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# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59) ## specificy version of autoconf
AC_INIT(seqkit, 1.0, jeremiah.wala@gmail.com)
AM_INIT_AUTOMAKE(foreign)
AC_CONFIG_SRCDIR([src/BamReader.cpp])
AC_CONFIG_HEADER([config.h])
AM_MAINTAINER_MODE([disable])
##m4_include([m4/m4_ax_openmp.m4])
LIB_VERSION=2:0
AC_SUBST([VERSION])
AC_SUBST([LIB_VERSION])
# Checks for programs.
AC_PROG_CXX ## test for cpp compiler
AC_PROG_CC ## test for C compiler
AC_PROG_RANLIB ## required if libraries are built in package
AC_PROG_LIBTOOL
# Check for headers
AC_LANG([C++])
AC_CHECK_HEADER([zlib.h])
# Check for libraries
AC_SEARCH_LIBS([gzopen],[z],,[AC_MSG_ERROR([libz not found, please install zlib (http://www.zlib.net/)])])
AC_SEARCH_LIBS([lzma_code],[lzma],,[AC_MSG_ERROR([liblzma not found, please install lzma (http://www.7-zip.org/sdk.html)])])
AC_SEARCH_LIBS([BZ2_bzBuffToBuffDecompress],[bz2],,[AC_MSG_ERROR([lib bz2 not found, please install])])
AC_SEARCH_LIBS([clock_gettime], [rt], [AC_DEFINE([HAVE_CLOCK_GETTIME], [1], [clock_getttime found])], )
# check for c++11
#AX_CXX_COMPILE_STDCXX_11(,[optional])
# Only fail on warnings when the --enable-development flag is passed into configure
AC_ARG_ENABLE(development, AS_HELP_STRING([--enable-development],
[Turn on development options, like failing compilation on warnings]))
if test "$enable_development"; then
fail_on_warning="-Werror"
fi
PKG_CHECK_MODULES([hts], [htslib])
# Set compiler flags.
AC_SUBST(AM_CXXFLAGS, "-g $fail_on_warning -std=c++11 -Wno-unknown-pragmas")
AC_SUBST(CXXFLAGS, "$CXXFLAGS")
AC_SUBST(CFLAGS, "$CFLAGS")
AC_SUBST(LDFLAGS, "$LDFLAGS")
# We always need to specify to link in external libraries
AC_SUBST(LIBS, "$LIBS -pthread")
AC_CONFIG_FILES([Makefile
src/Makefile
src/seqtools/Makefile
libseqlib.pc
])
AC_OUTPUT
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