfo = \
@@ -84,12 +135,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -238,10 +307,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -262,16 +332,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
PathOverlap$(EXEEXT): $(PathOverlap_OBJECTS) $(PathOverlap_DEPENDENCIES) $(EXTRA_PathOverlap_DEPENDENCIES)
@rm -f PathOverlap$(EXEEXT)
- $(CXXLINK) $(PathOverlap_OBJECTS) $(PathOverlap_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(PathOverlap_OBJECTS) $(PathOverlap_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -282,53 +354,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/PathOverlap-PathOverlap.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
PathOverlap-PathOverlap.o: PathOverlap.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathOverlap-PathOverlap.o -MD -MP -MF $(DEPDIR)/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo '$(srcdir)/'`PathOverlap.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PathOverlap-PathOverlap.Tpo $(DEPDIR)/PathOverlap-PathOverlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PathOverlap.cpp' object='PathOverlap-PathOverlap.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathOverlap-PathOverlap.o -MD -MP -MF $(DEPDIR)/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo '$(srcdir)/'`PathOverlap.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PathOverlap-PathOverlap.Tpo $(DEPDIR)/PathOverlap-PathOverlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PathOverlap.cpp' object='PathOverlap-PathOverlap.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo '$(srcdir)/'`PathOverlap.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo '$(srcdir)/'`PathOverlap.cpp
PathOverlap-PathOverlap.obj: PathOverlap.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathOverlap-PathOverlap.obj -MD -MP -MF $(DEPDIR)/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.obj `if test -f 'PathOverlap.cpp'; then $(CYGPATH_W) 'PathOverlap.cpp'; else $(CYGPATH_W) '$(srcdir)/PathOverlap.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PathOverlap-PathOverlap.Tpo $(DEPDIR)/PathOverlap-PathOverlap.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PathOverlap.cpp' object='PathOverlap-PathOverlap.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PathOverlap-PathOverlap.obj -MD -MP -MF $(DEPDIR)/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.obj `if test -f 'PathOverlap.cpp'; then $(CYGPATH_W) 'PathOverlap.cpp'; else $(CYGPATH_W) '$(srcdir)/PathOverlap.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PathOverlap-PathOverlap.Tpo $(DEPDIR)/PathOverlap-PathOverlap.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PathOverlap.cpp' object='PathOverlap-PathOverlap.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathOverlap-PathOverlap.obj `if test -f 'PathOverlap.cpp'; then $(CYGPATH_W) 'PathOverlap.cpp'; else $(CYGPATH_W) '$(srcdir)/PathOverlap.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PathOverlap_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PathOverlap-PathOverlap.obj `if test -f 'PathOverlap.cpp'; then $(CYGPATH_W) 'PathOverlap.cpp'; else $(CYGPATH_W) '$(srcdir)/PathOverlap.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -340,15 +401,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -357,9 +414,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -513,18 +571,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/PopBubbles/Makefile.in b/PopBubbles/Makefile.in
index 668592d..2e3a1ed 100644
--- a/PopBubbles/Makefile.in
+++ b/PopBubbles/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = PopBubbles$(EXEEXT)
subdir = PopBubbles
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -72,15 +99,39 @@ PopBubbles_DEPENDENCIES = $(top_builddir)/Graph/libgraph.a \
$(top_builddir)/dialign/libdialign.a
PopBubbles_LINK = $(CXXLD) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(PopBubbles_SOURCES)
DIST_SOURCES = $(PopBubbles_SOURCES)
am__can_run_installinfo = \
@@ -88,12 +139,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -244,10 +313,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -268,16 +338,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
PopBubbles$(EXEEXT): $(PopBubbles_OBJECTS) $(PopBubbles_DEPENDENCIES) $(EXTRA_PopBubbles_DEPENDENCIES)
@rm -f PopBubbles$(EXEEXT)
- $(PopBubbles_LINK) $(PopBubbles_OBJECTS) $(PopBubbles_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(PopBubbles_LINK) $(PopBubbles_OBJECTS) $(PopBubbles_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -288,53 +360,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/PopBubbles-PopBubbles.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
PopBubbles-PopBubbles.o: PopBubbles.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -MT PopBubbles-PopBubbles.o -MD -MP -MF $(DEPDIR)/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo '$(srcdir)/'`PopBubbles.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PopBubbles-PopBubbles.Tpo $(DEPDIR)/PopBubbles-PopBubbles.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PopBubbles.cpp' object='PopBubbles-PopBubbles.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -MT PopBubbles-PopBubbles.o -MD -MP -MF $(DEPDIR)/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo '$(srcdir)/'`PopBubbles.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PopBubbles-PopBubbles.Tpo $(DEPDIR)/PopBubbles-PopBubbles.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PopBubbles.cpp' object='PopBubbles-PopBubbles.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo '$(srcdir)/'`PopBubbles.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo '$(srcdir)/'`PopBubbles.cpp
PopBubbles-PopBubbles.obj: PopBubbles.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -MT PopBubbles-PopBubbles.obj -MD -MP -MF $(DEPDIR)/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.obj `if test -f 'PopBubbles.cpp'; then $(CYGPATH_W) 'PopBubbles.cpp'; else $(CYGPATH_W) '$(srcdir)/PopBubbles.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/PopBubbles-PopBubbles.Tpo $(DEPDIR)/PopBubbles-PopBubbles.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='PopBubbles.cpp' object='PopBubbles-PopBubbles.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -MT PopBubbles-PopBubbles.obj -MD -MP -MF $(DEPDIR)/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.obj `if test -f 'PopBubbles.cpp'; then $(CYGPATH_W) 'PopBubbles.cpp'; else $(CYGPATH_W) '$(srcdir)/PopBubbles.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/PopBubbles-PopBubbles.Tpo $(DEPDIR)/PopBubbles-PopBubbles.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='PopBubbles.cpp' object='PopBubbles-PopBubbles.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -c -o PopBubbles-PopBubbles.obj `if test -f 'PopBubbles.cpp'; then $(CYGPATH_W) 'PopBubbles.cpp'; else $(CYGPATH_W) '$(srcdir)/PopBubbles.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(PopBubbles_CPPFLAGS) $(CPPFLAGS) $(PopBubbles_CXXFLAGS) $(CXXFLAGS) -c -o PopBubbles-PopBubbles.obj `if test -f 'PopBubbles.cpp'; then $(CYGPATH_W) 'PopBubbles.cpp'; else $(CYGPATH_W) '$(srcdir)/PopBubbles.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -346,15 +407,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -363,9 +420,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -519,18 +577,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/PopBubbles/PopBubbles.cpp b/PopBubbles/PopBubbles.cpp
index 8f3d8b4..269dcd1 100644
--- a/PopBubbles/PopBubbles.cpp
+++ b/PopBubbles/PopBubbles.cpp
@@ -244,13 +244,18 @@ static pair<unsigned, unsigned> alignPair(
*/
static pair<unsigned, unsigned> alignMulti(const vector<string>& seqs)
{
- string alignment;
- unsigned matches;
- string consensus = dialign(seqs, alignment, matches);
+ string alignment = seqs[0];
+ unsigned matches = 0;
+ NWAlignment align;
+ for (unsigned j = 0; j < seqs.size() - 1; j++) {
+ matches = min(matches, alignGlobal(alignment,
+ seqs[j+1], align));
+ alignment = align.match_align;
+ }
if (opt::verbose > 2)
#pragma omp critical(cerr)
- cerr << alignment << consensus << '\n';
- return make_pair(matches, consensus.size());
+ cerr << align;
+ return make_pair(matches, alignment.size());
}
/** Align the specified sequences.
diff --git a/README.html b/README.html
index 6edf1ed..1eb37b0 100644
--- a/README.html
+++ b/README.html
@@ -81,8 +81,24 @@ abyss-pe k=25 name=test \
<a href="http://www.openmp.org">OpenMP</a> such as <a href="http://gcc.gnu.org">GCC</a>.</p>
<p>ABySS will receive an error when compiling with Boost 1.51.0 or 1.52.0
-since they contain a bug. Download an earlier version such as
-<a href="http://downloads.sourceforge.net/project/boost/boost/1.50.0/boost_1_50_0.tar.bz2">Boost 1.50.0</a>.</p>
+since they contain a bug. Later versions of Boost compile without error.</p>
+
+<h1 id="compilingabyssfromgithub">Compiling ABySS from GitHub</h1>
+
+<p>When installing ABySS from GitHub source the following tools are
+required:</p>
+
+<ul>
+<li><a href="http://www.gnu.org/software/autoconf">Autoconf</a></li>
+<li><a href="http://www.gnu.org/software/automake">Automake</a></li>
+</ul>
+
+<p>To generate the configure script and make files:</p>
+
+<pre><code>./autogen.sh
+</code></pre>
+
+<p>See “Compiling ABySS from source” for further steps.</p>
<h1 id="compilingabyssfromsource">Compiling ABySS from source</h1>
@@ -346,11 +362,13 @@ see doc/flowchart.pdf.</p>
<h1 id="mailinglist">Mailing List</h1>
<p>Subscribe to the
-<a href="http://groups.google.com/group/abyss-users">ABySS mailing list</a>,
+[ABySS mailing list]
+(http://groups.google.com/group/abyss-users),
<a href="mailto:abyss-users@googlegroups.com">abyss-users@googlegroups.com</a>.</p>
<p>For questions related to transcriptome assembly, contact the
-<a href="http://groups.google.com/group/trans-abyss">Trans-ABySS mailing list</a>,
+[Trans-ABySS mailing list]
+(http://groups.google.com/group/trans-abyss),
<a href="mailto:trans-abyss@googlegroups.com">trans-abyss@googlegroups.com</a>.</p>
<h1 id="authors">Authors</h1>
diff --git a/README.md b/README.md
index 04317d7..b9d6655 100644
--- a/README.md
+++ b/README.md
@@ -69,8 +69,22 @@ ABySS requires a C++ compiler that supports
[OpenMP](http://www.openmp.org) such as [GCC](http://gcc.gnu.org).
ABySS will receive an error when compiling with Boost 1.51.0 or 1.52.0
-since they contain a bug. Download an earlier version such as
-[Boost 1.50.0](http://downloads.sourceforge.net/project/boost/boost/1.50.0/boost_1_50_0.tar.bz2).
+since they contain a bug. Later versions of Boost compile without error.
+
+Compiling ABySS from GitHub
+===========================
+
+When installing ABySS from GitHub source the following tools are
+required:
+
+* [Autoconf](http://www.gnu.org/software/autoconf)
+* [Automake](http://www.gnu.org/software/automake)
+
+To generate the configure script and make files:
+
+ ./autogen.sh
+
+See "Compiling ABySS from source" for further steps.
