c_cpp/etc/jellyfish/Makefile.in

   1 # Makefile.in generated by automake 1.11 from Makefile.am.
   2 # @configure_input@
   3
   4 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
   5 # 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
   6 # Inc.
   7 # This Makefile.in is free software; the Free Software Foundation
   8 # gives unlimited permission to copy and/or distribute it,
   9 # with or without modifications, as long as this notice is preserved.
  10
  11 # This program is distributed in the hope that it will be useful,
  12 # but WITHOUT ANY WARRANTY, to the extent permitted by law; without
  13 # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
  14 # PARTICULAR PURPOSE.
  15
  16 @SET_MAKE@
  17
  18
  19
  20
  21 VPATH = @srcdir@
  22 pkgdatadir = $(datadir)/@PACKAGE@
  23 pkgincludedir = $(includedir)/@PACKAGE@
  24 pkglibdir = $(libdir)/@PACKAGE@
  25 pkglibexecdir = $(libexecdir)/@PACKAGE@
  26 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
  27 install_sh_DATA = $(install_sh) -c -m 644
  28 install_sh_PROGRAM = $(install_sh) -c
  29 install_sh_SCRIPT = $(install_sh) -c
  30 INSTALL_HEADER = $(INSTALL_DATA)
  31 transform = $(program_transform_name)
  32 NORMAL_INSTALL = :
  33 PRE_INSTALL = :
  34 POST_INSTALL = :
  35 NORMAL_UNINSTALL = :
  36 PRE_UNINSTALL = :
  37 POST_UNINSTALL = :
  38 build_triplet = @build@
  39 host_triplet = @host@
  40 bin_PROGRAMS = bin/jellyfish$(EXEEXT)
  41 check_PROGRAMS = bin/generate_sequence$(EXEEXT) \
  42         bin/test_double_fifo_input$(EXEEXT) \
  43         bin/test_read_parser$(EXEEXT) \
  44         bin/test_offsets_key_value$(EXEEXT)
  45 DIST_COMMON = README $(am__configure_deps) $(library_include_HEADERS) \
  46         $(noinst_HEADERS) $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
  47         $(srcdir)/config.h.in $(srcdir)/gtest.mk \
  48         $(srcdir)/jellyfish-1.1.pc.in $(top_srcdir)/configure \
  49         $(top_srcdir)/tests/compat.sh.in config.guess config.sub \
  50         depcomp install-sh ltmain.sh missing
  51 subdir = .
  52 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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  54         $(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
  55         $(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \
  56         $(top_srcdir)/configure.ac
  57 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
  58         $(ACLOCAL_M4)
  59 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
  60  configure.lineno config.status.lineno
  61 mkinstalldirs = $(install_sh) -d
  62 CONFIG_HEADER = config.h
  63 CONFIG_CLEAN_FILES = tests/compat.sh jellyfish-1.1.pc
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  83 am__base_list = \
  84   sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
  85   sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
  86 am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" \
  87         "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(pkgconfigdir)" \
  88         "$(DESTDIR)$(library_includedir)"
  89 LTLIBRARIES = $(lib_LTLIBRARIES)
  90 libgtest_la_LIBADD =
  91 am__dirstamp = $(am__leading_dot)dirstamp
  92 am_libgtest_la_OBJECTS =  \
  93         unit_tests/gtest/src/libgtest_la-gtest-all.lo
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  95 AM_V_lt = $(am__v_lt_$(V))
  96 am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
  97 am__v_lt_0 = --silent
  98 libgtest_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
  99         $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(libgtest_la_CXXFLAGS) \
 100         $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
 101 libgtest_main_la_DEPENDENCIES = libgtest.la
 102 am_libgtest_main_la_OBJECTS =  \
 103         unit_tests/gtest/src/libgtest_main_la-gtest_main.lo
 104 libgtest_main_la_OBJECTS = $(am_libgtest_main_la_OBJECTS)
 105 libgtest_main_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX \
 106         $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CXXLD) \
 107         $(libgtest_main_la_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
 108         $(LDFLAGS) -o $@
 109 libjellyfish_la_LIBADD =
 110 am_libjellyfish_la_OBJECTS =  \
 111         jellyfish/libjellyfish_la-square_binary_matrix.lo \
 112         jellyfish/libjellyfish_la-err.lo \
 113         jellyfish/libjellyfish_la-misc.lo \
 114         jellyfish/libjellyfish_la-storage.lo \
 115         jellyfish/libjellyfish_la-thread_exec.lo \
 116         jellyfish/libjellyfish_la-time.lo \
 117         jellyfish/libjellyfish_la-file_parser.lo \
 118         jellyfish/libjellyfish_la-read_parser.lo \
 119         jellyfish/libjellyfish_la-parse_read.lo \
 120         jellyfish/libjellyfish_la-half.lo \
 121         jellyfish/libjellyfish_la-mapped_file.lo \
 122         jellyfish/libjellyfish_la-parse_dna.lo \
 123         jellyfish/libjellyfish_la-parse_quake.lo \
 124         jellyfish/libjellyfish_la-parse_qual_dna.lo \
 125         jellyfish/libjellyfish_la-sequence_parser.lo \
 126         jellyfish/libjellyfish_la-seq_qual_parser.lo \
 127         jellyfish/libjellyfish_la-backtrace.lo \
 128         jellyfish/libjellyfish_la-floats.lo \
 129         jellyfish/libjellyfish_la-dbg.lo \
 130         jellyfish/libjellyfish_la-allocators_mmap.lo
 131 libjellyfish_la_OBJECTS = $(am_libjellyfish_la_OBJECTS)
 132 libjellyfish_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX \
 133         $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CXXLD) \
 134         $(AM_CXXFLAGS) $(CXXFLAGS) $(libjellyfish_la_LDFLAGS) \
 135         $(LDFLAGS) -o $@
 136 PROGRAMS = $(bin_PROGRAMS)
 137 am_bin_generate_sequence_OBJECTS =  \
 138         jellyfish/generate_sequence.$(OBJEXT) jellyfish/misc.$(OBJEXT) \
 139         jellyfish/mersenne.$(OBJEXT) \
