| 1 | # Put objects into subdirs |
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| 2 | AUTOMAKE_OPTIONS = subdir-objects |
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| 3 | |
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| 4 | # Default extension to use when no bla_SOURCES exists. |
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| 5 | AM_DEFAULT_SOURCE_EXT = .cpp |
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| 6 | |
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| 7 | # Macros (like boost) are in the m4 folder |
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| 8 | ACLOCAL_AMFLAGS = -I m4 |
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| 9 | |
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| 10 | # Common flags for preprocessor and linker |
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| 11 | AM_CPPFLAGS = \ |
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| 12 | -I$(top_srcdir)/include \ |
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| 13 | -DBOOST_TEST_DYN_LINK -DBOOST_TEST_MAIN \ |
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| 14 | $(BOOST_CPPFLAGS) \ |
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| 15 | $(ARB_CPPFLAGS) \ |
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| 16 | $(CODE_COVERAGE_CPPFLAGS) \ |
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| 17 | $(TBB_CPPFLAGS) \ |
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| 18 | $(TBB_MALLOC_CPPFLAGS) |
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| 19 | |
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| 20 | AM_LDFLAGS = \ |
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| 21 | $(BOOST_LDFLAGS) \ |
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| 22 | $(ARB_LDFLAGS) \ |
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| 23 | $(TBB_LDFLAGS) \ |
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| 24 | $(TBB_MALLOC_LDFLAGS) |
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| 25 | |
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| 26 | AM_CXXFLAGS = \ |
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| 27 | $(CODE_COVERAGE_CXXFLAGS) |
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| 28 | |
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| 29 | AM_CFLAGS = \ |
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| 30 | $(CODE_COVERAGE_CFLAGS) |
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| 31 | |
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| 32 | |
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| 33 | # Files to copy into distribution packages |
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| 34 | EXTRA_BINDIST = \ |
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| 35 | LICENSE \ |
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| 36 | CHANGELOG \ |
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| 37 | README \ |
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| 38 | arb_LICENSE.txt \ |
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| 39 | arb_PUBLIB_LICENSE.txt |
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| 40 | |
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| 41 | EXTRA_DIST = \ |
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| 42 | $(EXTRA_BINDIST) \ |
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| 43 | Makefile.am \ |
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| 44 | configure.ac \ |
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| 45 | autogen.sh \ |
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| 46 | tools \ |
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| 47 | test_data/ltp_reduced.arb.xz \ |
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| 48 | include \ |
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| 49 | tests |
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| 50 | |
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| 51 | CLEANFILES = \ |
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| 52 | CHANGELOG \ |
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| 53 | README |
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| 54 | |
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| 55 | ### TARGETS ### |
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| 56 | |
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| 57 | # calling pkglibdir our ARBHOME (.../lib/sina), we install |
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| 58 | # internal libs and binaries to .../bin and .../lib subdirs |
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| 59 | |
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| 60 | bin_PROGRAMS = src/sina |
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| 61 | lib_LTLIBRARIES = src/libsina.la |
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| 62 | |
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| 63 | if ENABLE_FAT_TAR |
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| 64 | arblibdir = $(libdir)/arb/lib |
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| 65 | |
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| 66 | bin_PROGRAMS += arb_pt_server arb_message |
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| 67 | arblib_DATA = \ |
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| 68 | arb_tcp.dat |
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| 69 | |
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| 70 | arb_message_SOURCES= |
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| 71 | arb_pt_server_SOURCES= |
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| 72 | endif |
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| 73 | |
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| 74 | ### TARGET CONFIGS ### |
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| 75 | |
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| 76 | src_libsina_la_SOURCES = \ |
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| 77 | src/align.cpp \ |
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| 78 | src/align.h \ |
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| 79 | src/aligned_base.cpp \ |
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| 80 | src/aligned_base.h \ |
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| 81 | src/alignment_stats.cpp \ |
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| 82 | src/alignment_stats.h \ |
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| 83 | src/buffer.h \ |
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| 84 | src/cache.h \ |
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| 85 | src/cseq.cpp \ |
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| 86 | src/cseq.h \ |
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| 87 | src/cseq_impl.h \ |
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| 88 | src/cseq_comparator.cpp \ |
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| 89 | src/cseq_comparator.h \ |
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| 90 | src/famfinder.h \ |
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| 91 | src/famfinder.cpp \ |
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| 92 | src/graph.h \ |
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| 93 | src/helpers.h \ |