Compiling ABySS from source
===========================
diff --git a/Scaffold/Makefile.in b/Scaffold/Makefile.in
index 664ed86..39eab1a 100644
--- a/Scaffold/Makefile.in
+++ b/Scaffold/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ POST_UNINSTALL = :
bin_PROGRAMS = abyss-scaffold$(EXEEXT) abyss-junction$(EXEEXT)
noinst_PROGRAMS = abyss-drawgraph$(EXEEXT)
subdir = Scaffold
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -77,15 +104,39 @@ abyss_scaffold_OBJECTS = $(am_abyss_scaffold_OBJECTS)
abyss_scaffold_DEPENDENCIES = $(top_builddir)/Common/libcommon.a
abyss_scaffold_LINK = $(CXXLD) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(abyss_drawgraph_SOURCES) $(abyss_junction_SOURCES) \
$(abyss_scaffold_SOURCES)
DIST_SOURCES = $(abyss_drawgraph_SOURCES) $(abyss_junction_SOURCES) \
@@ -95,12 +146,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -256,10 +325,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -280,7 +350,8 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
@@ -290,15 +361,18 @@ clean-binPROGRAMS:
clean-noinstPROGRAMS:
-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+
abyss-drawgraph$(EXEEXT): $(abyss_drawgraph_OBJECTS) $(abyss_drawgraph_DEPENDENCIES) $(EXTRA_abyss_drawgraph_DEPENDENCIES)
@rm -f abyss-drawgraph$(EXEEXT)
- $(CXXLINK) $(abyss_drawgraph_OBJECTS) $(abyss_drawgraph_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(abyss_drawgraph_OBJECTS) $(abyss_drawgraph_LDADD) $(LIBS)
+
abyss-junction$(EXEEXT): $(abyss_junction_OBJECTS) $(abyss_junction_DEPENDENCIES) $(EXTRA_abyss_junction_DEPENDENCIES)
@rm -f abyss-junction$(EXEEXT)
- $(abyss_junction_LINK) $(abyss_junction_OBJECTS) $(abyss_junction_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_junction_LINK) $(abyss_junction_OBJECTS) $(abyss_junction_LDADD) $(LIBS)
+
abyss-scaffold$(EXEEXT): $(abyss_scaffold_OBJECTS) $(abyss_scaffold_DEPENDENCIES) $(EXTRA_abyss_scaffold_DEPENDENCIES)
@rm -f abyss-scaffold$(EXEEXT)
- $(abyss_scaffold_LINK) $(abyss_scaffold_OBJECTS) $(abyss_scaffold_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(abyss_scaffold_LINK) $(abyss_scaffold_OBJECTS) $(abyss_scaffold_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -311,81 +385,70 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/abyss_scaffold-scaffold.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
abyss_drawgraph-drawgraph.o: drawgraph.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_drawgraph-drawgraph.o -MD -MP -MF $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo '$(srcdir)/'`drawgraph.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo $(DEPDIR)/abyss_drawgraph-drawgraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='drawgraph.cc' object='abyss_drawgraph-drawgraph.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_drawgraph-drawgraph.o -MD -MP -MF $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo '$(srcdir)/'`drawgraph.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo $(DEPDIR)/abyss_drawgraph-drawgraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='drawgraph.cc' object='abyss_drawgraph-drawgraph.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo '$(srcdir)/'`drawgraph.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo '$(srcdir)/'`drawgraph.cc
abyss_drawgraph-drawgraph.obj: drawgraph.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_drawgraph-drawgraph.obj -MD -MP -MF $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.obj `if test -f 'drawgraph.cc'; then $(CYGPATH_W) 'drawgraph.cc'; else $(CYGPATH_W) '$(srcdir)/drawgraph.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo $(DEPDIR)/abyss_drawgraph-drawgraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='drawgraph.cc' object='abyss_drawgraph-drawgraph.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT abyss_drawgraph-drawgraph.obj -MD -MP -MF $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.obj `if test -f 'drawgraph.cc'; then $(CYGPATH_W) 'drawgraph.cc'; else $(CYGPATH_W) '$(srcdir)/drawgraph.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_drawgraph-drawgraph.Tpo $(DEPDIR)/abyss_drawgraph-drawgraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='drawgraph.cc' object='abyss_drawgraph-drawgraph.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_drawgraph-drawgraph.obj `if test -f 'drawgraph.cc'; then $(CYGPATH_W) 'drawgraph.cc'; else $(CYGPATH_W) '$(srcdir)/drawgraph.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_drawgraph_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o abyss_drawgraph-drawgraph.obj `if test -f 'drawgraph.cc'; then $(CYGPATH_W) 'drawgraph.cc'; else $(CYGPATH_W) '$(srcdir)/drawgraph.cc'; fi`
abyss_junction-junction.o: junction.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -MT abyss_junction-junction.o -MD -MP -MF $(DEPDIR)/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo '$(srcdir)/'`junction.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_junction-junction.Tpo $(DEPDIR)/abyss_junction-junction.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='junction.cc' object='abyss_junction-junction.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -MT abyss_junction-junction.o -MD -MP -MF $(DEPDIR)/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo '$(srcdir)/'`junction.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_junction-junction.Tpo $(DEPDIR)/abyss_junction-junction.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='junction.cc' object='abyss_junction-junction.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo '$(srcdir)/'`junction.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo '$(srcdir)/'`junction.cc
abyss_junction-junction.obj: junction.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -MT abyss_junction-junction.obj -MD -MP -MF $(DEPDIR)/abyss_junction-junction.Tpo -c -o abyss_junction-junction.obj `if test -f 'junction.cc'; then $(CYGPATH_W) 'junction.cc'; else $(CYGPATH_W) '$(srcdir)/junction.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_junction-junction.Tpo $(DEPDIR)/abyss_junction-junction.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='junction.cc' object='abyss_junction-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -MT abyss_junction-junction.obj -MD -MP -MF $(DEPDIR)/abyss_junction-junction.Tpo -c -o abyss_junction-junction.obj `if test -f 'junction.cc'; then $(CYGPATH_W) 'junction.cc'; else $(CYGPATH_W) '$(srcdir)/junction.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_junction-junction.Tpo $(DEPDIR)/abyss_junction-junction.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='junction.cc' object='abyss_junction-junction.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -c -o abyss_junction-junction.obj `if test -f 'junction.cc'; then $(CYGPATH_W) 'junction.cc'; else $(CYGPATH_W) '$(srcdir)/junction.cc'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_junction_CPPFLAGS) $(CPPFLAGS) $(abyss_junction_CXXFLAGS) $(CXXFLAGS) -c -o abyss_junction-junction.obj `if test -f 'junction.cc'; then $(CYGPATH_W) 'junction.cc'; else $(CYGPATH_W) '$(srcdir)/junction.cc'; fi`
abyss_scaffold-scaffold.o: scaffold.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -MT abyss_scaffold-scaffold.o -MD -MP -MF $(DEPDIR)/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo '$(srcdir)/'`scaffold.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_scaffold-scaffold.Tpo $(DEPDIR)/abyss_scaffold-scaffold.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='scaffold.cc' object='abyss_scaffold-scaffold.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -MT abyss_scaffold-scaffold.o -MD -MP -MF $(DEPDIR)/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo '$(srcdir)/'`scaffold.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_scaffold-scaffold.Tpo $(DEPDIR)/abyss_scaffold-scaffold.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='scaffold.cc' object='abyss_scaffold-scaffold.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo '$(srcdir)/'`scaffold.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo '$(srcdir)/'`scaffold.cc
abyss_scaffold-scaffold.obj: scaffold.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -MT abyss_scaffold-scaffold.obj -MD -MP -MF $(DEPDIR)/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.obj `if test -f 'scaffold.cc'; then $(CYGPATH_W) 'scaffold.cc'; else $(CYGPATH_W) '$(srcdir)/scaffold.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/abyss_scaffold-scaffold.Tpo $(DEPDIR)/abyss_scaffold-scaffold.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='scaffold.cc' object='abyss_scaffold-scaffold.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -MT abyss_scaffold-scaffold.obj -MD -MP -MF $(DEPDIR)/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.obj `if test -f 'scaffold.cc'; then $(CYGPATH_W) 'scaffold.cc'; else $(CYGPATH_W) '$(srcdir)/scaffold.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/abyss_scaffold-scaffold.Tpo $(DEPDIR)/abyss_scaffold-scaffold.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='scaffold.cc' object='abyss_scaffold-scaffold.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -c -o abyss_scaffold-scaffold.obj `if test -f 'scaffold.cc'; then $(CYGPATH_W) 'scaffold.cc'; else $(CYGPATH_W) '$(srcdir)/scaffold.cc'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(abyss_scaffold_CPPFLAGS) $(CPPFLAGS) $(abyss_scaffold_CXXFLAGS) $(CXXFLAGS) -c -o abyss_scaffold-scaffold.obj `if test -f 'scaffold.cc'; then $(CYGPATH_W) 'scaffold.cc'; else $(CYGPATH_W) '$(srcdir)/scaffold.cc'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -397,15 +460,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -414,9 +473,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -571,18 +631,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstPROGRAMS cscopelist ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic clean-noinstPROGRAMS \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/SimpleGraph/Makefile.in b/SimpleGraph/Makefile.in
index 0073220..9569104 100644
--- a/SimpleGraph/Makefile.in
+++ b/SimpleGraph/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
bin_PROGRAMS = SimpleGraph$(EXEEXT)
subdir = SimpleGraph
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -69,15 +96,39 @@ SimpleGraph_DEPENDENCIES = $(top_builddir)/Graph/libgraph.a \
$(top_builddir)/Common/libcommon.a
SimpleGraph_LINK = $(CXXLD) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) \
$(SimpleGraph_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(SimpleGraph_SOURCES)
DIST_SOURCES = $(SimpleGraph_SOURCES)
am__can_run_installinfo = \
@@ -85,12 +136,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -237,10 +306,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p; \
- then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p \
+ ; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' \
+ -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -261,16 +331,18 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' `; \
+ -e 's/$$/$(EXEEXT)/' \
+ `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
SimpleGraph$(EXEEXT): $(SimpleGraph_OBJECTS) $(SimpleGraph_DEPENDENCIES) $(EXTRA_SimpleGraph_DEPENDENCIES)
@rm -f SimpleGraph$(EXEEXT)
- $(SimpleGraph_LINK) $(SimpleGraph_OBJECTS) $(SimpleGraph_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(SimpleGraph_LINK) $(SimpleGraph_OBJECTS) $(SimpleGraph_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -281,53 +353,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SimpleGraph-SimpleGraph.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
SimpleGraph-SimpleGraph.o: SimpleGraph.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -MT SimpleGraph-SimpleGraph.o -MD -MP -MF $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo '$(srcdir)/'`SimpleGraph.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo $(DEPDIR)/SimpleGraph-SimpleGraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SimpleGraph.cpp' object='SimpleGraph-SimpleGraph.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -MT SimpleGraph-SimpleGraph.o -MD -MP -MF $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo '$(srcdir)/'`SimpleGraph.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo $(DEPDIR)/SimpleGraph-SimpleGraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='SimpleGraph.cpp' object='SimpleGraph-SimpleGraph.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo '$(srcdir)/'`SimpleGraph.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo '$(srcdir)/'`SimpleGraph.cpp
SimpleGraph-SimpleGraph.obj: SimpleGraph.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -MT SimpleGraph-SimpleGraph.obj -MD -MP -MF $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.obj `if test -f 'SimpleGraph.cpp'; then $(CYGPATH_W) 'SimpleGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/SimpleGraph.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo $(DEPDIR)/SimpleGraph-SimpleGraph.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SimpleGraph.cpp' object='SimpleGraph-SimpleGraph.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -MT SimpleGraph-SimpleGraph.obj -MD -MP -MF $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.obj `if test -f 'SimpleGraph.cpp'; then $(CYGPATH_W) 'SimpleGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/SimpleGraph.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/SimpleGraph-SimpleGraph.Tpo $(DEPDIR)/SimpleGraph-SimpleGraph.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='SimpleGraph.cpp' object='SimpleGraph-SimpleGraph.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -c -o SimpleGraph-SimpleGraph.obj `if test -f 'SimpleGraph.cpp'; then $(CYGPATH_W) 'SimpleGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/SimpleGraph.cpp'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(SimpleGraph_CPPFLAGS) $(CPPFLAGS) $(SimpleGraph_CXXFLAGS) $(CXXFLAGS) -c -o SimpleGraph-SimpleGraph.obj `if test -f 'SimpleGraph.cpp'; then $(CYGPATH_W) 'SimpleGraph.cpp'; else $(CYGPATH_W) '$(srcdir)/SimpleGraph.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -339,15 +400,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -356,9 +413,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -512,18 +570,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic cscopelist ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/aclocal.m4 b/aclocal.m4
index 63b681e..83c8b4f 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,8 +1,7 @@
-# generated automatically by aclocal 1.12 -*- Autoconf -*-
+# generated automatically by aclocal 1.14 -*- Autoconf -*-
+
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation,
-# Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -12,6 +11,7 @@
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.