 140         jellyfish/square_binary_matrix.$(OBJEXT) \
 141         jellyfish/backtrace.$(OBJEXT) jellyfish/dbg.$(OBJEXT) \
 142         jellyfish/time.$(OBJEXT)
 143 bin_generate_sequence_OBJECTS = $(am_bin_generate_sequence_OBJECTS)
 144 bin_generate_sequence_LDADD = $(LDADD)
 145 am_bin_jellyfish_OBJECTS = jellyfish/jellyfish.$(OBJEXT) \
 146         jellyfish/stats_main.$(OBJEXT) jellyfish/hash_merge.$(OBJEXT) \
 147         jellyfish/storage.$(OBJEXT) jellyfish/misc.$(OBJEXT) \
 148         jellyfish/err.$(OBJEXT) jellyfish/mer_counter.$(OBJEXT) \
 149         jellyfish/histo_main.$(OBJEXT) jellyfish/dump_main.$(OBJEXT) \
 150         jellyfish/time.$(OBJEXT) jellyfish/thread_exec.$(OBJEXT) \
 151         jellyfish/query_main.$(OBJEXT) \
 152         jellyfish/square_binary_matrix.$(OBJEXT) \
 153         jellyfish/dump_fastq_main.$(OBJEXT) \
 154         jellyfish/histo_fastq_main.$(OBJEXT) jellyfish/cite.$(OBJEXT) \
 155         jellyfish/parse_dna.$(OBJEXT) jellyfish/file_parser.$(OBJEXT) \
 156         jellyfish/parse_quake.$(OBJEXT) \
 157         jellyfish/parse_qual_dna.$(OBJEXT) \
 158         jellyfish/sequence_parser.$(OBJEXT) \
 159         jellyfish/seq_qual_parser.$(OBJEXT) jellyfish/half.$(OBJEXT) \
 160         jellyfish/hash_fastq_merge.$(OBJEXT) jellyfish/dbg.$(OBJEXT) \
 161         jellyfish/mapped_file.$(OBJEXT) jellyfish/backtrace.$(OBJEXT) \
 162         jellyfish/floats.$(OBJEXT) jellyfish/allocators_mmap.$(OBJEXT) \
 163         jellyfish/yaggo.$(OBJEXT)
 164 bin_jellyfish_OBJECTS = $(am_bin_jellyfish_OBJECTS)
 165 bin_jellyfish_LDADD = $(LDADD)
 166 am_bin_test_double_fifo_input_OBJECTS =  \
 167         jellyfish/test_double_fifo_input.$(OBJEXT) \
 168         jellyfish/parse_dna.$(OBJEXT) jellyfish/file_parser.$(OBJEXT) \
 169         jellyfish/sequence_parser.$(OBJEXT) \
 170         jellyfish/backtrace.$(OBJEXT) jellyfish/thread_exec.$(OBJEXT) \
 171         jellyfish/dbg.$(OBJEXT) jellyfish/time.$(OBJEXT) \
 172         jellyfish/allocators_mmap.$(OBJEXT)
 173 bin_test_double_fifo_input_OBJECTS =  \
 174         $(am_bin_test_double_fifo_input_OBJECTS)
 175 bin_test_double_fifo_input_LDADD = $(LDADD)
 176 am_bin_test_offsets_key_value_OBJECTS = unit_tests/bin_test_offsets_key_value-test_offsets_key_value.$(OBJEXT)
 177 bin_test_offsets_key_value_OBJECTS =  \
 178         $(am_bin_test_offsets_key_value_OBJECTS)
 179 bin_test_offsets_key_value_DEPENDENCIES = libgtest_main.la
 180 bin_test_offsets_key_value_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX \
 181         $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CXXLD) \
 182         $(bin_test_offsets_key_value_CXXFLAGS) $(CXXFLAGS) \
 183         $(AM_LDFLAGS) $(LDFLAGS) -o $@
 184 am_bin_test_read_parser_OBJECTS =  \
 185         jellyfish/test_read_parser.$(OBJEXT) \
 186         jellyfish/file_parser.$(OBJEXT) \
 187         jellyfish/read_parser.$(OBJEXT) jellyfish/parse_read.$(OBJEXT) \
 188         jellyfish/dbg.$(OBJEXT) jellyfish/backtrace.$(OBJEXT) \
 189         jellyfish/time.$(OBJEXT)
 190 bin_test_read_parser_OBJECTS = $(am_bin_test_read_parser_OBJECTS)
 191 bin_test_read_parser_LDADD = $(LDADD)
 192 DEFAULT_INCLUDES = -I.@am__isrc@
 193 depcomp = $(SHELL) $(top_srcdir)/depcomp
 194 am__depfiles_maybe = depfiles
 195 am__mv = mv -f
 196 CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
 197         $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
 198 LTCXXCOMPILE = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
 199         $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) \
 200         $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
 201         $(AM_CXXFLAGS) $(CXXFLAGS)
 202 AM_V_CXX = $(am__v_CXX_$(V))
 203 am__v_CXX_ = $(am__v_CXX_$(AM_DEFAULT_VERBOSITY))
 204 am__v_CXX_0 = @echo "  CXX   " $@;
 205 AM_V_at = $(am__v_at_$(V))
 206 am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
 207 am__v_at_0 = @
 208 CXXLD = $(CXX)
 209 CXXLINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
 210         $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
 211         $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
 212 AM_V_CXXLD = $(am__v_CXXLD_$(V))
 213 am__v_CXXLD_ = $(am__v_CXXLD_$(AM_DEFAULT_VERBOSITY))
 214 am__v_CXXLD_0 = @echo "  CXXLD " $@;
 215 AM_V_GEN = $(am__v_GEN_$(V))
 216 am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
 217 am__v_GEN_0 = @echo "  GEN   " $@;
 218 SOURCES = $(libgtest_la_SOURCES) $(libgtest_main_la_SOURCES) \
 219         $(libjellyfish_la_SOURCES) $(bin_generate_sequence_SOURCES) \
 220         $(bin_jellyfish_SOURCES) $(bin_test_double_fifo_input_SOURCES) \
 221         $(bin_test_offsets_key_value_SOURCES) \
 222         $(bin_test_read_parser_SOURCES)
 223 DIST_SOURCES = $(libgtest_la_SOURCES) $(libgtest_main_la_SOURCES) \
 224         $(libjellyfish_la_SOURCES) $(bin_generate_sequence_SOURCES) \
 225         $(bin_jellyfish_SOURCES) $(bin_test_double_fifo_input_SOURCES) \
 226         $(bin_test_offsets_key_value_SOURCES) \
 227         $(bin_test_read_parser_SOURCES)
 228 man1dir = $(mandir)/man1
 229 NROFF = nroff
 230 MANS = $(man1_MANS)
 231 DATA = $(pkgconfig_DATA)
 232 HEADERS = $(library_include_HEADERS) $(noinst_HEADERS)
 233 ETAGS = etags
 234 CTAGS = ctags
 235 # If stdout is a non-dumb tty, use colors.  If test -t is not supported,
 236 # then this fails; a conservative approach.  Of course do not redirect
 237 # stdout here, just stderr.
 238 am__tty_colors = \
 239 red=; grn=; lgn=; blu=; std=; \
 240 test "X$(AM_COLOR_TESTS)" != Xno \
 241 && test "X$$TERM" != Xdumb \
 242 && { test "X$(AM_COLOR_TESTS)" = Xalways || test -t 1 2>/dev/null; } \
 243 && { \
 244   red='\e[0;31m'; \
 245   grn='\e[0;32m'; \
 246   lgn='\e[1;32m'; \
 247   blu='\e[1;34m'; \
 248   std='\e[m'; \
 249 }
 250 # Restructured Text title and section.
