Merge branch 'dev'

Author: molpopgen

.travis.yml

@@ -17,4 +17,9 @@ addons:
     - zlib1g-dev
 
 notifications:
-  email: false
+  email: false
+
+script:
+ - export LD_LIBRARY_PATH=$HOME/lib
+ - ./configure --prefix=$HOME && make && make check && make install
+ - $HOME/bin/libsequenceConfig --version

Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 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,
@@ -14,17 +14,7 @@
 
 @SET_MAKE@
 VPATH = @srcdir@
-am__is_gnu_make = { \
-  if test -z '$(MAKELEVEL)'; then \
-    false; \
-  elif test -n '$(MAKE_HOST)'; then \
-    true; \
-  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
-    true; \
-  else \
-    false; \
-  fi; \
-}
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -88,15 +78,18 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = .
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(top_srcdir)/configure $(am__configure_deps) \
+	$(srcdir)/config.h.in AUTHORS COPYING ChangeLog INSTALL \
+	compile config.guess config.sub depcomp install-sh missing \
+	ltmain.sh
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/ax_cxx_compile_stdxx_11.m4 \
 	$(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
 	$(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
 	$(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
-	$(am__configure_deps) $(am__DIST_COMMON)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
  configure.lineno config.status.lineno
 mkinstalldirs = $(install_sh) -d
@@ -160,9 +153,6 @@ ETAGS = etags
 CTAGS = ctags
 CSCOPE = cscope
 DIST_SUBDIRS = $(SUBDIRS)
-am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in AUTHORS \
-	COPYING ChangeLog INSTALL compile config.guess config.sub \
-	depcomp install-sh ltmain.sh missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -350,6 +340,7 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --foreign Makefile
+.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -580,15 +571,15 @@ dist-xz: distdir
 	$(am__post_remove_distdir)
 
 dist-tarZ: distdir
-	@echo WARNING: "Support for distribution archives compressed with" \
-		       "legacy program 'compress' is deprecated." >&2
+	@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 shar distribution archives is" \
-	               "deprecated." >&2
+	@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)
@@ -624,17 +615,17 @@ distcheck: dist
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
-	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
+	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,^[^:\\/]:[\\/],/,'` \
 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
 	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build/sub \
-	  && ../../configure \
+	  && $(am__cd) $(distdir)/_build \
+	  && ../configure \
 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
-	    --srcdir=../.. --prefix="$$dc_install_base" \
+	    --srcdir=.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
@@ -811,8 +802,6 @@ uninstall-am:
 	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
 	uninstall-am
 
-.PRECIOUS: Makefile
-
 
 libtool: $(LIBTOOL_DEPS)
 	$(SHELL) ./config.status libtool

REVISION_HISTORY.md

@@ -33,6 +33,12 @@ However:
 
 1. Sequence/SeqRegexes.hpp -- not working.  This will not be fixed until GCC supports <regex>.  The function is now currently implemented in a non-regex manner, which is lame, but it works.
 
+## libsequence 1.8.7
+
+* Sliding windows over physical distance now require an end position
+* A new unit test was added to test the new sliding window code
+* A test un test/UhapsTest.cc was commented out.  It is known to fail, but those parts of libsequence are not used yet anywhere else.  I'll deal with it later
+
 ## libsequence 1.8.6
 
 * Patch for Issue #7

Sequence/Coalescent/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 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,
@@ -15,17 +15,7 @@
 @SET_MAKE@
 
 VPATH = @srcdir@
-am__is_gnu_make = { \
-  if test -z '$(MAKELEVEL)'; then \
-    false; \
-  elif test -n '$(MAKE_HOST)'; then \
-    true; \
-  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
-    true; \
-  else \
-    false; \
-  fi; \
-}
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -88,15 +78,15 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = Sequence/Coalescent
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(pkginclude_HEADERS)
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/ax_cxx_compile_stdxx_11.m4 \
 	$(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
 	$(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
 	$(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(pkginclude_HEADERS) \
-	$(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config.h
 CONFIG_CLEAN_FILES =
@@ -185,7 +175,6 @@ am__define_uniq_tagged_files = \
 ETAGS = etags
 CTAGS = ctags
 DIST_SUBDIRS = $(SUBDIRS)
-am__DIST_COMMON = $(srcdir)/Makefile.in
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 am__relativize = \
   dir0=`pwd`; \
@@ -362,6 +351,7 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Sequence/Coalescent/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu Sequence/Coalescent/Makefile
+.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -681,8 +671,6 @@ uninstall-am: uninstall-pkgincludeHEADERS
 	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
 	uninstall-am uninstall-pkgincludeHEADERS
 
-.PRECIOUS: Makefile
-
 
 # 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.

Sequence/Coalescent/bits/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 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,
@@ -15,17 +15,7 @@
 @SET_MAKE@
 
 VPATH = @srcdir@
-am__is_gnu_make = { \
-  if test -z '$(MAKELEVEL)'; then \
-    false; \
-  elif test -n '$(MAKE_HOST)'; then \
-    true; \
-  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
-    true; \
-  else \
-    false; \
-  fi; \
-}
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -88,15 +78,15 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = Sequence/Coalescent/bits
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(pkginclude_HEADERS)
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/ax_cxx_compile_stdxx_11.m4 \
 	$(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
 	$(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
 	$(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(pkginclude_HEADERS) \
-	$(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config.h
 CONFIG_CLEAN_FILES =
@@ -168,7 +158,6 @@ am__define_uniq_tagged_files = \
   done | $(am__uniquify_input)`
 ETAGS = etags
 CTAGS = ctags
-am__DIST_COMMON = $(srcdir)/Makefile.in
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 pkgincludedir = $(prefix)/include/Sequence/Coalescent/bits
 ACLOCAL = @ACLOCAL@
@@ -313,6 +302,7 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Sequence/Coalescent/bits/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu Sequence/Coalescent/bits/Makefile
+.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -559,8 +549,6 @@ uninstall-am: uninstall-pkgincludeHEADERS
 	ps ps-am tags tags-am uninstall uninstall-am \
 	uninstall-pkgincludeHEADERS
 
-.PRECIOUS: Makefile
-
 
 # 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.

Sequence/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 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,
@@ -15,17 +15,7 @@
 @SET_MAKE@
 
 VPATH = @srcdir@
-am__is_gnu_make = { \
-  if test -z '$(MAKELEVEL)'; then \
-    false; \
-  elif test -n '$(MAKE_HOST)'; then \
-    true; \
-  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
-    true; \
-  else \
-    false; \
-  fi; \
-}
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -88,15 +78,15 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = Sequence
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(pkginclude_HEADERS)
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/ax_cxx_compile_stdxx_11.m4 \
 	$(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
 	$(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
 	$(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(pkginclude_HEADERS) \
-	$(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config.h
 CONFIG_CLEAN_FILES =
@@ -185,7 +175,6 @@ am__define_uniq_tagged_files = \
 ETAGS = etags
 CTAGS = ctags
 DIST_SUBDIRS = $(SUBDIRS)
-am__DIST_COMMON = $(srcdir)/Makefile.in
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 am__relativize = \
   dir0=`pwd`; \
@@ -418,6 +407,7 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Sequence/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --gnu Sequence/Makefile
+.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -737,8 +727,6 @@ uninstall-am: uninstall-pkgincludeHEADERS
 	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
 	uninstall-am uninstall-pkgincludeHEADERS
 
-.PRECIOUS: Makefile
-
 
 # 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.