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AM_LDFLAGS = -fopenmp -pthread
LIBS = $(top_srcdir)/lib/libassembly.a @LIBS@
AM_CXXFLAGS = -Wall -O3 -fopenmp -pthread
INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/gtest_src
shuffle_reads_SOURCES = $(top_srcdir)/src/tools/shuffle_reads.cpp
scaffold_SOURCES = $(top_srcdir)/src/tools/scaffold.cpp
validate_component_SOURCES = $(top_srcdir)/src/tools/validate_component.cpp
fa2fq_SOURCES = $(top_srcdir)/src/tools/fa2fq.cpp
validate_rna_SOURCES = $(top_srcdir)/src/tools/validate_rna.cpp
validate_contigs_mummer_SOURCES = $(top_srcdir)/src/tools/validate_contigs_mummer.cpp
print_graph_SOURCES = $(top_srcdir)/src/tools/print_graph.cpp
idba_tran_test_SOURCES = $(top_srcdir)/src/tools/idba_tran_test.cpp
sample_reads_SOURCES = $(top_srcdir)/src/tools/sample_reads.cpp
sort_psl_SOURCES = $(top_srcdir)/src/tools/sort_psl.cpp
sort_reads_SOURCES = $(top_srcdir)/src/tools/sort_reads.cpp
filter_contigs_SOURCES = $(top_srcdir)/src/tools/filter_contigs.cpp
parallel_rna_blat_SOURCES = $(top_srcdir)/src/tools/parallel_rna_blat.cpp
filter_blat_SOURCES = $(top_srcdir)/src/tools/filter_blat.cpp
split_fa_SOURCES = $(top_srcdir)/src/tools/split_fa.cpp
test_SOURCES = $(top_srcdir)/src/tools/test.cpp
validate_reads_blat_SOURCES = $(top_srcdir)/src/tools/validate_reads_blat.cpp
split_fq_SOURCES = $(top_srcdir)/src/tools/split_fq.cpp
fq2fa_SOURCES = $(top_srcdir)/src/release/fq2fa.cpp
validate_contigs_blat_SOURCES = $(top_srcdir)/src/release/validate_contigs_blat.cpp
idba_ud_SOURCES = $(top_srcdir)/src/release/idba_ud.cpp
raw_n50_SOURCES = $(top_srcdir)/src/release/raw_n50.cpp
idba_tran_SOURCES = $(top_srcdir)/src/release/idba_tran.cpp
idba_hybrid_SOURCES = $(top_srcdir)/src/release/idba_hybrid.cpp
parallel_blat_SOURCES = $(top_srcdir)/src/release/parallel_blat.cpp
sim_reads_tran_SOURCES = $(top_srcdir)/src/release/sim_reads_tran.cpp
filterfa_SOURCES = $(top_srcdir)/src/release/filterfa.cpp
idba_SOURCES = $(top_srcdir)/src/release/idba.cpp
split_scaffold_SOURCES = $(top_srcdir)/src/release/split_scaffold.cpp
sim_reads_SOURCES = $(top_srcdir)/src/release/sim_reads.cpp
bin_PROGRAMS = \
idba_hybrid
noinst_PROGRAMS = \
shuffle_reads \
scaffold \
validate_component \
fa2fq \
validate_rna \
validate_contigs_mummer \
print_graph \
idba_tran_test \
sample_reads \
sort_psl \
sort_reads \
filter_contigs \
parallel_rna_blat \
filter_blat \
split_fa \
test \
validate_reads_blat \
split_fq \
fq2fa \
validate_contigs_blat \
idba_ud \
raw_n50 \
idba_tran \
parallel_blat \
sim_reads_tran \
filterfa \
idba \
split_scaffold \
sim_reads
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