 251 am__rst_title = sed 's/.*/   &   /;h;s/./=/g;p;x;p;g;p;s/.*//'
 252 am__rst_section = sed 'p;s/./=/g;p;g'
 253 # Put stdin (possibly several lines separated by ".  ") in a box.
 254 am__text_box = $(AWK) '{                                \
 255   n = split($$0, lines, "\\.  "); max = 0;              \
 256   for (i = 1; i <= n; ++i)                              \
 257     if (max < length(lines[i]))                         \
 258       max = length(lines[i]);                           \
 259   for (i = 0; i < max; ++i) line = line "=";            \
 260   print line;                                           \
 261   for (i = 1; i <= n; ++i) if (lines[i]) print lines[i];\
 262   print line;                                           \
 263 }'
 264 # Solaris 10 'make', and several other traditional 'make' implementations,
 265 # pass "-e" to $(SHELL).  This contradicts POSIX.  Work around the problem
 266 # by disabling -e (using the XSI extension "set +e") if it's set.
 267 am__sh_e_setup = case $$- in *e*) set +e;; esac
 268 # To be inserted before the command running the test.  Creates the
 269 # directory for the log if needed.  Stores in $dir the directory
 270 # containing $f, in $tst the test, in $log the log, and passes
 271 # TESTS_ENVIRONMENT.  Save and restore TERM around use of
 272 # TESTS_ENVIRONMENT, in case that unsets it.
 273 am__check_pre = \
 274 $(am__sh_e_setup);                                      \
 275 $(am__vpath_adj_setup) $(am__vpath_adj)                 \
 276 srcdir=$(srcdir); export srcdir;                        \
 277 rm -f $@-t;                                             \
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 279   1 2 13 15;                                            \
 280 am__odir=`echo "./$@" | sed 's|/[^/]*$$||'`;            \
 281 test "x$$am__odir" = x. || $(MKDIR_P) "$$am__odir" || exit $$?; \
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 284 else dir="$(srcdir)/"; fi;                              \
 285 tst=$$dir$$f; log='$@'; __SAVED_TERM=$$TERM;            \
 286 $(TESTS_ENVIRONMENT)
 287 RECHECK_LOGS = $(TEST_LOGS)
 288 AM_RECURSIVE_TARGETS = check check-html recheck recheck-html
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 298 top_distdir = $(distdir)
 299 am__remove_distdir = \
 300   { test ! -d "$(distdir)" \
 301     || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
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 303 DIST_ARCHIVES = $(distdir).tar.gz
 304 GZIP_ENV = --best
 305 distuninstallcheck_listfiles = find . -type f -print
 306 distcleancheck_listfiles = find . -type f -print
 307 ACLOCAL = @ACLOCAL@
 308 AMTAR = @AMTAR@
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 311 AUTOCONF = @AUTOCONF@
 312 AUTOHEADER = @AUTOHEADER@
 313 AUTOMAKE = @AUTOMAKE@
 314 AWK = @AWK@
 315 CC = @CC@
 316 CCDEPMODE = @CCDEPMODE@
 317 CFLAGS = @CFLAGS@
 318 CPP = @CPP@
 319 CPPFLAGS = @CPPFLAGS@
 320 CXX = @CXX@
 321 CXXCPP = @CXXCPP@
 322 CXXDEPMODE = @CXXDEPMODE@
 323 CXXFLAGS = @CXXFLAGS@
 324 CYGPATH_W = @CYGPATH_W@
 325 DEFS = @DEFS@
 326 DEPDIR = @DEPDIR@
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 328 DUMPBIN = @DUMPBIN@
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 333 EXEEXT = @EXEEXT@
 334 FGREP = @FGREP@
 335 GREP = @GREP@
 336 INSTALL = @INSTALL@
 337 INSTALL_DATA = @INSTALL_DATA@
 338 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 339 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 340 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 341 LD = @LD@
 342 LDFLAGS = @LDFLAGS@
 343 LIBOBJS = @LIBOBJS@
 344 LIBS = @LIBS@
 345 LIBTOOL = @LIBTOOL@
 346 LIPO = @LIPO@
 347 LN_S = @LN_S@
 348 LTLIBOBJS = @LTLIBOBJS@
 349 MAKEINFO = @MAKEINFO@
 350 MD5 = @MD5@
 351 MKDIR_P = @MKDIR_P@
 352 NM = @NM@
 353 NMEDIT = @NMEDIT@
 354 OBJDUMP = @OBJDUMP@
 355 OBJEXT = @OBJEXT@
 356 OTOOL = @OTOOL@
 357 OTOOL64 = @OTOOL64@
 358 PACKAGE = @PACKAGE@
 359 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 360 PACKAGE_NAME = @PACKAGE_NAME@
 361 PACKAGE_STRING = @PACKAGE_STRING@
 362 PACKAGE_TARNAME = @PACKAGE_TARNAME@
 363 PACKAGE_VERSION = @PACKAGE_VERSION@
 364 PATH_SEPARATOR = @PATH_SEPARATOR@
 365 RANLIB = @RANLIB@
 366 SED = @SED@
 367 SET_MAKE = @SET_MAKE@
 368 SHELL = @SHELL@
 369 STRIP = @STRIP@
 370 VERSION = @VERSION@
 371 abs_builddir = @abs_builddir@
 372 abs_srcdir = @abs_srcdir@
 373 abs_top_builddir = @abs_top_builddir@
 374 abs_top_srcdir = @abs_top_srcdir@
 375 ac_ct_CC = @ac_ct_CC@
 376 ac_ct_CXX = @ac_ct_CXX@
 377 ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 378 am__include = @am__include@
 379 am__leading_dot = @am__leading_dot@
 380 am__quote = @am__quote@
 381 am__tar = @am__tar@
 382 am__untar = @am__untar@
 383 bindir = @bindir@
 384 build = @build@
 385 build_alias = @build_alias@
 386 build_cpu = @build_cpu@
 387 build_os = @build_os@
 388 build_vendor = @build_vendor@
 389 builddir = @builddir@
 390 datadir = @datadir@
 391 datarootdir = @datarootdir@
 392 docdir = @docdir@
 393 dvidir = @dvidir@
 394 exec_prefix = @exec_prefix@
 395 host = @host@
 396 host_alias = @host_alias@
 397 host_cpu = @host_cpu@
 398 host_os = @host_os@
 399 host_vendor = @host_vendor@
 400 htmldir = @htmldir@
 401 includedir = @includedir@
 402 infodir = @infodir@
 403 install_sh = @install_sh@
 404 libdir = @libdir@
 405 libexecdir = @libexecdir@
 406 localedir = @localedir@
 407 localstatedir = @localstatedir@
 408 lt_ECHO = @lt_ECHO@
 409 mandir = @mandir@
 410 mkdir_p = @mkdir_p@
 411 oldincludedir = @oldincludedir@
 412 pdfdir = @pdfdir@
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 414 program_transform_name = @program_transform_name@
 415 psdir = @psdir@
 416 sbindir = @sbindir@
 417 sharedstatedir = @sharedstatedir@
 418 srcdir = @srcdir@
 419 sysconfdir = @sysconfdir@
 420 target_alias = @target_alias@
 421 top_build_prefix = @top_build_prefix@
 422 top_builddir = @top_builddir@
 423 top_srcdir = @top_srcdir@
 424 ACLOCAL_AMFLAGS = -I m4
 425 EXTRA_DIST = m4/gnulib-cache.m4 doc/jellyfish.pdf doc/jellyfish.man \
 426         README LICENSE HalfLICENSE jellyfish/cite_cmdline.hpp \
 427         jellyfish/query_cmdline.hpp jellyfish/hash_merge_cmdline.hpp \
 428         jellyfish/histo_main_cmdline.hpp \
 429         jellyfish/stats_main_cmdline.hpp \
 430         jellyfish/histo_fastq_main_cmdline.hpp \
 431         jellyfish/dump_fastq_main_cmdline.hpp \
 432         jellyfish/count_main_cmdline.hpp \
 433         jellyfish/hash_fastq_merge_cmdline.hpp \
 434         jellyfish/dump_main_cmdline.hpp \
 435         jellyfish/double_fifo_input.hpp \
 436         jellyfish/simple_growing_array.hpp jellyfish/backtrace.hpp \
 437         jellyfish/noop_dumper.hpp jellyfish/yaggo.hpp \
 438         jellyfish/fstream_default.hpp jellyfish/randomc.h \
