LIBS = -lhts -lz -lpthread

CXXFLAGS = -g -std=c++11 -Wall -Wextra -Werror

TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search
check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search
check_primer_trim_SOURCES = test_primer_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_trim_SOURCES = test_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_quality_trim_SOURCES = check_quality_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_consensus_SOURCES = test_call_consensus_from_plup.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp
check_allele_depth_SOURCES = test_allele_depth.cpp ../src/allele_functions.cpp
check_consensus_threshold_SOURCES = test_consensus_threshold.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp
check_consensus_min_depth_SOURCES = test_consensus_min_depth.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp
check_consensus_seq_id_SOURCES = test_consensus_seq_id.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp
check_variants_SOURCES = test_variants.cpp ../src/call_variants.cpp ../src/allele_functions.cpp ../src/parse_gff.cpp ../src/ref_seq.cpp
check_common_variants_SOURCES = test_common_variants.cpp ../src/get_common_variants.cpp
check_primer_bed_SOURCES = test_primer_bed.cpp ../src/primer_bed.cpp
check_getmasked_SOURCES = test_getmasked.cpp ../src/get_masked_amplicons.cpp ../src/primer_bed.cpp
check_removereads_SOURCES = test_removereads.cpp ../src/remove_reads_from_amplicon.cpp ../src/primer_bed.cpp ../src/trim_primer_quality.cpp ../src/interval_tree.cpp
check_unpaired_trim_SOURCES = test_unpaired_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_primer_trim_edge_cases_SOURCES = test_primer_trim_edge_cases.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_isize_trim_SOURCES = test_isize_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_interval_tree_SOURCES = test_interval_tree.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp