Merge pull request #37 from andrewjpage/master

Reduce times input file is opened

Author: andrewjpage

VERSION

@@ -1 +1 @@
-2.0.3
+2.1.0

configure.ac

@@ -1,14 +1,25 @@
 AC_INIT([snp-sites], [1])
-AM_INIT_AUTOMAKE([foreign])
+AM_INIT_AUTOMAKE([foreign subdir-objects])
 AC_CONFIG_SRCDIR([configure.ac])
 AC_CONFIG_HEADERS([config.h])   
 AC_CONFIG_MACRO_DIR([m4])
 
+AC_CANONICAL_HOST
+
+case $host_os in
+	*linux*)
+		HOST_OS=linux
+		;;
+	*) ;;
+esac
+
+AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux])
+
+AC_CHECK_HEADERS([zlib.h math.h])
+
 AC_PROG_LIBTOOL
 AC_PROG_CC                                   
 AC_PROG_CXX
 
 AC_CONFIG_FILES([Makefile src/Makefile])
 AC_OUTPUT
-
-AC_CHECK_HEADERS([zlib.h math.h])

src/Makefile.am

@@ -1,23 +1,18 @@
-# ship these headers in the "make dist" target
-
-#This is how the header files were originaly being installed.
-#dist_data_DATA = alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h parse-phylip.h string-cat.h kseq.h
-
-#The problem with the above is that the header files end up in /usr/share, which is far from ideal.
-#They should all be installed to /usr/include/snp-sites/.
-#Having spoken to John Marshall, this is how it should be done
 snpsitesincludedir=$(includedir)/snp-sites
-snpsitesinclude_HEADERS=alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h parse-phylip.h string-cat.h kseq.h
-
+snpsitesinclude_HEADERS=alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h kseq.h
 
-# snp_sites is our top level progra
 bin_PROGRAMS = snp-sites
 snp_sites_SOURCES = main.c
-snp_sites_LDADD=-lm libsnp-sites.la -lz -lpthread -lrt
+
+
+snp_sites_LDADD =-lm libsnp-sites.la -lz -lpthread
+if HOST_LINUX
+snp_sites_LDADD += -lrt
+endif
 
 # libsnp_sites.so is our library
 lib_LTLIBRARIES = libsnp-sites.la
-libsnp_sites_la_SOURCES = alignment-file.c vcf.c phylib-of-snp-sites.c snp-sites.c fasta-of-snp-sites.c parse-phylip.c string-cat.c
+libsnp_sites_la_SOURCES = alignment-file.c vcf.c phylib-of-snp-sites.c snp-sites.c fasta-of-snp-sites.c
 libsnp_sites_la_LDFLAGS= -version-info 1:0
 
 # "make check" target
@@ -29,4 +24,8 @@ run_all_tests_SOURCES = \
 	../tests/helper-methods.c \
 	../tests/run-all-tests.c
 run_all_tests_CFLAGS = -I../tests
-run_all_tests_LDADD = -lm -lcheck -lsubunit libsnp-sites.la -lz -lpthread -lrt
+
+run_all_tests_LDADD = -lm -lcheck libsnp-sites.la -lz -lpthread
+if HOST_LINUX
+run_all_tests_LDADD += -lrt
+endif