 439         jellyfish/generate_sequence_cmdline.hpp $(TESTS) $(GTEST_SRC)
 440 man1_MANS = doc/jellyfish.man
 441 pkgconfigdir = $(libdir)/pkgconfig
 442 pkgconfig_DATA = jellyfish-1.1.pc
 443 AM_LDFLAGS = -lpthread
 444 AM_CPPFLAGS = -Wall -Werror -Wnon-virtual-dtor -I$(top_srcdir)
 445 AM_CXXFLAGS = -g -O3
 446 lib_LTLIBRARIES = libjellyfish.la
 447
 448 ########################################
 449 # Build Jellyfish the exec
 450 ########################################
 451 bin_jellyfish_SOURCES = jellyfish/jellyfish.cc jellyfish/stats_main.cc                  \
 452                     jellyfish/hash_merge.cc jellyfish/storage.cc jellyfish/misc.cc      \
 453                     jellyfish/err.cc jellyfish/mer_counter.cc jellyfish/histo_main.cc   \
 454                     jellyfish/dump_main.cc jellyfish/time.cc jellyfish/thread_exec.cc   \
 455                     jellyfish/query_main.cc jellyfish/square_binary_matrix.cc   \
 456                     jellyfish/dump_fastq_main.cc jellyfish/histo_fastq_main.cc  \
 457                     jellyfish/cite.cc jellyfish/parse_dna.cc jellyfish/file_parser.cc   \
 458                     jellyfish/parse_quake.cc jellyfish/parse_qual_dna.cc                \
 459                     jellyfish/sequence_parser.cc jellyfish/seq_qual_parser.cc   \
 460                     jellyfish/half.cpp jellyfish/hash_fastq_merge.cc jellyfish/dbg.cc   \
 461                     jellyfish/mapped_file.cc jellyfish/backtrace.cc jellyfish/floats.cc \
 462                     jellyfish/allocators_mmap.cc jellyfish/yaggo.cpp
 463
 464
 465 ########################################
 466 # Build Jellyfish the shared library
 467 ########################################
 468 libjellyfish_la_LDFLAGS = -version-info 1:0:0
 469 libjellyfish_la_SOURCES = jellyfish/square_binary_matrix.cc             \
 470                           jellyfish/err.cc jellyfish/misc.cc            \
 471                           jellyfish/storage.cc                          \
 472                           jellyfish/thread_exec.cc jellyfish/time.cc    \
 473                           jellyfish/file_parser.cc                      \
 474                           jellyfish/read_parser.cc                      \
 475                           jellyfish/parse_read.cc jellyfish/half.cpp    \
 476                           jellyfish/mapped_file.cc                      \
 477                           jellyfish/parse_dna.cc                        \
 478                           jellyfish/parse_quake.cc                      \
 479                           jellyfish/parse_qual_dna.cc                   \
 480                           jellyfish/sequence_parser.cc                  \
 481                           jellyfish/seq_qual_parser.cc                  \
 482                           jellyfish/backtrace.cc jellyfish/floats.cc    \
 483                           jellyfish/dbg.cc                              \
 484                           jellyfish/allocators_mmap.cc
 485
 486 libjellyfish_la_CPPFLAGS = $(AM_CPPFLAGS)
 487 library_includedir = $(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
 488 library_include_HEADERS = jellyfish/allocators_malloc.hpp                       \
 489                           jellyfish/allocators_mmap.hpp                 \
 490                           jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp \
 491                           jellyfish/compacted_dumper.hpp                        \
 492                           jellyfish/compacted_hash.hpp                  \
 493                           jellyfish/concurrent_queues.hpp                       \
 494                           jellyfish/direct_indexing_array.hpp                   \
 495                           jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp      \
 496                           jellyfish/dumper.hpp jellyfish/hash_function.hpp              \
 497                           jellyfish/hash.hpp jellyfish/heap.hpp                 \
 498                           jellyfish/invertible_hash_array.hpp                   \
 499                           jellyfish/locking_hash_counters.hpp                   \
 500                           jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp \
 501                           jellyfish/mer_counting.hpp jellyfish/err.hpp          \
 502                           jellyfish/misc.hpp jellyfish/offsets_key_value.hpp    \
 503                           jellyfish/reversible_hash_function.hpp                \
 504                           jellyfish/sorted_dumper.hpp                           \
 505                           jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp      \
 506                           jellyfish/thread_exec.hpp jellyfish/time.hpp          \
 507                           jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp             \
 508                           jellyfish/capped_integer.hpp                  \
 509                           jellyfish/aligned_values_array.hpp                    \
 510                           jellyfish/fastq_dumper.hpp jellyfish/floats.hpp               \
 511                           jellyfish/circular_buffer.hpp jellyfish/counter.hpp   \
 512                           jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp             \
 513                           jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp        \
 514                           jellyfish/sequence_parser.hpp                 \
 515                           jellyfish/seq_qual_parser.hpp                 \
 516                           jellyfish/double_fifo_input.hpp                       \
 517                           jellyfish/read_parser.hpp jellyfish/parse_read.hpp    \
 518                           jellyfish/simple_growing_array.hpp jellyfish/toFloat.h        \
 519                           jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h           \
 520                           jellyfish/backtrace.hpp
 521
 522
 523 ########################################
 524 # Build tests
 525 ########################################
 526 bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc jellyfish/misc.cc        \
 527                             jellyfish/mersenne.cpp                              \
 528                             jellyfish/square_binary_matrix.cc                   \
 529                             jellyfish/backtrace.cc jellyfish/dbg.cc jellyfish/time.cc
 530
 531 bin_test_double_fifo_input_SOURCES = jellyfish/test_double_fifo_input.cc                \
 532                                  jellyfish/parse_dna.cc jellyfish/file_parser.cc        \
 533                                  jellyfish/sequence_parser.cc                   \