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| 94 | src/idset.h \ |
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| 95 | src/mesh.h \ |
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| 96 | src/mesh_debug.h \ |
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| 97 | src/mseq.cpp \ |
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| 98 | src/mseq.h \ |
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| 99 | src/progress.h \ |
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| 100 | src/pseq.cpp \ |
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| 101 | src/pseq.h \ |
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| 102 | src/query_arb.cpp \ |
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| 103 | src/query_arb.h \ |
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| 104 | src/query_pt.cpp \ |
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| 105 | src/query_pt.h \ |
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| 106 | src/rw_fasta.cpp \ |
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| 107 | src/rw_fasta.h \ |
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| 108 | src/rw_arb.cpp \ |
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| 109 | src/rw_arb.h \ |
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| 110 | src/rw_csv.cpp \ |
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| 111 | src/rw_csv.h \ |
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| 112 | src/log.cpp \ |
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| 113 | src/log.h \ |
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| 114 | src/scoring_schemes.h \ |
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| 115 | src/search.h \ |
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| 116 | src/search.cpp \ |
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| 117 | src/search_filter.cpp \ |
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| 118 | src/search_filter.h \ |
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| 119 | src/tempfile.h \ |
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| 120 | src/timer.h \ |
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| 121 | src/tray.cpp \ |
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| 122 | src/tray.h \ |
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| 123 | src/kmer.h \ |
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| 124 | src/kmer_search.cpp \ |
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| 125 | src/kmer_search.h |
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| 126 | |
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| 127 | src_libsina_la_LDFLAGS = \ |
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| 128 | $(ARB_LDFLAGS) \ |
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| 129 | $(BOOST_LDFLAGS) |
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| 130 | |
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| 131 | src_libsina_la_LIBADD = \ |
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| 132 | $(Z_LIB) \ |
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| 133 | $(ARB_LIBS) \ |
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| 134 | $(BOOST_PROGRAM_OPTIONS_LIB) \ |
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| 135 | $(BOOST_THREAD_LIB) \ |
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| 136 | $(BOOST_IOSTREAMS_LIB) \ |
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| 137 | $(BOOST_SYSTEM_LIB) \ |
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| 138 | $(BOOST_FILESYSTEM_LIB) \ |
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| 139 | $(TBB_LIB) \ |
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| 140 | $(TBB_MALLOC_LIB) |
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| 141 | |
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| 142 | sina_libs = \ |
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| 143 | src/libsina.la \ |
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| 144 | $(ARB_PROBE_LIBS) \ |
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| 145 | $(ARB_HELIX_LIBS) \ |
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| 146 | $(ARB_LIBS) \ |
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| 147 | $(CODE_COVERAGE_LIBS) |
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| 148 | |
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| 149 | src_sina_LDADD = $(sina_libs) |
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| 150 | |
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| 151 | arb_pt_server$(EXEEXT): $(ARBHOME)/bin/arb_pt_server$(EXEEXT) |
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| 152 | cp $< $@ |
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| 153 | arb_message$(EXEEXT): $(ARBHOME)/bin/arb_message$(EXEXT) |
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| 154 | cp $< $@ |
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| 155 | arb_tcp.dat: $(ARBHOME)/lib/arb_tcp.dat |
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| 156 | cp $< $@ |
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| 157 | |
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| 158 | |
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| 159 | @CODE_COVERAGE_RULES@ |
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| 160 | CODE_COVERAGE_DIRECTORY = $(top_builddir)/src |
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| 161 | CODE_COVERAGE_OUTPUT_DIRECTORY = $(top_builddir)/coverage |
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| 162 | CODE_COVERAGE_OUTPUT_FILE = $(top_builddir)/coverage.info |
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| 163 | header_paths = $(abspath $(patsubst -I%,%,$(filter -I%,$(AM_CPPFLAGS) $(CPPFLAGS)))) |
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| 164 | CODE_COVERAGE_IGNORE_PATTERN = \ |
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| 165 | $(patsubst %,%/\*,$(header_paths) /usr) \ |
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| 166 | \*/c++/\* \ |
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| 167 | \*unit_tests\* \ |
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| 168 | \*include\* |
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| 169 | |
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| 170 | ### DOCUMENTATION ### |
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| 171 | |
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| 172 | DOC_SOURCE = \ |
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| 173 | doc/source/conf.py \ |
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| 174 | doc/source/index.rst \ |
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| 175 | doc/source/fields.rst \ |
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| 176 | doc/source/install.rst \ |
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| 177 | doc/source/commandline.rst \ |
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| 178 | doc/source/CHANGELOG.rst \ |
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| 179 | doc/source/README.rst \ |
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| 180 | README.rst |
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| 181 | |
