Author: Andreas Tille <tille@debian.org>,
        Adrian Bunk <bunk@debian.org>
Last-Update: Sat, 18 Aug 2018 02:26:01 +0300
Description: Add autoconf stuff to enable simple library creation

--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,16 @@
+lib_LTLIBRARIES  = libfastahack.la
+
+libfastahackdir=$(includedir)/fastahack
+libfastahack_HEADERS=Fasta.h LargeFileSupport.h Region.h split.h
+libfastahack_la_SOURCES = Fasta.cpp split.cpp
+libfastahack_la_LDFLAGS = -version-info @LIB_VERSION@
+
+libfastahack_la_CPPFLAGS = $(INCLUDES)
+
+bin_PROGRAMS = fastahack
+fastahack_SOURCES = FastaHack.cpp
+LDADD = libfastahack.la -ldisorder
+
+pkgconfigdir=$(libdir)/pkgconfig
+pkgconfig_DATA = libfastahack.pc
+
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,61 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_INIT(fastahack, 0.0, erik.garrison@bc.edu)
+AC_CONFIG_HEADERS([config.h])
+
+AC_PREREQ(2.57)
+
+#	Directory that contains install-sh and other auxiliary files
+AC_CONFIG_AUX_DIR([config])
+
+################################################################################
+#	According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)
+#		this macro should be after AC_INIT but before AM_INIT_AUTOMAKE
+################################################################################
+AC_CONFIG_MACRO_DIR(config)
+
+AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
+
+LIB_VERSION=0:0
+
+AC_SUBST([VERSION])
+AC_SUBST([LIB_VERSION])
+
+AC_SUBST([VERSION])
+
+# Checks for programs.
+AC_PROG_LN_S
+AC_PROG_INSTALL
+AC_PROG_LIBTOOL
+
+################################################################################
+# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
+#	the AX_CXXFLAGS macro below.
+# So we cache the argument to configure
+#	here in ARG_CXX_FLAGS (so that our macro does not override them)
+################################################################################
+ARG_CXX_FLAGS="$CXXFLAGS"
+AC_PROG_CXX
+
+#Ranlib handled by check for libtool
+CXXFLAGS="$ARG_CXX_FLAGS"
+AX_CXXFLAGS
+
+AC_SUBST(CXXFLAGS)
+
+CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"
+# Checks for libraries.
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([stdlib.h])
+
+AC_PROG_MAKE_SET
+
+AC_CONFIG_FILES([
+	Makefile
+	libfastahack.pc
+	])
+AC_OUTPUT
+
--- /dev/null
+++ b/libfastahack.pc.in
@@ -0,0 +1,11 @@
+prefix=@prefix@
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include/fastahack
+
+
+Name: libfastahack
+Version: @VERSION@
+Description: utilities for indexing and sequence extraction from FASTA files
+Libs: -L${libdir} -lfastahack
+Cflags: -I${includedir}
--- a/Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-
-# Use ?= to allow overriding from the env or command-line
-CXX ?=		g++
-CXXFLAGS ?=	-O3
-PREFIX ?=	./stage
-STRIP_CMD ?=	strip
-INSTALL ?=	install -c
-MKDIR ?=	mkdir -p
-
-# Required flags that we shouldn't override
-CXXFLAGS +=	-D_FILE_OFFSET_BITS=64
-
-OBJS =	Fasta.o FastaHack.o split.o disorder.o
-
-all:	fastahack
-
-fastahack: $(OBJS)
-	$(CXX) $(CXXFLAGS) $(OBJS) -o fastahack
-
-FastaHack.o: Fasta.h FastaHack.cpp
-	$(CXX) $(CXXFLAGS) -c FastaHack.cpp
-
-Fasta.o: Fasta.h Fasta.cpp
-	$(CXX) $(CXXFLAGS) -c Fasta.cpp
-
-split.o: split.h split.cpp
-	$(CXX) $(CXXFLAGS) -c split.cpp
-
-disorder.o: disorder.c disorder.h
-	$(CXX) $(CXXFLAGS) -c disorder.c
-
-install: fastahack
-	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
-	$(INSTALL) fastahack $(DESTDIR)$(PREFIX)/bin
-
-install-strip: install
-	$(STRIP_CMD) $(DESTDIR)$(PREFIX)/bin/fastahack
-
-clean:
-	rm -rf fastahack *.o stage
-
-.PHONY: clean