 534                                  jellyfish/backtrace.cc jellyfish/thread_exec.cc        \
 535                                  jellyfish/dbg.cc jellyfish/time.cc                     \
 536                                  jellyfish/allocators_mmap.cc
 537
 538 bin_test_read_parser_SOURCES = jellyfish/test_read_parser.cc jellyfish/file_parser.cc   \
 539                            jellyfish/read_parser.cc jellyfish/parse_read.cc             \
 540                            jellyfish/dbg.cc jellyfish/backtrace.cc jellyfish/time.cc
 541
 542
 543 ########################################
 544 # Tests
 545 ########################################
 546 TEST_EXTENSIONS = .sh
 547 SH_LOG_COMPILER = /bin/sh
 548 AM_SH_LOG_FLAGS =
 549
 550 ########################################
 551 # Unit tests
 552 ########################################
 553 TESTS = tests/generate_sequence.sh tests/serial_hashing.sh \
 554         tests/parallel_hashing.sh tests/serial_direct_indexing.sh \
 555         tests/parallel_direct_indexing.sh tests/raw_hash.sh \
 556         tests/generate_fastq_sequence.sh \
 557         tests/parallel_fastq_hashing.sh tests/multi_file.sh \
 558         tests/multi_file_fastq.sh tests/from_stream.sh \
 559         tests/parallel_fastq_sequence_hashing.sh \
 560         tests/from_stream_fastq.sh tests/merge.sh tests/min_qual.sh \
 561         tests/big.sh tests/parsers.sh unit_tests/unit_tests.sh
 562 bin_test_offsets_key_value_SOURCES = unit_tests/test_offsets_key_value.cc
 563 bin_test_offsets_key_value_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests/gtest
 564 bin_test_offsets_key_value_LDADD = libgtest_main.la
 565
 566 ##############################
 567 # Gtest build.
 568 ##############################
 569 # Build rules for libraries.
 570 check_LTLIBRARIES = libgtest.la libgtest_main.la
 571 libgtest_la_SOURCES = unit_tests/gtest/src/gtest-all.cc
 572 libgtest_main_la_SOURCES = unit_tests/gtest/src/gtest_main.cc
 573 libgtest_main_la_LIBADD = libgtest.la
 574 libgtest_la_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest \
 575 -I$(top_srcdir)/unit_tests/gtest/include
 576
 577 libgtest_main_la_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest    \
 578 -I$(top_srcdir)/unit_tests/gtest/include
 579
 580
 581 # gtest source files that we don't compile directly.  They are
 582 # #included by gtest-all.cc.
 583 GTEST_SRC = unit_tests/gtest/src/gtest-death-test.cc    \
 584             unit_tests/gtest/src/gtest-filepath.cc      \
 585             unit_tests/gtest/src/gtest-internal-inl.h   \
 586             unit_tests/gtest/src/gtest-port.cc          \
 587             unit_tests/gtest/src/gtest-printers.cc      \
 588             unit_tests/gtest/src/gtest-test-part.cc     \
 589             unit_tests/gtest/src/gtest-typed-test.cc    \
 590             unit_tests/gtest/src/gtest.cc
 591
 592
 593 # Headers, not installed
 594 GTEST_I = unit_tests/gtest/include/gtest
 595 noinst_HEADERS = $(GTEST_I)/gtest-death-test.h                          \
 596                  $(GTEST_I)/gtest-message.h                             \
 597                  $(GTEST_I)/gtest-param-test.h                          \
 598                  $(GTEST_I)/gtest-printers.h $(GTEST_I)/gtest-spi.h     \
 599                  $(GTEST_I)/gtest-test-part.h                           \
 600                  $(GTEST_I)/gtest-typed-test.h $(GTEST_I)/gtest.h       \
 601                  $(GTEST_I)/gtest_pred_impl.h $(GTEST_I)/gtest_prod.h   \
 602                  $(GTEST_I)/internal/gtest-death-test-internal.h        \
 603                  $(GTEST_I)/internal/gtest-filepath.h                   \
 604                  $(GTEST_I)/internal/gtest-internal.h                   \
 605                  $(GTEST_I)/internal/gtest-linked_ptr.h                 \
 606                  $(GTEST_I)/internal/gtest-param-util-generated.h       \
 607                  $(GTEST_I)/internal/gtest-param-util.h                 \
 608                  $(GTEST_I)/internal/gtest-port.h                       \
 609                  $(GTEST_I)/internal/gtest-string.h                     \
 610                  $(GTEST_I)/internal/gtest-tuple.h                      \
 611                  $(GTEST_I)/internal/gtest-type-util.h
 612
 613 all: config.h
 614         $(MAKE) $(AM_MAKEFLAGS) all-am
 615
 616 .SUFFIXES:
 617 .SUFFIXES: .cc .cpp .html .lo .log .o .obj .sh .sh$(EXEEXT)
 618 am--refresh:
 619         @:
 620 $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am $(srcdir)/gtest.mk $(am__configure_deps)
 621         @for dep in $?; do \
 622           case '$(am__configure_deps)' in \
 623             *$$dep*) \
 624               echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \
 625               $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \
 626                 && exit 0; \
 627               exit 1;; \
 628           esac; \
 629         done; \
 630         echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
 631         $(am__cd) $(top_srcdir) && \
 632           $(AUTOMAKE) --foreign Makefile
 633 .PRECIOUS: Makefile
 634 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 635         @case '$?' in \
 636           *config.status*) \
 637             echo ' $(SHELL) ./config.status'; \
 638             $(SHELL) ./config.status;; \
 639           *) \
 640             echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
 641             cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
 642         esac;
 643
 644 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
 645         $(SHELL) ./config.status --recheck
 646
 647 $(top_srcdir)/configure:  $(am__configure_deps)
 648         $(am__cd) $(srcdir) && $(AUTOCONF)
 649 $(ACLOCAL_M4):  $(am__aclocal_m4_deps)
 650         $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
 651 $(am__aclocal_m4_deps):
 652
 653 config.h: stamp-h1
 654         @if test ! -f $@; then \
 655           rm -f stamp-h1; \
 656           $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
 657         else :; fi
 658
 659 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
 660         @rm -f stamp-h1
 661         cd $(top_builddir) && $(SHELL) ./config.status config.h
 662 $(srcdir)/config.h.in:  $(am__configure_deps)
 663         ($(am__cd) $(top_srcdir) && $(AUTOHEADER))
 664         rm -f stamp-h1
 665         touch $@
 666
 667 distclean-hdr:
 668         -rm -f config.h stamp-h1
 669 tests/compat.sh: $(top_builddir)/config.status $(top_srcdir)/tests/compat.sh.in
 670         cd $(top_builddir) && $(SHELL) ./config.status $@
 671 jellyfish-1.1.pc: $(top_builddir)/config.status $(srcdir)/jellyfish-1.1.pc.in
 672         cd $(top_builddir) && $(SHELL) ./config.status $@
 673