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| 182 | doc_DATA := $(filter %.txt,$(DOC_SOURCE:doc/source/%.rst=doc/text/%.txt)) |
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| 183 | |
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| 184 | EXTRA_DIST += $(DOC_SOURCE) |
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| 185 | |
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| 186 | man1_MANS = doc/man/sina.1 |
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| 187 | |
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| 188 | |
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| 189 | $(doc_DATA): doc/build.stamp |
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| 190 | doc/build.stamp: $(DOC_SOURCE) |
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| 191 | $(SPHINX_BUILD) -M text $$(dirname $<) doc |
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| 192 | touch $@ |
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| 193 | CLEANFILES += doc/build.stamp |
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| 194 | |
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| 195 | $(man1_MANS): $(DOC_SOURCE) |
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| 196 | $(SPHINX_BUILD) -M man $$(dirname $<) doc |
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| 197 | |
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| 198 | %: doc/text/%.txt |
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| 199 | cp $< $@ |
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| 200 | |
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| 201 | |
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| 202 | |
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| 203 | CLEANFILES += sina-manual.log |
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| 204 | LATEXTOMAN=$(top_srcdir)/tools/latex2man |
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| 205 | |
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| 206 | export TEXINPUTS=$(top_srcdir):$(top_srcdir)/tools/: |
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| 207 | |
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| 208 | CLEANFILES += $(doc_DATA) $(check_DATA) $(man1_MANS) |
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| 209 | |
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| 210 | clean-local-docs: |
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| 211 | rm -rf doc/doctrees |
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| 212 | |
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| 213 | |
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| 214 | ### PACKAGE ### |
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| 215 | |
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| 216 | |
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| 217 | dist-hook: |
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| 218 | find $(distdir) \( -name \*~ -or -name \*.log -or -name \*.arb \) -delete |
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| 219 | |
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| 220 | |
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| 221 | BINDISTFILES = |
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| 222 | bindistdir = $(PACKAGE)-$(VERSION)-$(OSNAME) |
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| 223 | |
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| 224 | bindistdir: all |
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| 225 | rm -rf $(bindistdir) |
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| 226 | mkdir $(bindistdir) |
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| 227 | $(MAKE) DESTDIR=$(abspath $(bindistdir)) install |
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| 228 | mv -f $(bindistdir)/$(prefix)/* $(bindistdir) |
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| 229 | cd $(bindistdir); for f in bin/sina share/doc/sina*; do \ |
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| 230 | test -f $$f && $(LN_S) $$f; done || true |
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| 231 | for f in $(EXTRA_BINDIST); do \ |
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| 232 | cp -fpR $(top_srcdir)/$$f $(bindistdir)/$$f 2>/dev/null || \ |
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| 233 | cp -fpR $(top_builddir)/$$f $(bindistdir)/$$f; done; \ |
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| 234 | find $(bindistdir) -depth -type d -empty -exec rmdir {} \; |
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| 235 | binaries=$$(find $(bindistdir) -type f -exec file --mime {} \; | \ |
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| 236 | $(GREP) -E "application/x-.*(mach|executable|sharedlib)" | cut -d: -f1); \ |
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| 237 | export LDPATHS="$(subst -L,,$(filter -L%, $(BOOST_LDFLAGS)))"; \ |
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| 238 | for binary in $$binaries; do $(top_srcdir)/tools/fix_libpaths.sh "$$binary"; done; \ |
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| 239 | find $(bindistdir) \( -name \*.la -or -name \*.a \) -delete |
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| 240 | |
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| 241 | tar_allow_lns = $${TAR-tar} cof - "$$tardir" |
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| 242 | bindist-gzip: bindistdir |
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| 243 | tardir=$(bindistdir) && $(tar_allow_lns) | GZIP=$(GZIP_ENV) gzip -c >$(bindistdir).tar.gz |
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| 244 | rm -rf $(bindistdir) |
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| 245 | bindist-bzip2: bindistdir |
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| 246 | tardir=$(bindistdir) && $(tar_allow_lns) | BZIP2=$${BZIP2--9} bzip2 -c >$(bindistdir).tar.bz2 |
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| 247 | rm -rf $(bindistdir) |
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| 248 | |
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| 249 | |
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| 250 | .PHONY: bindistdir bindist-gzip bindist-bzip2 |
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| 251 | |
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| 252 | |
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| 253 | ### Unit Tests ### |
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| 254 | |
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| 255 | test_libs = \ |
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| 256 | $(sina_libs) \ |
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| 257 | $(BOOST_UNIT_TEST_FRAMEWORK_LIB) \ |
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| 258 | $(BOOST_SYSTEM_LIB) |
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| 259 | |
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| 260 | LOG_COMPILER = $(top_srcdir)/tools/test_driver.sh |
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| 261 | |
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| 262 | TEST_LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) \ |
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| 263 | $(top_srcdir)/build-aux/tap-driver.sh --comments |
