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bin_PROGRAMS = abyss-index abyss-map abyss-map-ssq abyss-overlap
abyss_index_CPPFLAGS = -I$(top_srcdir) \
-I$(top_srcdir)/Common \
-I$(top_srcdir)/DataLayer \
-I$(top_srcdir)/FMIndex
abyss_index_LDADD = \
$(top_builddir)/FMIndex/libfmindex.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
abyss_index_SOURCES = index.cc
abyss_map_CPPFLAGS = -I$(top_srcdir) \
-I$(top_srcdir)/Common \
-I$(top_srcdir)/DataLayer \
-I$(top_srcdir)/FMIndex
abyss_map_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
abyss_map_LDADD = \
$(top_builddir)/FMIndex/libfmindex.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a \
$(top_builddir)/DataBase/libdb.a \
$(SQLITE_LIBS)
abyss_map_SOURCES = map.cc
abyss_map_ssq_CPPFLAGS = $(abyss_map_CPPFLAGS) \
-D SAM_SEQ_QUAL=1
abyss_map_ssq_CXXFLAGS = $(abyss_map_CXXFLAGS)
abyss_map_ssq_LDADD = $(abyss_map_LDADD)
abyss_map_ssq_SOURCES = $(abyss_map_SOURCES)
abyss_overlap_CPPFLAGS = -I$(top_srcdir) \
-I$(top_srcdir)/Common \
-I$(top_srcdir)/DataLayer \
-I$(top_srcdir)/FMIndex
abyss_overlap_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
abyss_overlap_LDADD = \
$(top_builddir)/FMIndex/libfmindex.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
abyss_overlap_SOURCES = overlap.cc
CXXFLAGS += -Wno-deprecated-declarations
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