 674 clean-checkLTLIBRARIES:
 675         -test -z "$(check_LTLIBRARIES)" || rm -f $(check_LTLIBRARIES)
 676         @list='$(check_LTLIBRARIES)'; for p in $$list; do \
 677           dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
 678           test "$$dir" != "$$p" || dir=.; \
 679           echo "rm -f \"$${dir}/so_locations\""; \
 680           rm -f "$${dir}/so_locations"; \
 681         done
 682 install-libLTLIBRARIES: $(lib_LTLIBRARIES)
 683         @$(NORMAL_INSTALL)
 684         test -z "$(libdir)" || $(MKDIR_P) "$(DESTDIR)$(libdir)"
 685         @list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
 686         list2=; for p in $$list; do \
 687           if test -f $$p; then \
 688             list2="$$list2 $$p"; \
 689           else :; fi; \
 690         done; \
 691         test -z "$$list2" || { \
 692           echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
 693           $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
 694         }
 695
 696 uninstall-libLTLIBRARIES:
 697         @$(NORMAL_UNINSTALL)
 698         @list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
 699         for p in $$list; do \
 700           $(am__strip_dir) \
 701           echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
 702           $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
 703         done
 704
 705 clean-libLTLIBRARIES:
 706         -test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
 707         @list='$(lib_LTLIBRARIES)'; for p in $$list; do \
 708           dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
 709           test "$$dir" != "$$p" || dir=.; \
 710           echo "rm -f \"$${dir}/so_locations\""; \
 711           rm -f "$${dir}/so_locations"; \
 712         done
 713 unit_tests/gtest/src/$(am__dirstamp):
 714         @$(MKDIR_P) unit_tests/gtest/src
 715         @: > unit_tests/gtest/src/$(am__dirstamp)
 716 unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp):
 717         @$(MKDIR_P) unit_tests/gtest/src/$(DEPDIR)
 718         @: > unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
 719 unit_tests/gtest/src/libgtest_la-gtest-all.lo:  \
 720         unit_tests/gtest/src/$(am__dirstamp) \
 721         unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
 722 libgtest.la: $(libgtest_la_OBJECTS) $(libgtest_la_DEPENDENCIES)
 723         $(AM_V_CXXLD)$(libgtest_la_LINK)  $(libgtest_la_OBJECTS) $(libgtest_la_LIBADD) $(LIBS)
 724 unit_tests/gtest/src/libgtest_main_la-gtest_main.lo:  \
 725         unit_tests/gtest/src/$(am__dirstamp) \
 726         unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
 727 libgtest_main.la: $(libgtest_main_la_OBJECTS) $(libgtest_main_la_DEPENDENCIES)
 728         $(AM_V_CXXLD)$(libgtest_main_la_LINK)  $(libgtest_main_la_OBJECTS) $(libgtest_main_la_LIBADD) $(LIBS)
 729 jellyfish/$(am__dirstamp):
 730         @$(MKDIR_P) jellyfish
 731         @: > jellyfish/$(am__dirstamp)
 732 jellyfish/$(DEPDIR)/$(am__dirstamp):
 733         @$(MKDIR_P) jellyfish/$(DEPDIR)
 734         @: > jellyfish/$(DEPDIR)/$(am__dirstamp)
 735 jellyfish/libjellyfish_la-square_binary_matrix.lo:  \
 736         jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
 737 jellyfish/libjellyfish_la-err.lo: jellyfish/$(am__dirstamp) \
 738         jellyfish/$(DEPDIR)/$(am__dirstamp)
 739 jellyfish/libjellyfish_la-misc.lo: jellyfish/$(am__dirstamp) \
 740         jellyfish/$(DEPDIR)/$(am__dirstamp)
 741 jellyfish/libjellyfish_la-storage.lo: jellyfish/$(am__dirstamp) \
 742         jellyfish/$(DEPDIR)/$(am__dirstamp)
 743 jellyfish/libjellyfish_la-thread_exec.lo: jellyfish/$(am__dirstamp) \
 744         jellyfish/$(DEPDIR)/$(am__dirstamp)
 745 jellyfish/libjellyfish_la-time.lo: jellyfish/$(am__dirstamp) \
 746         jellyfish/$(DEPDIR)/$(am__dirstamp)
 747 jellyfish/libjellyfish_la-file_parser.lo: jellyfish/$(am__dirstamp) \
 748         jellyfish/$(DEPDIR)/$(am__dirstamp)
 749 jellyfish/libjellyfish_la-read_parser.lo: jellyfish/$(am__dirstamp) \
 750         jellyfish/$(DEPDIR)/$(am__dirstamp)
 751 jellyfish/libjellyfish_la-parse_read.lo: jellyfish/$(am__dirstamp) \
 752         jellyfish/$(DEPDIR)/$(am__dirstamp)
 753 jellyfish/libjellyfish_la-half.lo: jellyfish/$(am__dirstamp) \
 754         jellyfish/$(DEPDIR)/$(am__dirstamp)
 755 jellyfish/libjellyfish_la-mapped_file.lo: jellyfish/$(am__dirstamp) \
 756         jellyfish/$(DEPDIR)/$(am__dirstamp)
 757 jellyfish/libjellyfish_la-parse_dna.lo: jellyfish/$(am__dirstamp) \
 758         jellyfish/$(DEPDIR)/$(am__dirstamp)
 759 jellyfish/libjellyfish_la-parse_quake.lo: jellyfish/$(am__dirstamp) \
 760         jellyfish/$(DEPDIR)/$(am__dirstamp)
 761 jellyfish/libjellyfish_la-parse_qual_dna.lo:  \
 762         jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
 763 jellyfish/libjellyfish_la-sequence_parser.lo:  \
 764         jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
 765 jellyfish/libjellyfish_la-seq_qual_parser.lo:  \
 766         jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
 767 jellyfish/libjellyfish_la-backtrace.lo: jellyfish/$(am__dirstamp) \
 768         jellyfish/$(DEPDIR)/$(am__dirstamp)
 769 jellyfish/libjellyfish_la-floats.lo: jellyfish/$(am__dirstamp) \
 770         jellyfish/$(DEPDIR)/$(am__dirstamp)
 771 jellyfish/libjellyfish_la-dbg.lo: jellyfish/$(am__dirstamp) \
 772         jellyfish/$(DEPDIR)/$(am__dirstamp)
 773 jellyfish/libjellyfish_la-allocators_mmap.lo:  \
 774         jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
 775 libjellyfish.la: $(libjellyfish_la_OBJECTS) $(libjellyfish_la_DEPENDENCIES)
 776         $(AM_V_CXXLD)$(libjellyfish_la_LINK) -rpath $(libdir) $(libjellyfish_la_OBJECTS) $(libjellyfish_la_LIBADD) $(LIBS)
 777 install-binPROGRAMS: $(bin_PROGRAMS)
 778         @$(NORMAL_INSTALL)
 779         test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
 780         @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
 781         for p in $$list; do echo "$$p $$p"; done | \
 782         sed 's/$(EXEEXT)$$//' | \
 783         while read p p1; do if test -f $$p || test -f $$p1; \
 784           then echo "$$p"; echo "$$p"; else :; fi; \
 785         done | \
 786         sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
 787             -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
 788         sed 'N;N;N;s,\n, ,g' | \
 789         $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
 790           { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
 791             if ($$2 == $$4) files[d] = files[d] " " $$1; \
 792             else { print "f", $$3 "/" $$4, $$1; } } \
 793           END { for (d in files) print "f", d, files[d] }' | \
 794         while read type dir files; do \
 795             if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