+m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])])
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
@@ -20,24 +20,22 @@ You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.])])
-# Copyright (C) 2002-2012 Free Software Foundation, Inc.
+# Copyright (C) 2002-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 8
-
# AM_AUTOMAKE_VERSION(VERSION)
# ----------------------------
# Automake X.Y traces this macro to ensure aclocal.m4 has been
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.12'
+[am__api_version='1.14'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.12], [],
+m4_if([$1], [1.14], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -53,21 +51,19 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.12])dnl
+[AM_AUTOMAKE_VERSION([1.14])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001-2012 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 2
-
# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
# $ac_aux_dir to '$srcdir/foo'. In other projects, it is set to
# '$srcdir', '$srcdir/..', or '$srcdir/../..'.
@@ -115,14 +111,12 @@ am_aux_dir=`cd $ac_aux_dir && pwd`
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997-2012 Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 10
-
# AM_CONDITIONAL(NAME, SHELL-CONDITION)
# -------------------------------------
# Define a conditional.
@@ -148,13 +142,12 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999-2012 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 16
# There are a few dirty hacks below to avoid letting 'AC_PROG_CC' be
# written in clear, in which case automake, when reading aclocal.m4,
@@ -166,7 +159,7 @@ fi])])
# _AM_DEPENDENCIES(NAME)
# ----------------------
# See how the compiler implements dependency checking.
-# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# NAME is "CC", "CXX", "OBJC", "OBJCXX", "UPC", or "GJC".
# We try a few techniques and use that to set a single cache variable.
#
# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
@@ -182,6 +175,7 @@ AC_REQUIRE([AM_DEP_TRACK])dnl
m4_if([$1], [CC], [depcc="$CC" am_compiler_list=],
[$1], [CXX], [depcc="$CXX" am_compiler_list=],
[$1], [OBJC], [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+ [$1], [OBJCXX], [depcc="$OBJCXX" am_compiler_list='gcc3 gcc'],
[$1], [UPC], [depcc="$UPC" am_compiler_list=],
[$1], [GCJ], [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
[depcc="$$1" am_compiler_list=])
@@ -339,19 +333,18 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999-2012 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 6
# _AM_OUTPUT_DEPENDENCY_COMMANDS
# ------------------------------
AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
[{
- # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # Older Autoconf quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
@@ -380,7 +373,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "am__include" && continue
+ test -z "$am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
@@ -416,17 +409,21 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996-2012 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 18
-
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
+m4_define([AC_PROG_CC],
+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -439,7 +436,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# arguments mandatory, and then we can depend on a new Autoconf
# release and drop the old call support.
AC_DEFUN([AM_INIT_AUTOMAKE],
-[AC_PREREQ([2.62])dnl
+[AC_PREREQ([2.65])dnl
dnl Autoconf wants to disallow AM_ names. We explicitly allow
dnl the ones we care about.
m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
@@ -468,7 +465,9 @@ AC_SUBST([CYGPATH_W])
# Define the identity of the package.
dnl Distinguish between old-style and new-style calls.
m4_ifval([$2],
-[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+[AC_DIAGNOSE([obsolete],
+ [$0: two- and three-arguments forms are deprecated.])
+m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
AC_SUBST([PACKAGE], [$1])dnl
AC_SUBST([VERSION], [$2])],
[_AM_SET_OPTIONS([$1])dnl
@@ -494,7 +493,12 @@ AM_MISSING_PROG([AUTOHEADER], [autoheader])
AM_MISSING_PROG([MAKEINFO], [makeinfo])
AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
-AC_REQUIRE([AM_PROG_MKDIR_P])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+# For better backward compatibility. To be removed once Automake 1.9.x
+# dies out for good. For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
@@ -506,25 +510,70 @@ _AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
_AM_IF_OPTION([no-dependencies],,
[AC_PROVIDE_IFELSE([AC_PROG_CC],
[_AM_DEPENDENCIES([CC])],
- [define([AC_PROG_CC],
- defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
+ [m4_define([AC_PROG_CC],
+ m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
AC_PROVIDE_IFELSE([AC_PROG_CXX],
[_AM_DEPENDENCIES([CXX])],
- [define([AC_PROG_CXX],
- defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
+ [m4_define([AC_PROG_CXX],
+ m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
AC_PROVIDE_IFELSE([AC_PROG_OBJC],
[_AM_DEPENDENCIES([OBJC])],
- [define([AC_PROG_OBJC],
- defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
+ [m4_define([AC_PROG_OBJC],
+ m4_defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
+ [_AM_DEPENDENCIES([OBJCXX])],
+ [m4_define([AC_PROG_OBJCXX],
+ m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
])
-_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
-dnl The 'parallel-tests' driver may need to know about EXEEXT, so add the
-dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro
-dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
+AC_REQUIRE([AM_SILENT_RULES])dnl
+dnl The testsuite driver may need to know about EXEEXT, so add the
+dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This
+dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
-])
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+ fi
+fi])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
@@ -532,7 +581,6 @@ dnl mangled by Autoconf and run in a shell conditional statement.
m4_define([_AC_COMPILER_EXEEXT],
m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
-
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
# that is generated. The stamp files are numbered to have different names.
@@ -554,14 +602,12 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001-2012 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 8
-
# AM_PROG_INSTALL_SH
# ------------------
# Define $install_sh.
@@ -577,14 +623,12 @@ if test x"${install_sh}" != xset; then
fi
AC_SUBST([install_sh])])
-# Copyright (C) 2003-2012 Free Software Foundation, Inc.
+# Copyright (C) 2003-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 2
-
# Check whether the underlying file-system supports filenames
# with a leading dot. For instance MS-DOS doesn't.
AC_DEFUN([AM_SET_LEADING_DOT],
@@ -600,14 +644,12 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001-2012 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 5
-
# AM_MAKE_INCLUDE()
# -----------------
# Check to see how make treats includes.
@@ -652,14 +694,12 @@ rm -f confinc confmf
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997-2012 Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 7
-
# AM_MISSING_PROG(NAME, PROGRAM)
# ------------------------------
AC_DEFUN([AM_MISSING_PROG],
@@ -667,11 +707,10 @@ AC_DEFUN([AM_MISSING_PROG],
$1=${$1-"${am_missing_run}$2"}
AC_SUBST($1)])
-
# AM_MISSING_HAS_RUN
# ------------------
-# Define MISSING if not defined so far and test if it supports --run.
-# If it does, set am_missing_run to use it, otherwise, to nothing.
+# Define MISSING if not defined so far and test if it is modern enough.
+# If it is, set am_missing_run to use it, otherwise, to nothing.
AC_DEFUN([AM_MISSING_HAS_RUN],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([missing])dnl
@@ -684,52 +723,22 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
- am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
else
am_missing_run=
AC_MSG_WARN(['missing' script is too old or missing])
fi
])
-# Copyright (C) 2003-2012 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# serial 2
-
-# AM_PROG_MKDIR_P
-# ---------------
-# Check for 'mkdir -p'.
-AC_DEFUN([AM_PROG_MKDIR_P],
-[AC_PREREQ([2.60])dnl
-AC_REQUIRE([AC_PROG_MKDIR_P])dnl
-dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
-dnl while keeping a definition of mkdir_p for backward compatibility.
-dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
-dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
-dnl Makefile.ins that do not define MKDIR_P, so we do our own
-dnl adjustment using top_builddir (which is defined more often than
-dnl MKDIR_P).
-AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
-case $mkdir_p in
- [[\\/$]]* | ?:[[\\/]]*) ;;
- */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-esac
-])
-
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001-2012 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 6
-
# _AM_MANGLE_OPTION(NAME)
# -----------------------
AC_DEFUN([_AM_MANGLE_OPTION],
@@ -753,15 +762,77 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-# Check to make sure that the build environment is sane. -*- Autoconf -*-
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# _AM_PROG_CC_C_O
+# ---------------
+# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
+# to automatically call this.
+AC_DEFUN([_AM_PROG_CC_C_O],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+AC_LANG_PUSH([C])dnl
+AC_CACHE_CHECK(
+ [whether $CC understands -c and -o together],
+ [am_cv_prog_cc_c_o],
+ [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i])
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+AC_LANG_POP([C])])
-# Copyright (C) 1996-2012 Free Software Foundation, Inc.
+# For backward compatibility.
+AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
+
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 9
+# AM_RUN_LOG(COMMAND)
+# -------------------
+# Run COMMAND, save the exit status in ac_status, and log it.
+# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
+AC_DEFUN([AM_RUN_LOG],
+[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
+ ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ (exit $ac_status); }])
+
+# Check to make sure that the build environment is sane. -*- Autoconf -*-
+
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
# AM_SANITY_CHECK
# ---------------
@@ -838,13 +909,71 @@ AC_CONFIG_COMMANDS_PRE(
rm -f conftest.file
])
-# Copyright (C) 2001-2012 Free Software Foundation, Inc.
+# Copyright (C) 2009-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 2
+# AM_SILENT_RULES([DEFAULT])
+# --------------------------
+# Enable less verbose build rules; with the default set to DEFAULT
+# ("yes" being less verbose, "no" or empty being verbose).
+AC_DEFUN([AM_SILENT_RULES],
+[AC_ARG_ENABLE([silent-rules], [dnl
+AS_HELP_STRING(
+ [--enable-silent-rules],
+ [less verbose build output (undo: "make V=1")])
+AS_HELP_STRING(
+ [--disable-silent-rules],
+ [verbose build output (undo: "make V=0")])dnl
+])
+case $enable_silent_rules in @%:@ (((
+ yes) AM_DEFAULT_VERBOSITY=0;;
+ no) AM_DEFAULT_VERBOSITY=1;;
+ *) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
+esac
+dnl
+dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
+dnl do not support nested variable expansions.
+dnl See automake bug#9928 and bug#10237.
+am_make=${MAKE-make}
+AC_CACHE_CHECK([whether $am_make supports nested variables],
+ [am_cv_make_support_nested_variables],
+ [if AS_ECHO([['TRUE=$(BAR$(V))
+BAR0=false
+BAR1=true
+V=1
+am__doit:
+ @$(TRUE)
+.PHONY: am__doit']]) | $am_make -f - >/dev/null 2>&1; then
+ am_cv_make_support_nested_variables=yes
+else
+ am_cv_make_support_nested_variables=no
+fi])
+if test $am_cv_make_support_nested_variables = yes; then
+ dnl Using '$V' instead of '$(V)' breaks IRIX make.
+ AM_V='$(V)'
+ AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
+else
+ AM_V=$AM_DEFAULT_VERBOSITY
+ AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
+fi
+AC_SUBST([AM_V])dnl
+AM_SUBST_NOTMAKE([AM_V])dnl
+AC_SUBST([AM_DEFAULT_V])dnl
+AM_SUBST_NOTMAKE([AM_DEFAULT_V])dnl
+AC_SUBST([AM_DEFAULT_VERBOSITY])dnl
+AM_BACKSLASH='\'
+AC_SUBST([AM_BACKSLASH])dnl
+_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
+])
+
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
# AM_PROG_INSTALL_STRIP
# ---------------------
@@ -868,14 +997,12 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006-2012 Free Software Foundation, Inc.
+# Copyright (C) 2006-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 3
-
# _AM_SUBST_NOTMAKE(VARIABLE)
# ---------------------------
# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
@@ -889,14 +1016,12 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004-2012 Free Software Foundation, Inc.
