Makefile_backup

CXXFLAGS=-std=c++11 -stdlib=libc++

all: process_vcf_latest

process_vcf_latest: process_vcf.o process_vcf_abba_baba.o process_vcf_get_aa_seq.o process_vcf_cbs.o process_vcf_fill_aa.o process_vcf_join_multiFasta.o process_vcf_utils.o process_vcf_IUPAC.o process_vcf_annotation_tools.o process_vcf_print_routines.o process_vcf_stats.o process_vcf_stats_functions.o process_vcf_filter.o process_vcf_variant_sharing.o process_vcf_testing.o process_vcf_massoko.o process_vcf_get_sequences.o process_vcf_coding_sequences.o process_vcf_sequenom.o process_vcf_use_map.o process_vcf_fixed_search.o process_vcf_search_sex.o process_vcf_mt_sequences.o process_vcf_stats_testing.o process_vcf_reorder.o process_vcf_vcf_from_sequenom.o process_vcf_fst.o process_vcf_merge.o
	g++ process_vcf.o process_vcf_abba_baba.o process_vcf_get_aa_seq.o process_vcf_cbs.o process_vcf_fill_aa.o process_vcf_join_multiFasta.o process_vcf_utils.o process_vcf_IUPAC.o process_vcf_annotation_tools.o process_vcf_print_routines.o process_vcf_stats.o process_vcf_stats_functions.o process_vcf_filter.o process_vcf_variant_sharing.o process_vcf_testing.o process_vcf_massoko.o process_vcf_get_sequences.o process_vcf_coding_sequences.o process_vcf_sequenom.o process_vcf_use_map.o process_vcf_fixed_search.o process_vcf_search_sex.o process_vcf_mt_sequences.o process_vcf_stats_testing.o process_vcf_reorder.o process_vcf_vcf_from_sequenom.o process_vcf_fst.o process_vcf_merge.o -o process_vcf_latest -lz

process_vcf.o: process_vcf.cpp
	g++ -c process_vcf.cpp


process_vcf_abba_baba.o: process_vcf_abba_baba.cpp process_vcf_abba_baba.h process_vcf_stats_utils.h
	g++ -c process_vcf_abba_baba.cpp

process_vcf_get_aa_seq.o: process_vcf_get_aa_seq.cpp process_vcf_get_aa_seq.h
	g++ -c process_vcf_get_aa_seq.cpp

process_vcf_cbs.o: process_vcf_cbs.cpp process_vcf_seq_utils.h process_vcf_utils.h process_vcf_stats_utils.h
	g++ -c process_vcf_cbs.cpp

process_vcf_utils.o: process_vcf_utils.cpp
	g++ -c process_vcf_utils.cpp ${CXXFLAGS}

process_vcf_fst.o: process_vcf_fst.cpp process_vcf_fst.h process_vcf_annotation_tools.h process_vcf_stats_utils.h
	g++ -c process_vcf_fst.cpp ${CXXFLAGS}

process_vcf_IUPAC.o: process_vcf_IUPAC.cpp
	g++ -c process_vcf_IUPAC.cpp

process_vcf_annotation_tools.o: process_vcf_annotation_tools.cpp
	g++ -c process_vcf_annotation_tools.cpp

process_vcf_print_routines.o: process_vcf_print_routines.cpp
	g++ -c process_vcf_print_routines.cpp

process_vcf_stats.o: process_vcf_stats.cpp
	g++ -c process_vcf_stats.cpp

process_vcf_stats_functions.o: process_vcf_stats_functions.cpp
	g++ -c process_vcf_stats_functions.cpp

process_vcf_fill_aa.o: process_vcf_fill_aa.cpp process_vcf_fill_aa.h
	g++ -c process_vcf_fill_aa.cpp

process_vcf_filter.o: process_vcf_filter.cpp
	g++ -c process_vcf_filter.cpp

process_vcf_join_multiFasta.o: process_vcf_join_multiFasta.cpp 
	g++ -c process_vcf_join_multiFasta.cpp

process_vcf_variant_sharing.o: process_vcf_variant_sharing.cpp
	g++ -c process_vcf_variant_sharing.cpp

process_vcf_testing.o: process_vcf_testing.cpp
	g++ -c process_vcf_testing.cpp

process_vcf_massoko.o: process_vcf_massoko.cpp
	g++ -c process_vcf_massoko.cpp

process_vcf_get_sequences.o: process_vcf_get_sequences.cpp process_vcf_seq_utils.h 
	g++ -c process_vcf_get_sequences.cpp

process_vcf_coding_sequences.o: process_vcf_coding_sequences.cpp process_vcf_IUPAC.h process_vcf_annotation_tools.h process_vcf_seq_utils.h
	g++ -c process_vcf_coding_sequences.cpp

process_vcf_sequenom.o: process_vcf_sequenom.cpp
	g++ -c process_vcf_sequenom.cpp

process_vcf_use_map.o: process_vcf_use_map.cpp
	g++ -c process_vcf_use_map.cpp

process_vcf_fixed_search.o: process_vcf_fixed_search.cpp
	g++ -c process_vcf_fixed_search.cpp

process_vcf_search_sex.o: process_vcf_search_sex.cpp process_vcf_search_sex.h process_vcf_stats_utils.h process_vcf_utils.h
	g++ -c process_vcf_search_sex.cpp

process_vcf_reorder.o: process_vcf_reorder.cpp
	g++ -c process_vcf_reorder.cpp

process_vcf_mt_sequences.o: process_vcf_mt_sequences.cpp
	g++ -c process_vcf_mt_sequences.cpp

process_vcf_stats_testing.o: process_vcf_stats_testing.cpp process_vcf_stats_utils.h
	g++ -c process_vcf_stats_testing.cpp

process_vcf_vcf_from_sequenom.o: process_vcf_vcf_from_sequenom.cpp process_vcf_vcf_from_sequenom.h
	g++ -c process_vcf_vcf_from_sequenom.cpp

process_vcf_merge.o: process_vcf_merge.cpp
	g++ -c process_vcf_merge.cpp