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| 264 | |
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| 265 | check_PROGRAMS = \ |
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| 266 | src/unit_tests/cseq_test \ |
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| 267 | src/unit_tests/cseq_comparator_test \ |
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| 268 | src/unit_tests/idset_test \ |
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| 269 | src/unit_tests/kmer_test \ |
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| 270 | src/unit_tests/kmer_search_test \ |
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| 271 | src/unit_tests/famfinder_test \ |
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| 272 | src/unit_tests/progress_test \ |
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| 273 | src/unit_tests/rw_csv_test \ |
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| 274 | src/unit_tests/query_arb_test |
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| 275 | |
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| 276 | src_unit_tests_cseq_test_LDADD = $(test_libs) |
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| 277 | src_unit_tests_cseq_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 278 | src_unit_tests_cseq_comparator_test_LDADD = $(test_libs) |
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| 279 | src_unit_tests_cseq_comparator_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 280 | src_unit_tests_idset_test_LDADD = $(test_libs) |
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| 281 | src_unit_tests_idset_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 282 | src_unit_tests_kmer_test_LDADD = $(test_libs) |
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| 283 | src_unit_tests_kmer_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 284 | src_unit_tests_kmer_search_test_LDADD = $(test_libs) |
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| 285 | src_unit_tests_kmer_search_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 286 | src_unit_tests_famfinder_test_LDADD = $(test_libs) |
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| 287 | src_unit_tests_famfinder_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 288 | src_unit_tests_rw_csv_test_LDADD = $(test_libs) |
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| 289 | src_unit_tests_rw_csv_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 290 | src_unit_tests_query_arb_test_LDADD = $(test_libs) |
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| 291 | src_unit_tests_query_arb_test_LDFLAGS = $(ARB_LDFLAGS) |
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| 292 | src_unit_tests_progress_test_LDADD = $(BOOST_UNIT_TEST_FRAMEWORK_LIB) |
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| 293 | |
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| 294 | test_scripts = \ |
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| 295 | tests/readwrite.test \ |
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| 296 | tests/align.test \ |
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| 297 | tests/search.test \ |
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| 298 | tests/infocommands.test \ |
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| 299 | tests/accuracy_kmer.test \ |
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| 300 | tests/accuracy.test |
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| 301 | |
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| 302 | |
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| 303 | check_DATA = test_data/ltp_reduced.arb |
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| 304 | |
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| 305 | TESTS = $(check_PROGRAMS) $(test_scripts) |
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| 306 | |
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| 307 | ## add `make check-filtered P=<pattern>` |
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| 308 | P ?= / |
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| 309 | # call contains, MATCH, WORDS - filters by substr |
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| 310 | contains = $(foreach v,$(2),$(if $(findstring $(1),$(v)),$(v),)) |
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| 311 | # call strip_term - removes leading ^ and trailing $ |
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| 312 | strip_term = $(patsubst ^%,%,$(patsubst %$$,%,$(1))) |
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| 313 | # call add_term - adds leading ^ and trailing $ |
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| 314 | add_term = $(patsubst %,^%$$,$(1)) |
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| 315 | # call contains_term MATCH WORDS - filters by substr with ^ and $ matching start/end |
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| 316 | contains_term = $(call strip_term,$(call contains,$(1),$(call add_term,$(2)))) |
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| 317 | filtered_tests = $(foreach v,$(P),$(call contains_term,$(v),$(TEST_LOGS))) |
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| 318 | check-filtered: |
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| 319 | $(MAKE) $(AM_MAKEFLAGS) check TEST_LOGS="$(filtered_tests)" |
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| 320 | .PHONY: check-filtered |
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| 321 | |
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| 322 | ## pass ARGS to tests |
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| 323 | TEST_ARGS := $(check_DATA) $(TEST_EXTRA_ARGS) |
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| 324 | export TEST_ARGS |
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| 325 | $(test_scripts): $(bin_PROGRAMS) $(check_DATA) tests/test_helper.sh |
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| 326 | |
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| 327 | ## unzip source test data into build folder |
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| 328 | test_data/%: test_data/%.xz |
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| 329 | mkdir -p $$(dirname $@) |
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| 330 | unxz -c $< > $@ |
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| 331 | |
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| 332 | clean-local: clean-local-check clean-local-docs |
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| 333 | |
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| 334 | clean-local-check: |
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| 335 | rm -f test.*.xml |
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| 336 | rm -f test_data/ltp_reduced.arb.* |
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| 337 | rm -f test_data/ltp_reduced.sidx |
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| 338 | |
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| 339 | .PHONY: clean-local-check clean-local-docs |
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| 340 | |
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| 341 | |
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