+# Copyright (C) 2004-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 3
-
# _AM_PROG_TAR(FORMAT)
# --------------------
# Check how to create a tarball in format FORMAT.
@@ -910,76 +1035,114 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Substitute a variable $(am__untar) that extract such
# a tarball read from stdin.
# $(am__untar) < result.tar
+#
AC_DEFUN([_AM_PROG_TAR],
[# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AC_SUBST([AMTAR], ['$${TAR-tar}'])
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
- [m4_case([$1], [ustar],, [pax],,
- [m4_fatal([Unknown tar format])])
-AC_MSG_CHECKING([how to create a $1 tar archive])
-# Loop over all known methods to create a tar archive until one works.
+
+# We'll loop over all known methods to create a tar archive until one works.
_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-_am_tools=${am_cv_prog_tar_$1-$_am_tools}
-# Do not fold the above two line into one, because Tru64 sh and
-# Solaris sh will not grok spaces in the rhs of '-'.
-for _am_tool in $_am_tools
-do
- case $_am_tool in
- gnutar)
- for _am_tar in tar gnutar gtar;
- do
- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
+m4_if([$1], [v7],
+ [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
+
+ [m4_case([$1],
+ [ustar],
+ [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
+ # There is notably a 21 bits limit for the UID and the GID. In fact,
+ # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
+ # and bug#13588).
+ am_max_uid=2097151 # 2^21 - 1
+ am_max_gid=$am_max_uid
+ # The $UID and $GID variables are not portable, so we need to resort
+ # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
+ # below are definitely unexpected, so allow the users to see them
+ # (that is, avoid stderr redirection).
+ am_uid=`id -u || echo unknown`
+ am_gid=`id -g || echo unknown`
+ AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
+ if test $am_uid -le $am_max_uid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi
+ AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
+ if test $am_gid -le $am_max_gid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi],
+
+ [pax],
+ [],
+
+ [m4_fatal([Unknown tar format])])
+
+ AC_MSG_CHECKING([how to create a $1 tar archive])
+
+ # Go ahead even if we have the value already cached. We do so because we
+ # need to set the values for the 'am__tar' and 'am__untar' variables.
+ _am_tools=${am_cv_prog_tar_$1-$_am_tools}
+
+ for _am_tool in $_am_tools; do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar; do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
- # tar/untar a dummy directory, and stop if the command works
- rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ AM_RUN_LOG([cat conftest.dir/file])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+ done
rm -rf conftest.dir
- if test -s conftest.tar; then
- AM_RUN_LOG([$am__untar <conftest.tar])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
-done
-rm -rf conftest.dir
-AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
-AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+ AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+ AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+
AC_SUBST([am__tar])
AC_SUBST([am__untar])
]) # _AM_PROG_TAR
diff --git a/bin/Makefile.in b/bin/Makefile.in
index 3e6e142..1a1795f 100644
--- a/bin/Makefile.in
+++ b/bin/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
esac; \
- test $$am__dry = yes; \
- }
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -50,8 +77,8 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = bin
-DIST_COMMON = $(dist_bin_SCRIPTS) $(dist_noinst_SCRIPTS) \
- $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(dist_bin_SCRIPTS) $(dist_noinst_SCRIPTS)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -89,6 +116,18 @@ am__uninstall_files_from_dir = { \
}
am__installdirs = "$(DESTDIR)$(bindir)"
SCRIPTS = $(dist_bin_SCRIPTS) $(dist_noinst_SCRIPTS)
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
SOURCES =
DIST_SOURCES =
am__can_run_installinfo = \
@@ -96,10 +135,12 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -277,11 +318,9 @@ uninstall-dist_binSCRIPTS:
files=`for p in $$list; do echo "$$p"; done | \
sed -e 's,.*/,,;$(transform)'`; \
dir='$(DESTDIR)$(bindir)'; $(am__uninstall_files_from_dir)
-tags: TAGS
-TAGS:
+tags TAGS:
-ctags: CTAGS
-CTAGS:
+ctags CTAGS:
cscope cscopelist:
@@ -421,17 +460,17 @@ uninstall-am: uninstall-dist_binSCRIPTS
.MAKE: install-am install-strip
-.PHONY: all all-am check check-am clean clean-generic distclean \
- distclean-generic distdir dvi dvi-am html html-am info info-am \
- install install-am install-data install-data-am \
- install-dist_binSCRIPTS install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
- pdf-am ps ps-am uninstall uninstall-am \
- uninstall-dist_binSCRIPTS
+.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
+ ctags-am distclean distclean-generic distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-dist_binSCRIPTS install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am tags-am uninstall \
+ uninstall-am uninstall-dist_binSCRIPTS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/bin/abyss-pe b/bin/abyss-pe
index 82f3f93..73339ba 100755
--- a/bin/abyss-pe
+++ b/bin/abyss-pe
@@ -234,7 +234,7 @@ Report bugs to <abyss-users at bcgsc.ca>.\n'
version:
@printf '\
-abyss-pe (ABySS) 1.3.5\n\
+abyss-pe (ABySS) 1.3.6\n\
Written by Shaun Jackman.\n\
\n\
Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n'
diff --git a/compile b/compile
new file mode 100755
index 0000000..531136b
--- /dev/null
+++ b/compile
@@ -0,0 +1,347 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-10-14.11; # UTC
+
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey at cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake at gnu.org> or send patches to
+# <automake-patches at gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" "" $nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+ file=$1
+ case $file in
+ / | /[!/]*) # absolute file, and not a UNC file
+ if test -z "$file_conv"; then
+ # lazily determine how to convert abs files
+ case `uname -s` in
+ MINGW*)
+ file_conv=mingw
+ ;;
+ CYGWIN*)
+ file_conv=cygwin
+ ;;
+ *)
+ file_conv=wine
+ ;;
+ esac
+ fi
+ case $file_conv/,$2, in
+ *,$file_conv,*)
+ ;;
+ mingw/*)
+ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+ ;;
+ cygwin/*)
+ file=`cygpath -m "$file" || echo "$file"`
+ ;;
+ wine/*)
+ file=`winepath -w "$file" || echo "$file"`
+ ;;
+ esac
+ ;;
+ esac
+}
+
+# func_cl_dashL linkdir
+# Make cl look for libraries in LINKDIR
+func_cl_dashL ()
+{
+ func_file_conv "$1"
+ if test -z "$lib_path"; then
+ lib_path=$file
+ else
+ lib_path="$lib_path;$file"
+ fi
+ linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+ lib=$1
+ found=no
+ save_IFS=$IFS
+ IFS=';'
+ for dir in $lib_path $LIB
+ do
+ IFS=$save_IFS
+ if $shared && test -f "$dir/$lib.dll.lib"; then
+ found=yes
+ lib=$dir/$lib.dll.lib
+ break
+ fi
+ if test -f "$dir/$lib.lib"; then
+ found=yes
+ lib=$dir/$lib.lib
+ break
+ fi
+ if test -f "$dir/lib$lib.a"; then
+ found=yes
+ lib=$dir/lib$lib.a
+ break
+ fi
+ done
+ IFS=$save_IFS
+
+ if test "$found" != yes; then
+ lib=$lib.lib
+ fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+ # Assume a capable shell
+ lib_path=
+ shared=:
+ linker_opts=
+ for arg
+ do
+ if test -n "$eat"; then
+ eat=
+ else
+ case $1 in
+ -o)
+ # configure might choose to run compile as 'compile cc -o foo foo.c'.
+ eat=1
+ case $2 in
+ *.o | *.[oO][bB][jJ])
+ func_file_conv "$2"
+ set x "$@" -Fo"$file"
+ shift
+ ;;
+ *)
+ func_file_conv "$2"
+ set x "$@" -Fe"$file"
+ shift
+ ;;
+ esac
+ ;;
+ -I)
+ eat=1
+ func_file_conv "$2" mingw
+ set x "$@" -I"$file"
+ shift
+ ;;
+ -I*)
+ func_file_conv "${1#-I}" mingw
+ set x "$@" -I"$file"
+ shift
+ ;;
+ -l)
+ eat=1
+ func_cl_dashl "$2"
+ set x "$@" "$lib"
+ shift
+ ;;
+ -l*)
+ func_cl_dashl "${1#-l}"
+ set x "$@" "$lib"
+ shift
+ ;;
+ -L)
+ eat=1
+ func_cl_dashL "$2"
+ ;;
+ -L*)
+ func_cl_dashL "${1#-L}"
+ ;;
+ -static)
+ shared=false
+ ;;
+ -Wl,*)
+ arg=${1#-Wl,}
+ save_ifs="$IFS"; IFS=','
+ for flag in $arg; do
+ IFS="$save_ifs"
+ linker_opts="$linker_opts $flag"
+ done
+ IFS="$save_ifs"
+ ;;
+ -Xlinker)
+ eat=1
+ linker_opts="$linker_opts $2"
+ ;;
+ -*)
+ set x "$@" "$1"
+ shift
+ ;;
+ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+ func_file_conv "$1"
+ set x "$@" -Tp"$file"
+ shift
+ ;;
+ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+ func_file_conv "$1" mingw
+ set x "$@" "$file"
+ shift
+ ;;
+ *)
+ set x "$@" "$1"
+ shift
+ ;;
+ esac
+ fi
+ shift
+ done
+ if test -n "$linker_opts"; then
+ linker_opts="-link$linker_opts"
+ fi
+ exec "$@" $linker_opts
+ exit 1
+}
+
+eat=
+
+case $1 in
+ '')
+ echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "compile $scriptversion"
+ exit $?
+ ;;
+ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+ func_cl_wrapper "$@" # Doesn't return...
+ ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+ if test -n "$eat"; then
+ eat=
+ else
+ case $1 in
+ -o)
+ # configure might choose to run compile as 'compile cc -o foo foo.c'.
+ # So we strip '-o arg' only if arg is an object.
+ eat=1
+ case $2 in
+ *.o | *.obj)
+ ofile=$2
+ ;;
+ *)
+ set x "$@" -o "$2"
+ shift
+ ;;
+ esac
+ ;;
+ *.c)
+ cfile=$1
+ set x "$@" "$1"
+ shift
+ ;;
+ *)
+ set x "$@" "$1"
+ shift
+ ;;
+ esac
+ fi
+ shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+ # If no '-o' option was seen then we might have been invoked from a
+ # pattern rule where we don't need one. That is ok -- this is a
+ # normal compilation that the losing compiler can handle. If no
+ # '.c' file was seen then we are probably linking. That is also
+ # ok.
+ exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file. Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+ if mkdir "$lockdir" >/dev/null 2>&1; then
+ break
+ fi
+ sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/config.h.in b/config.h.in
index 1b14e80..809f1f0 100644
--- a/config.h.in
+++ b/config.h.in
@@ -3,9 +3,6 @@
/* Define if building universal (internal helper macro) */
#undef AC_APPLE_UNIVERSAL_BUILD
-/* Define to use the popcnt instruction */
-#undef ENABLE_POPCNT
-
/* Width of bits of the FM-index in bits */
#undef FMBITS
@@ -64,6 +61,9 @@
/* Define to 1 if you have the `mpich' library (-lmpich). */
#undef HAVE_LIBMPICH
+/* Define to 1 if you have the `mpl' library (-lmpl). */
+#undef HAVE_LIBMPL
+
/* Define to 1 if you have the `pthread' library (-lpthread). */
#undef HAVE_LIBPTHREAD
@@ -83,6 +83,9 @@
/* Define to 1 if you have the <mpi.h> header file. */
#undef HAVE_MPI_H
+/* Define to 0 if you do not have popcnt. */
+#undef HAVE_POPCNT
+
/* Define to 1 if you have the `pow' function. */
#undef HAVE_POW
diff --git a/configure b/configure
index 0698b28..ff3d00c 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for ABySS 1.3.5.
+# Generated by GNU Autoconf 2.69 for ABySS 1.3.6.