 796             test -z "$$files" || { \
 797             echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
 798             $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
 799             } \
 800         ; done
 801
 802 uninstall-binPROGRAMS:
 803         @$(NORMAL_UNINSTALL)
 804         @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
 805         files=`for p in $$list; do echo "$$p"; done | \
 806           sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
 807               -e 's/$$/$(EXEEXT)/' `; \
 808         test -n "$$list" || exit 0; \
 809         echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
 810         cd "$(DESTDIR)$(bindir)" && rm -f $$files
 811
 812 clean-binPROGRAMS:
 813         @list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
 814         echo " rm -f" $$list; \
 815         rm -f $$list || exit $$?; \
 816         test -n "$(EXEEXT)" || exit 0; \
 817         list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
 818         echo " rm -f" $$list; \
 819         rm -f $$list
 820
 821 clean-checkPROGRAMS:
 822         @list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
 823         echo " rm -f" $$list; \
 824         rm -f $$list || exit $$?; \
 825         test -n "$(EXEEXT)" || exit 0; \
 826         list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
 827         echo " rm -f" $$list; \
 828         rm -f $$list
 829 jellyfish/generate_sequence.$(OBJEXT): jellyfish/$(am__dirstamp) \
 830         jellyfish/$(DEPDIR)/$(am__dirstamp)
 831 jellyfish/misc.$(OBJEXT): jellyfish/$(am__dirstamp) \
 832         jellyfish/$(DEPDIR)/$(am__dirstamp)
 833 jellyfish/mersenne.$(OBJEXT): jellyfish/$(am__dirstamp) \
 834         jellyfish/$(DEPDIR)/$(am__dirstamp)
 835 jellyfish/square_binary_matrix.$(OBJEXT): jellyfish/$(am__dirstamp) \
 836         jellyfish/$(DEPDIR)/$(am__dirstamp)
 837 jellyfish/backtrace.$(OBJEXT): jellyfish/$(am__dirstamp) \
 838         jellyfish/$(DEPDIR)/$(am__dirstamp)
 839 jellyfish/dbg.$(OBJEXT): jellyfish/$(am__dirstamp) \
 840         jellyfish/$(DEPDIR)/$(am__dirstamp)
 841 jellyfish/time.$(OBJEXT): jellyfish/$(am__dirstamp) \
 842         jellyfish/$(DEPDIR)/$(am__dirstamp)
 843 bin/$(am__dirstamp):
 844         @$(MKDIR_P) bin
 845         @: > bin/$(am__dirstamp)
 846 bin/generate_sequence$(EXEEXT): $(bin_generate_sequence_OBJECTS) $(bin_generate_sequence_DEPENDENCIES) bin/$(am__dirstamp)
 847         @rm -f bin/generate_sequence$(EXEEXT)
 848         $(AM_V_CXXLD)$(CXXLINK) $(bin_generate_sequence_OBJECTS) $(bin_generate_sequence_LDADD) $(LIBS)
 849 jellyfish/jellyfish.$(OBJEXT): jellyfish/$(am__dirstamp) \
 850         jellyfish/$(DEPDIR)/$(am__dirstamp)
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1111 unit_tests/gtest/src/libgtest_main_la-gtest_main.lo: unit_tests/gtest/src/gtest_main.cc
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1119 jellyfish/libjellyfish_la-square_binary_matrix.lo: jellyfish/square_binary_matrix.cc
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1127 jellyfish/libjellyfish_la-err.lo: jellyfish/err.cc
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1131 @AMDEP_TRUE@@am__fastdepCXX_FALSE@      source='jellyfish/err.cc' object='jellyfish/libjellyfish_la-err.lo' libtool=yes @AMDEPBACKSLASH@
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1135 jellyfish/libjellyfish_la-misc.lo: jellyfish/misc.cc
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1142
1143 jellyfish/libjellyfish_la-storage.lo: jellyfish/storage.cc
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1150
1151 jellyfish/libjellyfish_la-thread_exec.lo: jellyfish/thread_exec.cc
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1155 @AMDEP_TRUE@@am__fastdepCXX_FALSE@      source='jellyfish/thread_exec.cc' object='jellyfish/libjellyfish_la-thread_exec.lo' libtool=yes @AMDEPBACKSLASH@
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1158
1159 jellyfish/libjellyfish_la-time.lo: jellyfish/time.cc
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1166
1167 jellyfish/libjellyfish_la-file_parser.lo: jellyfish/file_parser.cc
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1175 jellyfish/libjellyfish_la-read_parser.lo: jellyfish/read_parser.cc
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1183 jellyfish/libjellyfish_la-parse_read.lo: jellyfish/parse_read.cc
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1191 jellyfish/libjellyfish_la-half.lo: jellyfish/half.cpp
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1199 jellyfish/libjellyfish_la-mapped_file.lo: jellyfish/mapped_file.cc
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1207 jellyfish/libjellyfish_la-parse_dna.lo: jellyfish/parse_dna.cc
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1215 jellyfish/libjellyfish_la-parse_quake.lo: jellyfish/parse_quake.cc
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1222
1223 jellyfish/libjellyfish_la-parse_qual_dna.lo: jellyfish/parse_qual_dna.cc
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1230
1231 jellyfish/libjellyfish_la-sequence_parser.lo: jellyfish/sequence_parser.cc
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1238
1239 jellyfish/libjellyfish_la-seq_qual_parser.lo: jellyfish/seq_qual_parser.cc
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1247 jellyfish/libjellyfish_la-backtrace.lo: jellyfish/backtrace.cc
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1255 jellyfish/libjellyfish_la-floats.lo: jellyfish/floats.cc
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1263 jellyfish/libjellyfish_la-dbg.lo: jellyfish/dbg.cc
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1271 jellyfish/libjellyfish_la-allocators_mmap.lo: jellyfish/allocators_mmap.cc
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1278
1279 unit_tests/bin_test_offsets_key_value-test_offsets_key_value.o: unit_tests/test_offsets_key_value.cc
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1423         unique=`for i in $$list; do \
1424             if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
1425           done | \
1426           $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
1427               END { if (nonempty) { for (i in files) print i; }; }'`; \
1428         shift; \
1429         if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
1430           test -n "$$unique" || unique=$$empty_fix; \
1431           if test $$# -gt 0; then \
1432             $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
1433               "$$@" $$unique; \
1434           else \
1435             $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
1436               $$unique; \
1437           fi; \
1438         fi
1439 ctags: CTAGS
1440 CTAGS:  $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
