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noinst_LIBRARIES = libalign.a
libalign_a_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
libalign_a_SOURCES = \
alignGlobal.cc alignGlobal.h \
dialign.cpp dialign.h dna_diag_prob.cc \
smith_waterman.cpp smith_waterman.h Options.h
bin_PROGRAMS = abyss-align abyss-mergepairs
abyss_align_CPPFLAGS = -I$(top_srcdir) \
-I$(top_srcdir)/Common \
-I$(top_srcdir)/DataLayer
abyss_align_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
abyss_align_LDADD = $(builddir)/libalign.a \
$(top_builddir)/dialign/libdialign.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
abyss_align_SOURCES = align.cc
abyss_mergepairs_CPPFLAGS = -I$(top_srcdir) \
-I$(top_srcdir)/Common \
-I$(top_srcdir)/DataLayer
abyss_mergepairs_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
abyss_mergepairs_LDADD = $(builddir)/libalign.a \
$(top_builddir)/dialign/libdialign.a \
$(top_builddir)/DataLayer/libdatalayer.a \
$(top_builddir)/Common/libcommon.a
abyss_mergepairs_SOURCES = mergepairs.cc
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