#
# Report bugs to <abyss-users at bcgsc.ca>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='ABySS'
PACKAGE_TARNAME='abyss'
-PACKAGE_VERSION='1.3.5'
-PACKAGE_STRING='ABySS 1.3.5'
+PACKAGE_VERSION='1.3.6'
+PACKAGE_STRING='ABySS 1.3.6'
PACKAGE_BUGREPORT='abyss-users at bcgsc.ca'
PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss'
@@ -662,6 +662,10 @@ CPPFLAGS
LDFLAGS
CFLAGS
CC
+AM_BACKSLASH
+AM_DEFAULT_VERBOSITY
+AM_DEFAULT_V
+AM_V
am__untar
am__tar
AMTAR
@@ -726,6 +730,7 @@ SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
+enable_silent_rules
enable_dependency_tracking
with_boost
with_mpi
@@ -733,7 +738,6 @@ enable_mpich
enable_lammpi
enable_fm
enable_maxk
-enable_popcnt
enable_samseqqual
enable_openmp
'
@@ -1290,7 +1294,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures ABySS 1.3.5 to adapt to many kinds of systems.
+\`configure' configures ABySS 1.3.6 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1356,7 +1360,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of ABySS 1.3.5:";;
+ short | recursive ) echo "Configuration of ABySS 1.3.6:";;
esac
cat <<\_ACEOF
@@ -1364,6 +1368,8 @@ Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --enable-silent-rules less verbose build output (undo: "make V=1")
+ --disable-silent-rules verbose build output (undo: "make V=0")
--enable-dependency-tracking
do not reject slow dependency extractors
--disable-dependency-tracking
@@ -1373,7 +1379,6 @@ Optional Features:
--enable-fm specify the width of the FM-index in bits (default
is 64-bit)
--enable-maxk=N set the maximum k-mer length (default is 64)
- --disable-popcnt do not use the popcnt instruction
--enable-samseqqual enable SAM sequence and quality fields
--disable-openmp do not use OpenMP
@@ -1464,7 +1469,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-ABySS configure 1.3.5
+ABySS configure 1.3.6
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2275,7 +2280,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by ABySS $as_me 1.3.5, which was
+It was created by ABySS $as_me 1.3.6, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2623,7 +2628,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-am__api_version='1.12'
+am__api_version='1.14'
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
@@ -2836,8 +2841,8 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
- am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
else
am_missing_run=
{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
@@ -2995,12 +3000,6 @@ fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
$as_echo "$MKDIR_P" >&6; }
-mkdir_p="$MKDIR_P"
-case $mkdir_p in
- [\\/$]* | ?:[\\/]*) ;;
- */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-esac
-
for ac_prog in gawk mawk nawk awk
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
@@ -3083,6 +3082,45 @@ else
fi
rmdir .tst 2>/dev/null
+# Check whether --enable-silent-rules was given.
+if test "${enable_silent_rules+set}" = set; then :
+ enableval=$enable_silent_rules;
+fi
+
+case $enable_silent_rules in # (((
+ yes) AM_DEFAULT_VERBOSITY=0;;
+ no) AM_DEFAULT_VERBOSITY=1;;
+ *) AM_DEFAULT_VERBOSITY=1;;
+esac
+am_make=${MAKE-make}
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
+$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
+if ${am_cv_make_support_nested_variables+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if $as_echo 'TRUE=$(BAR$(V))
+BAR0=false
+BAR1=true
+V=1
+am__doit:
+ @$(TRUE)
+.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then
+ am_cv_make_support_nested_variables=yes
+else
+ am_cv_make_support_nested_variables=no
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
+$as_echo "$am_cv_make_support_nested_variables" >&6; }
+if test $am_cv_make_support_nested_variables = yes; then
+ AM_V='$(V)'
+ AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
+else
+ AM_V=$AM_DEFAULT_VERBOSITY
+ AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
+fi
+AM_BACKSLASH='\'
+
if test "`cd $srcdir && pwd`" != "`pwd`"; then
# Use -I$(srcdir) only when $(srcdir) != ., so that make's output
# is not polluted with repeated "-I."
@@ -3105,7 +3143,7 @@ fi
# Define the identity of the package.
PACKAGE='abyss'
- VERSION='1.3.5'
+ VERSION='1.3.6'
cat >>confdefs.h <<_ACEOF
@@ -3133,12 +3171,22 @@ AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+# For better backward compatibility. To be removed once Automake 1.9.x
+# dies out for good. For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+mkdir_p='$(MKDIR_P)'
+
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AMTAR='$${TAR-tar}'
+
+# We'll loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar pax cpio none'
+
am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
@@ -3146,6 +3194,48 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
+ fi
+fi
+
ac_config_headers="$ac_config_headers config.h"
@@ -3980,6 +4070,65 @@ ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
+$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
+if ${am_cv_prog_cc_c_o+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
+ ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
+$as_echo "$am_cv_prog_cc_c_o" >&6; }
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
DEPDIR="${am__leading_dot}deps"
ac_config_commands="$ac_config_commands depfiles"
@@ -6360,17 +6509,6 @@ cat >>confdefs.h <<_ACEOF
_ACEOF
-# Check whether --enable-popcnt was given.
-if test "${enable_popcnt+set}" = set; then :
- enableval=$enable_popcnt;
-fi
-
-if test "$enable_popcnt" != no; then
-
-$as_echo "#define ENABLE_POPCNT 1" >>confdefs.h
-
-fi
-
# Check whether --enable-samseqqual was given.
if test "${enable_samseqqual+set}" = set; then :
enableval=$enable_samseqqual;
@@ -6453,6 +6591,51 @@ _ACEOF
fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for MPL_env2int in -lmpl" >&5
+$as_echo_n "checking for MPL_env2int in -lmpl... " >&6; }
+if ${ac_cv_lib_mpl_MPL_env2int+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lmpl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char MPL_env2int ();
+int
+main ()
+{
+return MPL_env2int ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_mpl_MPL_env2int=yes
+else
+ ac_cv_lib_mpl_MPL_env2int=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mpl_MPL_env2int" >&5
+$as_echo "$ac_cv_lib_mpl_MPL_env2int" >&6; }
+if test "x$ac_cv_lib_mpl_MPL_env2int" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBMPL 1
+_ACEOF
+
+ LIBS="-lmpl $LIBS"
+
+fi
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for MPI_Init in -lmpich" >&5
$as_echo_n "checking for MPI_Init in -lmpich... " >&6; }
if ${ac_cv_lib_mpich_MPI_Init+:} false; then :
@@ -6906,6 +7089,30 @@ _ACEOF
fi
+# Check for popcnt instruction.
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdint.h>,
+ uint64_t x = 0;
+int
+main ()
+{
+__asm__("popcnt %1,%0" : "=r" (x) : "r" (x));
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+$as_echo "#define HAVE_POPCNT 1" >>confdefs.h
+
+else
+
+$as_echo "#define HAVE_POPCNT 0" >>confdefs.h
+
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
# Check for the hash table implementation.
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
@@ -7697,7 +7904,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by ABySS $as_me 1.3.5, which was
+This file was extended by ABySS $as_me 1.3.6, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -7764,7 +7971,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-ABySS config.status 1.3.5
+ABySS config.status 1.3.6
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -8520,7 +8727,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
case $ac_file$ac_mode in
"depfiles":C) test x"$AMDEP_TRUE" != x"" || {
- # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # Older Autoconf quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
@@ -8571,7 +8778,7 @@ $as_echo X"$mf" |
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "am__include" && continue
+ test -z "$am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
diff --git a/configure.ac b/configure.ac
index 16b9d55..79e64fe 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
AC_PREREQ(2.59)
-AC_INIT(ABySS, 1.3.5, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 1.3.6, abyss-users at bcgsc.ca, abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AM_INIT_AUTOMAKE(foreign)
AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])
@@ -84,12 +84,6 @@ AC_ARG_ENABLE(maxk, AS_HELP_STRING([--enable-maxk=N],
[], [enable_maxk=64])
AC_DEFINE_UNQUOTED(MAX_KMER, [$enable_maxk], [maximum k-mer length])
-AC_ARG_ENABLE(popcnt, AS_HELP_STRING([--disable-popcnt],
- [do not use the popcnt instruction]))
-if test "$enable_popcnt" != no; then
- AC_DEFINE(ENABLE_POPCNT, 1, [Define to use the popcnt instruction])
-fi
-
AC_ARG_ENABLE(samseqqual,
AS_HELP_STRING([--enable-samseqqual],
[enable SAM sequence and quality fields]),
@@ -110,6 +104,7 @@ AC_DEFINE(OMPI_SKIP_MPICXX, 1,
AC_CHECK_HEADERS([mpi.h])
if test "$enable_mpich"; then
AC_CHECK_LIB([pthread], [pthread_create])
+ AC_CHECK_LIB([mpl], [MPL_env2int])
AC_CHECK_LIB([mpich], [MPI_Init])
ac_cv_lib_mpi_MPI_Init=$ac_cv_lib_mpich_MPI_Init
elif test "$enable_lammpi"; then
@@ -137,6 +132,14 @@ AC_CHECK_FUNC(ceilf, [], AC_DEFINE(ceilf, [ceil],
# Check for the dynamic linking library.
AC_CHECK_LIB([dl], [dlsym])
+# Check for popcnt instruction.
+AC_COMPILE_IFELSE(
+ [AC_LANG_PROGRAM([[#include <stdint.h>],
+ [uint64_t x = 0;]],
+ [[__asm__("popcnt %1,%0" : "=r" (x) : "r" (x));]])],
+ [AC_DEFINE([HAVE_POPCNT], 1, [Define to 1 if you have popcnt.])],
+ [AC_DEFINE([HAVE_POPCNT], 0, [Define to 0 if you do not have popcnt.])])
+
# Check for the hash table implementation.
AC_LANG([C++])
AC_CHECK_HEADERS([ \
diff --git a/depcomp b/depcomp
index debb6ff..4ebd5b3 100755
--- a/depcomp
+++ b/depcomp
@@ -1,9 +1,9 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2012-03-27.16; # UTC
+scriptversion=2013-05-30.07; # UTC
-# Copyright (C) 1999-2012 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -27,9 +27,9 @@ scriptversion=2012-03-27.16; # UTC
case $1 in
'')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
- exit 1;
- ;;
+ echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
@@ -56,11 +56,65 @@ EOF
;;
esac
+# Get the directory component of the given path, and save it in the
+# global variables '$dir'. Note that this directory component will
+# be either empty or ending with a '/' character. This is deliberate.
+set_dir_from ()
+{
+ case $1 in
+ */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
+ *) dir=;;
+ esac
+}
+
+# Get the suffix-stripped basename of the given path, and save it the
+# global variable '$base'.
+set_base_from ()
+{
+ base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
+}
+
+# If no dependency file was actually created by the compiler invocation,
+# we still have to create a dummy depfile, to avoid errors with the
+# Makefile "include basename.Plo" scheme.
+make_dummy_depfile ()
+{
+ echo "#dummy" > "$depfile"
+}
+
+# Factor out some common post-processing of the generated depfile.
+# Requires the auxiliary global variable '$tmpdepfile' to be set.
+aix_post_process_depfile ()
+{
+ # If the compiler actually managed to produce a dependency file,
+ # post-process it.
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form 'foo.o: dependency.h'.
+ # Do two passes, one to just change these to
+ # $object: dependency.h
+ # and one to simply output
+ # dependency.h:
+ # which is needed to avoid the deleted-header problem.
+ { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
+ sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
+ } > "$depfile"
+ rm -f "$tmpdepfile"
+ else
+ make_dummy_depfile
+ fi
+}
+
# A tabulation character.
tab=' '
# A newline character.
nl='
'
+# Character ranges might be problematic outside the C locale.
+# These definitions help.
+upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
+lower=abcdefghijklmnopqrstuvwxyz
+digits=0123456789
+alpha=${upper}${lower}
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
@@ -74,6 +128,9 @@ tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
+# Avoid interferences from the environment.
+gccflag= dashmflag=
+
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
@@ -85,32 +142,32 @@ if test "$depmode" = hp; then
fi
if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvisualcpp
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u='sed s,\\\\,/,g'
+ depmode=msvisualcpp
fi
if test "$depmode" = msvc7msys; then
- # This is just like msvc7 but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvc7
+ # This is just like msvc7 but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u='sed s,\\\\,/,g'
+ depmode=msvc7
fi
if test "$depmode" = xlc; then
- # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency informations.
- gccflag=-qmakedep=gcc,-MF
- depmode=gcc
+ # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
+ gccflag=-qmakedep=gcc,-MF
+ depmode=gcc
fi
case "$depmode" in
@@ -133,8 +190,7 @@ gcc3)
done
"$@"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -142,13 +198,17 @@ gcc3)
;;
gcc)
+## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
+## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
+## (see the conditional assignment to $gccflag above).
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say).
+## -MM, not -M (despite what the docs say). Also, it might not be
+## supported by the other compilers which use the 'gcc' depmode.
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
@@ -156,15 +216,14 @@ gcc)
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
+ # The second -e expression handles DOS-style file names with drive
+ # letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the "deleted header file" problem.
@@ -173,15 +232,15 @@ gcc)
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
- tr ' ' "$nl" < "$tmpdepfile" |
## Some versions of gcc put a space before the ':'. On the theory
## that the space means something, we add a space to the output as
## well. hp depmode also adds that space, but also prefixes the VPATH
## to the object. Take care to not repeat it in the output.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -199,8 +258,7 @@ sgi)
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -208,7 +266,6 @@ sgi)
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
-
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
@@ -216,19 +273,15 @@ sgi)
# the IRIX cc adds comments like '#:fec' to the end of the
# dependency line.
tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
- tr "$nl" ' ' >> "$depfile"
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
+ | tr "$nl" ' ' >> "$depfile"
echo >> "$depfile"
-
# The second pass generates a dummy entry for each header file.
tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
+ make_dummy_depfile
fi
rm -f "$tmpdepfile"
;;
@@ -246,9 +299,8 @@ aix)
# current directory. Also, the AIX compiler puts '$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
@@ -261,9 +313,7 @@ aix)
"$@" -M
fi
stat=$?
-
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
@@ -272,65 +322,113 @@ aix)
do
test -f "$tmpdepfile" && break
done
- if test -f "$tmpdepfile"; then
- # Each line is of the form 'foo.o: dependent.h'.
- # Do two passes, one to just change these to
- # '$object: dependent.h' and one to simply 'dependent.h:'.
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- sed -e 's,^.*\.[a-z]*:['"$tab"' ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
+ aix_post_process_depfile
+ ;;
+
+tcc)
+ # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
+ # FIXME: That version still under development at the moment of writing.
+ # Make that this statement remains true also for stable, released
+ # versions.
+ # It will wrap lines (doesn't matter whether long or short) with a
+ # trailing '\', as in:
+ #
+ # foo.o : \
+ # foo.c \
+ # foo.h \
+ #
+ # It will put a trailing '\' even on the last line, and will use leading
+ # spaces rather than leading tabs (at least since its commit 0394caf7
+ # "Emit spaces for -MD").
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile"
+ exit $stat
fi
+ rm -f "$depfile"
+ # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
+ # We have to change lines of the first kind to '$object: \'.
+ sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
+ # And for each line of the second kind, we have to emit a 'dep.h:'
+ # dummy dependency, to avoid the deleted-header problem.
+ sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
rm -f "$tmpdepfile"
;;
-icc)
- # Intel's C compiler anf tcc (Tiny C Compiler) understand '-MD -MF file'.
- # However on
- # $CC -MD -MF foo.d -c -o sub/foo.o sub/foo.c
- # ICC 7.0 will fill foo.d with something like
- # foo.o: sub/foo.c
- # foo.o: sub/foo.h
- # which is wrong. We want
- # sub/foo.o: sub/foo.c
- # sub/foo.o: sub/foo.h
- # sub/foo.c:
- # sub/foo.h:
- # ICC 7.1 will output
+## The order of this option in the case statement is important, since the
+## shell code in configure will try each of these formats in the order
+## listed in this file. A plain '-MD' option would be understood by many
+## compilers, so we must ensure this comes after the gcc and icc options.
+pgcc)
+ # Portland's C compiler understands '-MD'.
+ # Will always output deps to 'file.d' where file is the root name of the
+ # source file under compilation, even if file resides in a subdirectory.
+ # The object file name does not affect the name of the '.d' file.
+ # pgcc 10.2 will output
# foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using '\':
+ # and will wrap long lines using '\' :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
- # tcc 0.9.26 (FIXME still under development at the moment of writing)
- # will emit a similar output, but also prepend the continuation lines
- # with horizontal tabulation characters.
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
+ set_dir_from "$object"
+ # Use the source, not the object, to determine the base name, since
+ # that's sadly what pgcc will do too.
+ set_base_from "$source"
+ tmpdepfile=$base.d
+
+ # For projects that build the same source file twice into different object
+ # files, the pgcc approach of using the *source* file root name can cause
+ # problems in parallel builds. Use a locking strategy to avoid stomping on
+ # the same $tmpdepfile.
+ lockdir=$base.d-lock
+ trap "
+ echo '$0: caught signal, cleaning up...' >&2
+ rmdir '$lockdir'
+ exit 1
+ " 1 2 13 15
+ numtries=100
+ i=$numtries
+ while test $i -gt 0; do
+ # mkdir is a portable test-and-set.
+ if mkdir "$lockdir" 2>/dev/null; then
+ # This process acquired the lock.
+ "$@" -MD
+ stat=$?
+ # Release the lock.
+ rmdir "$lockdir"
+ break
+ else
+ # If the lock is being held by a different process, wait
+ # until the winning process is done or we timeout.
+ while test -d "$lockdir" && test $i -gt 0; do
+ sleep 1
+ i=`expr $i - 1`
+ done
+ fi
+ i=`expr $i - 1`
+ done
+ trap - 1 2 13 15
+ if test $i -le 0; then
+ echo "$0: failed to acquire lock after $numtries attempts" >&2
+ echo "$0: check lockdir '$lockdir'" >&2
+ exit 1
+ fi
+
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
- # Each line is of the form 'foo.o: dependent.h',
- # or 'foo.o: dep1.h dep2.h \', or ' dep3.h dep4.h \'.
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
- # '$object: dependent.h' and one to simply 'dependent.h:'.
- sed -e "s/^[ $tab][ $tab]*/ /" -e "s,^[^:]*:,$object :," \
- < "$tmpdepfile" > "$depfile"
- sed '
- s/[ '"$tab"'][ '"$tab"']*/ /g
- s/^ *//
- s/ *\\*$//
- s/^[^:]*: *//
- /^$/d
- /:$/d
- s/$/ :/
- ' < "$tmpdepfile" >> "$depfile"
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -341,9 +439,8 @@ hp2)
# 'foo.d', which lands next to the object file, wherever that
# happens to be.
# Much of this is similar to the tru64 case; see comments there.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
@@ -354,8 +451,7 @@ hp2)
"$@" +Maked
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
@@ -365,76 +461,61 @@ hp2)
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
# Add 'dependent.h:' lines.
sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
- echo "#dummy" > "$depfile"
+ make_dummy_depfile
fi
rm -f "$tmpdepfile" "$tmpdepfile2"
;;
tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in 'foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
- if test "$libtool" = yes; then
- # With Tru64 cc, shared objects can also be used to make a
- # static library. This mechanism is used in libtool 1.4 series to
- # handle both shared and static libraries in a single compilation.
- # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
- #
- # With libtool 1.5 this exception was removed, and libtool now
- # generates 2 separate objects for the 2 libraries. These two
- # compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
- tmpdepfile2=$dir$base.o.d # libtool 1.5
- tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
- tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.o.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- tmpdepfile4=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- sed -e 's,^.*\.[a-z]*:['"$tab"' ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in 'foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ set_dir_from "$object"
+ set_base_from "$object"
+
+ if test "$libtool" = yes; then
+ # Libtool generates 2 separate objects for the 2 libraries. These
+ # two compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir$base.o.d # libtool 1.5
+ tmpdepfile2=$dir.libs/$base.o.d # Likewise.
+ tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ # Same post-processing that is required for AIX mode.
+ aix_post_process_depfile
+ ;;
msvc7)
if test "$libtool" = yes; then
@@ -445,8 +526,7 @@ msvc7)
"$@" $showIncludes > "$tmpdepfile"
stat=$?
grep -v '^Note: including file: ' "$tmpdepfile"
- if test "$stat" = 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -472,6 +552,7 @@ $ {
G
p
}' >> "$depfile"
+ echo >> "$depfile" # make sure the fragment doesn't end with a backslash
rm -f "$tmpdepfile"
;;
@@ -523,13 +604,14 @@ dashmstdout)
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
"$@" $dashmflag |
- sed 's:^['"$tab"' ]*[^:'"$tab"' ][^:][^:]*\:['"$tab"' ]*:'"$object"'\: :' > "$tmpdepfile"
+ sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
- tr ' ' "$nl" < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this sed invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -582,10 +664,12 @@ makedepend)
# makedepend may prepend the VPATH from the source file name to the object.
# No need to regex-escape $object, excess matching of '.' is harmless.
sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
- sed '1,2d' "$tmpdepfile" | tr ' ' "$nl" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process the last invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed '1,2d' "$tmpdepfile" \
+ | tr ' ' "$nl" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
@@ -621,10 +705,10 @@ cpp)
esac
done
- "$@" -E |
- sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
- sed '$ s: \\$::' > "$tmpdepfile"
+ "$@" -E \
+ | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ | sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
@@ -656,15 +740,15 @@ msvisualcpp)
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
+ set fnord "$@"
+ shift
+ shift
+ ;;
*)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
esac
done
"$@" -E 2>/dev/null |
diff --git a/dialign/Makefile.in b/dialign/Makefile.in
index e43e67c..7369f7d 100644
--- a/dialign/Makefile.in
+++ b/dialign/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,23 +16,51 @@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -52,7 +79,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
noinst_PROGRAMS = dialign$(EXEEXT)
subdir = dialign
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -65,6 +92,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libdialign_a_AR = $(AR) $(ARFLAGS)
libdialign_a_LIBADD =
am_libdialign_a_OBJECTS = alig.$(OBJEXT) assemble.$(OBJEXT) \
@@ -75,14 +106,34 @@ PROGRAMS = $(noinst_PROGRAMS)
am_dialign_OBJECTS = museq.$(OBJEXT)
dialign_OBJECTS = $(am_dialign_OBJECTS)
dialign_DEPENDENCIES = libdialign.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_ at AM_V@)
+am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
+am__v_CC_0 = @echo " CC " $@;
+am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
+am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
+am__v_CCLD_0 = @echo " CCLD " $@;
+am__v_CCLD_1 =
SOURCES = $(libdialign_a_SOURCES) $(dialign_SOURCES)
DIST_SOURCES = $(libdialign_a_SOURCES) $(dialign_SOURCES)
am__can_run_installinfo = \
@@ -90,12 +141,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -240,16 +309,18 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libdialign.a: $(libdialign_a_OBJECTS) $(libdialign_a_DEPENDENCIES) $(EXTRA_libdialign_a_DEPENDENCIES)
- -rm -f libdialign.a
- $(libdialign_a_AR) libdialign.a $(libdialign_a_OBJECTS) $(libdialign_a_LIBADD)
- $(RANLIB) libdialign.a
+ $(AM_V_at)-rm -f libdialign.a
+ $(AM_V_AR)$(libdialign_a_AR) libdialign.a $(libdialign_a_OBJECTS) $(libdialign_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libdialign.a
clean-noinstPROGRAMS:
-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+
dialign$(EXEEXT): $(dialign_OBJECTS) $(dialign_DEPENDENCIES) $(EXTRA_dialign_DEPENDENCIES)
@rm -f dialign$(EXEEXT)
- $(LINK) $(dialign_OBJECTS) $(dialign_LDADD) $(LIBS)
+ $(AM_V_CCLD)$(LINK) $(dialign_OBJECTS) $(dialign_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -268,39 +339,28 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/translate.Po at am__quote@
.c.o:
- at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCC_FALSE@ $(COMPILE) -c $<
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(COMPILE) -c -o $@ $<
.c.obj:
- at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(COMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -312,15 +372,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -329,9 +385,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -483,18 +540,18 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstLIBRARIES clean-noinstPROGRAMS cscopelist ctags \
- distclean distclean-compile distclean-generic distclean-tags \
- distdir dvi dvi-am html html-am info info-am install \
- install-am install-data install-data-am install-dvi \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstLIBRARIES clean-noinstPROGRAMS cscopelist-am ctags \
+ ctags-am distclean distclean-compile distclean-generic \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
install-dvi-am install-exec install-exec-am install-html \
install-html-am install-info install-info-am install-man \
install-pdf install-pdf-am install-ps install-ps-am \
install-strip installcheck installcheck-am installdirs \
maintainer-clean maintainer-clean-generic mostlyclean \
mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am
+ tags tags-am uninstall uninstall-am
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/doc/ABYSS.1 b/doc/ABYSS.1
index 8136ad4..7a3d970 100644
--- a/doc/ABYSS.1
+++ b/doc/ABYSS.1
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2013-Mar" "ABYSS (ABySS) 1.3.5" "User Commands"
+.TH ABYSS "1" "2013-Jul" "ABYSS (ABySS) 1.3.6" "User Commands"
.SH NAME
ABYSS \- assemble short reads into contigs
.SH SYNOPSIS
diff --git a/doc/Makefile.in b/doc/Makefile.in
index 586d129..79fa43b 100644
--- a/doc/Makefile.in
+++ b/doc/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
esac; \
- test $$am__dry = yes; \
- }
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -50,8 +77,8 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = doc
-DIST_COMMON = $(dist_doc_DATA) $(dist_man_MANS) $(srcdir)/Makefile.am \
- $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(dist_man_MANS) $(dist_doc_DATA)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -60,6 +87,18 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
SOURCES =
DIST_SOURCES =
am__can_run_installinfo = \
@@ -99,10 +138,12 @@ am__installdirs = "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(docdir)"
NROFF = nroff
MANS = $(dist_man_MANS)
DATA = $(dist_doc_DATA)
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -295,29 +336,14 @@ uninstall-dist_docDATA:
@list='$(dist_doc_DATA)'; test -n "$(docdir)" || list=; \
files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
dir='$(DESTDIR)$(docdir)'; $(am__uninstall_files_from_dir)
-tags: TAGS
-TAGS:
+tags TAGS:
-ctags: CTAGS
-CTAGS:
+ctags CTAGS:
cscope cscopelist:
distdir: $(DISTFILES)
- @list='$(MANS)'; if test -n "$$list"; then \
- list=`for p in $$list; do \
- if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
- if test -f "$$d$$p"; then echo "$$d$$p"; else :; fi; done`; \
- if test -n "$$list" && \
- grep 'ab help2man is required to generate this page' $$list >/dev/null; then \
- echo "error: found man pages containing the 'missing help2man' replacement text:" >&2; \
- grep -l 'ab help2man is required to generate this page' $$list | sed 's/^/ /' >&2; \
- echo " to fix them, install help2man, remove and regenerate the man pages;" >&2; \
- echo " typically 'make maintainer-clean' will remove them" >&2; \
- exit 1; \
- else :; fi; \
- else :; fi
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
@@ -454,17 +480,18 @@ uninstall-man: uninstall-man1
.MAKE: install-am install-strip
-.PHONY: all all-am check check-am clean clean-generic distclean \
- distclean-generic distdir dvi dvi-am html html-am info info-am \
- install install-am install-data install-data-am \
- install-dist_docDATA install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-man1 install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
- pdf-am ps ps-am uninstall uninstall-am uninstall-dist_docDATA \
- uninstall-man uninstall-man1
+.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
+ ctags-am distclean distclean-generic distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-dist_docDATA install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-man1 install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags-am \
+ uninstall uninstall-am uninstall-dist_docDATA uninstall-man \
+ uninstall-man1
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1
index 42c76cc..fdf6439 100644
--- a/doc/abyss-pe.1
+++ b/doc/abyss-pe.1
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2013-Mar" "abyss-pe (ABySS) 1.3.5" "User Commands"
+.TH abyss-pe "1" "2013-Jul" "abyss-pe (ABySS) 1.3.6" "User Commands"
.SH NAME
abyss-pe - assemble reads into contigs
.SH SYNOPSIS
diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1
index 6e8ecb2..71c315a 100644
--- a/doc/abyss-tofastq.1
+++ b/doc/abyss-tofastq.1
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2013-Mar" "ABySS 1.3.5" "User Commands"
+.TH abyss-tofastq "1" "2013-Jul" "ABySS 1.3.6" "User Commands"
.SH NAME
abyss-tofastq \- convert various file formats to FASTQ format
.br
diff --git a/doxygen.conf b/doxygen.conf
index 9f08a71..a3cb1de 100644
--- a/doxygen.conf
+++ b/doxygen.conf
@@ -1096,7 +1096,7 @@ HIDE_UNDOC_RELATIONS = YES
# toolkit from AT&T and Lucent Bell Labs. The other options in this section
# have no effect if this option is set to NO (the default)
-HAVE_DOT = NO
+HAVE_DOT = YES
# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
@@ -1121,12 +1121,12 @@ GROUP_GRAPHS = YES
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
-UML_LOOK = NO
+UML_LOOK = YES
# If set to YES, the inheritance and collaboration graphs will show the
# relations between templates and their instances.
-TEMPLATE_RELATIONS = NO
+TEMPLATE_RELATIONS = YES
# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
# tags are set to YES then doxygen will generate a graph for each documented
@@ -1148,7 +1148,7 @@ INCLUDED_BY_GRAPH = YES
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
-CALL_GRAPH = NO
+CALL_GRAPH = YES
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will
# generate a caller dependency graph for every global function or class method.
@@ -1156,7 +1156,7 @@ CALL_GRAPH = NO
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
-CALLER_GRAPH = NO
+CALLER_GRAPH = YES
# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
# will graphical hierarchy of all classes instead of a textual one.
@@ -1221,14 +1221,14 @@ MAX_DOT_GRAPH_DEPTH = 0
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
-DOT_TRANSPARENT = NO
+DOT_TRANSPARENT = YES
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10)
# support this, this feature is disabled by default.
-DOT_MULTI_TARGETS = NO
+DOT_MULTI_TARGETS = YES
# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
# generate a legend page explaining the meaning of the various boxes and
@@ -1249,4 +1249,4 @@ DOT_CLEANUP = YES
# The SEARCHENGINE tag specifies whether or not a search engine should be
# used. If set to NO the values of all tags below this one will be ignored.
-SEARCHENGINE = NO
+SEARCHENGINE = YES
diff --git a/kmerprint/Makefile.in b/kmerprint/Makefile.in
index 95a81fb..c2b5ccc 100644
--- a/kmerprint/Makefile.in
+++ b/kmerprint/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.12 from Makefile.am.
+# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -16,23 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
-am__make_dryrun = \
- { \
- am__dry=no; \
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
- echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \
- | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
- *) \
- for am__flg in $$MAKEFLAGS; do \
- case $$am__flg in \
- *=*|--*) ;; \
- *n*) am__dry=yes; break;; \
- esac; \
- done;; \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
esac; \
- test $$am__dry = yes; \
- }
+ done; \
+ test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -51,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
noinst_PROGRAMS = kmerprint$(EXEEXT)
subdir = kmerprint
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -66,15 +93,39 @@ am_kmerprint_OBJECTS = kmerprint-kmerprint.$(OBJEXT)
kmerprint_OBJECTS = $(am_kmerprint_OBJECTS)
kmerprint_DEPENDENCIES = $(top_builddir)/Assembly/libassembly.a \
$(top_builddir)/Common/libcommon.a
+AM_V_P = $(am__v_P_ at AM_V@)
+am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_ at AM_V@)
+am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
+am__v_GEN_0 = @echo " GEN " $@;
+am__v_GEN_1 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+AM_V_lt = $(am__v_lt_ at AM_V@)
+am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+AM_V_CXX = $(am__v_CXX_ at AM_V@)
+am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
+am__v_CXX_0 = @echo " CXX " $@;
+am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
+AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
+am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
+am__v_CXXLD_0 = @echo " CXXLD " $@;
+am__v_CXXLD_1 =
SOURCES = $(kmerprint_SOURCES)
DIST_SOURCES = $(kmerprint_SOURCES)
am__can_run_installinfo = \
@@ -82,12 +133,30 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
AM_CXXFLAGS = @AM_CXXFLAGS@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -227,9 +296,10 @@ $(am__aclocal_m4_deps):
clean-noinstPROGRAMS:
-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+
kmerprint$(EXEEXT): $(kmerprint_OBJECTS) $(kmerprint_DEPENDENCIES) $(EXTRA_kmerprint_DEPENDENCIES)
@rm -f kmerprint$(EXEEXT)
- $(CXXLINK) $(kmerprint_OBJECTS) $(kmerprint_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(kmerprint_OBJECTS) $(kmerprint_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -240,53 +310,42 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/kmerprint-kmerprint.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
kmerprint-kmerprint.o: kmerprint.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT kmerprint-kmerprint.o -MD -MP -MF $(DEPDIR)/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo '$(srcdir)/'`kmerprint.cc
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/kmerprint-kmerprint.Tpo $(DEPDIR)/kmerprint-kmerprint.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='kmerprint.cc' object='kmerprint-kmerprint.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT kmerprint-kmerprint.o -MD -MP -MF $(DEPDIR)/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo '$(srcdir)/'`kmerprint.cc
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/kmerprint-kmerprint.Tpo $(DEPDIR)/kmerprint-kmerprint.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='kmerprint.cc' object='kmerprint-kmerprint.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo '$(srcdir)/'`kmerprint.cc
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo '$(srcdir)/'`kmerprint.cc
kmerprint-kmerprint.obj: kmerprint.cc
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT kmerprint-kmerprint.obj -MD -MP -MF $(DEPDIR)/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.obj `if test -f 'kmerprint.cc'; then $(CYGPATH_W) 'kmerprint.cc'; else $(CYGPATH_W) '$(srcdir)/kmerprint.cc'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/kmerprint-kmerprint.Tpo $(DEPDIR)/kmerprint-kmerprint.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='kmerprint.cc' object='kmerprint-kmerprint.obj' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT kmerprint-kmerprint.obj -MD -MP -MF $(DEPDIR)/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.obj `if test -f 'kmerprint.cc'; then $(CYGPATH_W) 'kmerprint.cc'; else $(CYGPATH_W) '$(srcdir)/kmerprint.cc'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/kmerprint-kmerprint.Tpo $(DEPDIR)/kmerprint-kmerprint.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='kmerprint.cc' object='kmerprint-kmerprint.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o kmerprint-kmerprint.obj `if test -f 'kmerprint.cc'; then $(CYGPATH_W) 'kmerprint.cc'; else $(CYGPATH_W) '$(srcdir)/kmerprint.cc'; fi`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
- mkid -fID $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(kmerprint_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o kmerprint-kmerprint.obj `if test -f 'kmerprint.cc'; then $(CYGPATH_W) 'kmerprint.cc'; else $(CYGPATH_W) '$(srcdir)/kmerprint.cc'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -298,15 +357,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | \
- $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -315,9 +370,10 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
-cscopelist: $(HEADERS) $(SOURCES) $(LISP)
- list='$(SOURCES) $(HEADERS) $(LISP)'; \
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
@@ -468,8 +524,8 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstPROGRAMS cscopelist ctags distclean \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstPROGRAMS cscopelist-am ctags ctags-am distclean \
distclean-compile distclean-generic distclean-tags distdir dvi \
dvi-am html html-am info info-am install install-am \
install-data install-data-am install-dvi install-dvi-am \
@@ -478,7 +534,7 @@ uninstall-am:
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
diff --git a/missing b/missing
index 9a55648..cdea514 100755
--- a/missing
+++ b/missing
@@ -1,10 +1,10 @@
#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
+# Common wrapper for a few potentially missing GNU programs.
-scriptversion=2012-01-06.18; # UTC
+scriptversion=2012-06-26.16; # UTC
-# Copyright (C) 1996-2012 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Originally written by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -29,61 +29,33 @@ if test $# -eq 0; then
exit 1
fi
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, 'missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
- configure_ac=configure.ac
-else
- configure_ac=configure.in
-fi
+case $1 in
-msg="missing on your system"
+ --is-lightweight)
+ # Used by our autoconf macros to check whether the available missing
+ # script is modern enough.
+ exit 0
+ ;;
-case $1 in
---run)
- # Try to run requested program, and just exit if it succeeds.
- run=
- shift
- "$@" && exit 0
- # Exit code 63 means version mismatch. This often happens
- # when the user try to use an ancient version of a tool on
- # a file that requires a minimum version. In this case we
- # we should proceed has if the program had been absent, or
- # if --run hadn't been passed.
- if test $? = 63; then
- run=:
- msg="probably too old"
- fi
- ;;
+ --run)
+ # Back-compat with the calling convention used by older automake.
+ shift
+ ;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
-Handle 'PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
+Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
+to PROGRAM being missing or too old.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
- --run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
- aclocal touch file 'aclocal.m4'
- autoconf touch file 'configure'
- autoheader touch file 'config.h.in'
- autom4te touch the output file, or create a stub one
- automake touch all 'Makefile.in' files
- bison create 'y.tab.[ch]', if possible, from existing .[ch]
- flex create 'lex.yy.c', if possible, from existing .c
- help2man touch the output file
- lex create 'lex.yy.c', if possible, from existing .c
- makeinfo touch the output file
- yacc create 'y.tab.[ch]', if possible, from existing .[ch]
+ aclocal autoconf autoheader autom4te automake makeinfo
+ bison yacc flex lex help2man
Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
'g' are ignored when checking the name.
@@ -98,228 +70,141 @@ Send bug reports to <bug-automake at gnu.org>."
;;
-*)
- echo 1>&2 "$0: Unknown '$1' option"
+ echo 1>&2 "$0: unknown '$1' option"
echo 1>&2 "Try '$0 --help' for more information"
exit 1
;;
esac
-# normalize program name to check for.
-program=`echo "$1" | sed '
- s/^gnu-//; t
- s/^gnu//; t
- s/^g//; t'`
-
-# Now exit if we have it, but it failed. Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program). This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
- lex*|yacc*)
- # Not GNU programs, they don't have --version.
- ;;
-
- *)
- if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
- # We have it, but it failed.
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- # Could not run --version or --help. This is probably someone
- # running '$TOOL --version' or '$TOOL --help' to check whether
- # $TOOL exists and not knowing $TOOL uses missing.
- exit 1
- fi
- ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
- aclocal*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified 'acinclude.m4' or '${configure_ac}'. You might want
- to install the Automake and Perl packages. Grab them from
- any GNU archive site."
- touch aclocal.m4
- ;;
-
- autoconf*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified '${configure_ac}'. You might want to install the
- Autoconf and GNU m4 packages. Grab them from any GNU
- archive site."
- touch configure
- ;;
-
- autoheader*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified 'acconfig.h' or '${configure_ac}'. You might want
- to install the Autoconf and GNU m4 packages. Grab them
- from any GNU archive site."
- files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
- test -z "$files" && files="config.h"
- touch_files=
- for f in $files; do
- case $f in
- *:*) touch_files="$touch_files "`echo "$f" |
- sed -e 's/^[^:]*://' -e 's/:.*//'`;;
- *) touch_files="$touch_files $f.in";;
- esac
- done
- touch $touch_files
- ;;
-
- automake*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified 'Makefile.am', 'acinclude.m4' or '${configure_ac}'.
- You might want to install the Automake and Perl packages.
- Grab them from any GNU archive site."
- find . -type f -name Makefile.am -print |
- sed 's/\.am$/.in/' |
- while read f; do touch "$f"; done
- ;;
-
- autom4te*)
- echo 1>&2 "\
-WARNING: '$1' is needed, but is $msg.
- You might have modified some files without having the
- proper tools for further handling them.
- You can get '$1' as part of Autoconf from any GNU
- archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo "#! /bin/sh"
- echo "# Created by GNU Automake missing as a replacement of"
- echo "# $ $@"
- echo "exit 0"
- chmod +x $file
- exit 1
- fi
- ;;
-
- bison*|yacc*)
- echo 1>&2 "\
-WARNING: '$1' $msg. You should only need it if
- you modified a '.y' file. You may need the Bison package
- in order for those modifications to take effect. You can get
- Bison from any GNU archive site."
- rm -f y.tab.c y.tab.h
- if test $# -ne 1; then
- eval LASTARG=\${$#}
- case $LASTARG in
- *.y)
- SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.c
- fi
- SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.h
- fi
- ;;
- esac
- fi
- if test ! -f y.tab.h; then
- echo >y.tab.h
- fi
- if test ! -f y.tab.c; then
- echo 'main() { return 0; }' >y.tab.c
- fi
- ;;
-
- lex*|flex*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified a '.l' file. You may need the Flex package
- in order for those modifications to take effect. You can get
- Flex from any GNU archive site."
- rm -f lex.yy.c
- if test $# -ne 1; then
- eval LASTARG=\${$#}
- case $LASTARG in
- *.l)
- SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" lex.yy.c
- fi
- ;;
- esac
- fi
- if test ! -f lex.yy.c; then
- echo 'main() { return 0; }' >lex.yy.c
- fi
- ;;
-
- help2man*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified a dependency of a manual page. You may need the
- Help2man package in order for those modifications to take
- effect. You can get Help2man from any GNU archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo ".ab help2man is required to generate this page"
- exit $?
- fi
- ;;
-
- makeinfo*)
- echo 1>&2 "\
-WARNING: '$1' is $msg. You should only need it if
- you modified a '.texi' or '.texinfo' file, or any other file
- indirectly affecting the aspect of the manual. The spurious
- call might also be the consequence of using a buggy 'make' (AIX,
- DU, IRIX). You might want to install the Texinfo package or
- the GNU make package. Grab either from any GNU archive site."
- # The file to touch is that specified with -o ...
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -z "$file"; then
- # ... or it is the one specified with @setfilename ...
- infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
- file=`sed -n '
- /^@setfilename/{
- s/.* \([^ ]*\) *$/\1/
- p
- q
- }' $infile`
- # ... or it is derived from the source name (dir/f.texi becomes f.info)
- test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
- fi
- # If the file does not exist, the user really needs makeinfo;
- # let's fail without touching anything.
- test -f $file || exit 1
- touch $file
- ;;
+# Run the given program, remember its exit status.
+"$@"; st=$?
+
+# If it succeeded, we are done.
+test $st -eq 0 && exit 0
+
+# Also exit now if we it failed (or wasn't found), and '--version' was
+# passed; such an option is passed most likely to detect whether the
+# program is present and works.
+case $2 in --version|--help) exit $st;; esac
+
+# Exit code 63 means version mismatch. This often happens when the user
+# tries to use an ancient version of a tool on a file that requires a
+# minimum version.
+if test $st -eq 63; then
+ msg="probably too old"
+elif test $st -eq 127; then
+ # Program was missing.
+ msg="missing on your system"
+else
+ # Program was found and executed, but failed. Give up.
+ exit $st
+fi
- *)
- echo 1>&2 "\
-WARNING: '$1' is needed, and is $msg.
- You might have modified some files without having the
- proper tools for further handling them. Check the 'README' file,
- it often tells you about the needed prerequisites for installing
- this package. You may also peek at any GNU archive site, in case
- some other package would contain this missing '$1' program."
- exit 1
+perl_URL=http://www.perl.org/
+flex_URL=http://flex.sourceforge.net/
+gnu_software_URL=http://www.gnu.org/software
+
+program_details ()
+{
+ case $1 in
+ aclocal|automake)
+ echo "The '$1' program is part of the GNU Automake package:"
+ echo "<$gnu_software_URL/automake>"
+ echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/autoconf>"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ autoconf|autom4te|autoheader)
+ echo "The '$1' program is part of the GNU Autoconf package:"
+ echo "<$gnu_software_URL/autoconf/>"
+ echo "It also requires GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ esac
+}
+
+give_advice ()
+{
+ # Normalize program name to check for.
+ normalized_program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+ printf '%s\n' "'$1' is $msg."
+
+ configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
+ case $normalized_program in
+ autoconf*)
+ echo "You should only need it if you modified 'configure.ac',"
+ echo "or m4 files included by it."
+ program_details 'autoconf'
+ ;;
+ autoheader*)
+ echo "You should only need it if you modified 'acconfig.h' or"
+ echo "$configure_deps."
+ program_details 'autoheader'
+ ;;
+ automake*)
+ echo "You should only need it if you modified 'Makefile.am' or"
+ echo "$configure_deps."
+ program_details 'automake'
+ ;;
+ aclocal*)
+ echo "You should only need it if you modified 'acinclude.m4' or"
+ echo "$configure_deps."
+ program_details 'aclocal'
+ ;;
+ autom4te*)
+ echo "You might have modified some maintainer files that require"
+ echo "the 'automa4te' program to be rebuilt."
+ program_details 'autom4te'
+ ;;
+ bison*|yacc*)
+ echo "You should only need it if you modified a '.y' file."
+ echo "You may want to install the GNU Bison package:"
+ echo "<$gnu_software_URL/bison/>"
+ ;;
+ lex*|flex*)
+ echo "You should only need it if you modified a '.l' file."
+ echo "You may want to install the Fast Lexical Analyzer package:"
+ echo "<$flex_URL>"
+ ;;
+ help2man*)
+ echo "You should only need it if you modified a dependency" \
+ "of a man page."
+ echo "You may want to install the GNU Help2man package:"
+ echo "<$gnu_software_URL/help2man/>"
;;
-esac
-
-exit 0
+ makeinfo*)
+ echo "You should only need it if you modified a '.texi' file, or"
+ echo "any other file indirectly affecting the aspect of the manual."
+ echo "You might want to install the Texinfo package:"
+ echo "<$gnu_software_URL/texinfo/>"
+ echo "The spurious makeinfo call might also be the consequence of"
+ echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
+ echo "want to install GNU make:"
+ echo "<$gnu_software_URL/make/>"
+ ;;
+ *)
+ echo "You might have modified some files without having the proper"
+ echo "tools for further handling them. Check the 'README' file, it"
+ echo "often tells you about the needed prerequisites for installing"
+ echo "this package. You may also peek at any GNU archive site, in"
+ echo "case some other package contains this missing '$1' program."
+ ;;
+ esac
+}
+
+give_advice "$1" | sed -e '1s/^/WARNING: /' \
+ -e '2,$s/^/ /' >&2
+
+# Propagate the correct exit status (expected to be 127 for a program
+# not found, 63 for a program that failed due to version mismatch).
+exit $st
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/abyss.git
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