1441                 $(TAGS_FILES) $(LISP)
1442         list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
1443         unique=`for i in $$list; do \
1444             if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
1445           done | \
1446           $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
1447               END { if (nonempty) { for (i in files) print i; }; }'`; \
1448         test -z "$(CTAGS_ARGS)$$unique" \
1449           || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
1450              $$unique
1451
1452 GTAGS:
1453         here=`$(am__cd) $(top_builddir) && pwd` \
1454           && $(am__cd) $(top_srcdir) \
1455           && gtags -i $(GTAGS_ARGS) "$$here"
1456
1457 distclean-tags:
1458         -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
1459
1460 # To be appended to the command running the test.  Handle the stdout
1461 # and stderr redirection, and catch the exit status.
1462 am__check_post =                                        \
1463 >$@-t 2>&1;                                             \
1464 estatus=$$?;                                            \
1465 if test -n '$(DISABLE_HARD_ERRORS)'                     \
1466    && test $$estatus -eq 99; then                       \
1467   estatus=1;                                            \
1468 fi;                                                     \
1469 TERM=$$__SAVED_TERM; export TERM;                       \
1470 $(am__tty_colors);                                      \
1471 xfailed=PASS;                                           \
1472 case " $(XFAIL_TESTS) " in                              \
1473   *[\ \ ]$$f[\ \        ]* | *[\ \      ]$$dir$$f[\ \   ]*) \
1474     xfailed=XFAIL;;                                     \
1475 esac;                                                   \
1476 case $$estatus:$$xfailed in                             \
1477     0:XFAIL) col=$$red; res=XPASS;;                     \
1478     0:*)     col=$$grn; res=PASS ;;                     \
1479     77:*)    col=$$blu; res=SKIP ;;                     \
1480     99:*)    col=$$red; res=FAIL ;;                     \
1481     *:XFAIL) col=$$lgn; res=XFAIL;;                     \
1482     *:*)     col=$$red; res=FAIL ;;                     \
1483 esac;                                                   \
1484 echo "$${col}$$res$${std}: $$f";                        \
1485 echo "$$res: $$f (exit: $$estatus)" |                   \
1486   $(am__rst_section) >$@;                               \
1487 cat $@-t >>$@;                                          \
1488 rm -f $@-t
1489
1490 $(TEST_SUITE_LOG): $(TEST_LOGS)
1491         @$(am__sh_e_setup);                                             \
1492         list='$(TEST_LOGS)';                                            \
1493         results=`for f in $$list; do                                    \
1494                    read line < $$f && echo "$$line" || echo FAIL;       \
1495                  done`;                                                 \
1496         all=`echo "$$results" | sed '/^$$/d' | wc -l | sed -e 's/^[      ]*//'`; \
1497         fail=`echo "$$results" | grep -c '^FAIL'`;                      \
1498         pass=`echo "$$results" | grep -c '^PASS'`;                      \
1499         skip=`echo "$$results" | grep -c '^SKIP'`;                      \
1500         xfail=`echo "$$results" | grep -c '^XFAIL'`;                    \
1501         xpass=`echo "$$results" | grep -c '^XPASS'`;                    \
1502         failures=`expr $$fail + $$xpass`;                               \
1503         all=`expr $$all - $$skip`;                                      \
1504         if test "$$all" -eq 1; then tests=test; All=;                   \
1505         else tests=tests; All="All "; fi;                               \
1506         case fail=$$fail:xpass=$$xpass:xfail=$$xfail in                 \
1507           fail=0:xpass=0:xfail=0)                                       \
1508             msg="$$All$$all $$tests passed.  ";                         \
1509             exit=true;;                                                 \
1510           fail=0:xpass=0:xfail=*)                                       \
1511             msg="$$All$$all $$tests behaved as expected";               \
1512             if test "$$xfail" -eq 1; then xfailures=failure;            \
1513             else xfailures=failures; fi;                                \
1514             msg="$$msg ($$xfail expected $$xfailures).  ";              \
1515             exit=true;;                                                 \
1516           fail=*:xpass=0:xfail=*)                                       \
1517             msg="$$fail of $$all $$tests failed.  ";                    \
1518             exit=false;;                                                \
1519           fail=*:xpass=*:xfail=*)                                       \
1520             msg="$$failures of $$all $$tests did not behave as expected"; \
1521             if test "$$xpass" -eq 1; then xpasses=pass;                 \
1522             else xpasses=passes; fi;                                    \
1523             msg="$$msg ($$xpass unexpected $$xpasses).  ";              \
1524             exit=false;;                                                \
1525           *)                                                            \
1526             echo >&2 "incorrect case"; exit 4;;                         \
1527         esac;                                                           \
1528         if test "$$skip" -ne 0; then                                    \
1529           if test "$$skip" -eq 1; then                                  \
1530             msg="$$msg($$skip test was not run).  ";                    \
1531           else                                                          \
1532             msg="$$msg($$skip tests were not run).  ";                  \
1533           fi;                                                           \
1534         fi;                                                             \
1535         {                                                               \
1536           echo "$(PACKAGE_STRING): $(subdir)/$(TEST_SUITE_LOG)" |       \
1537             $(am__rst_title);                                           \
1538           echo "$$msg";                                                 \
1539           echo;                                                         \
1540           echo ".. contents:: :depth: 2";                               \
1541           echo;                                                         \
1542           for f in $$list; do                                           \
1543             read line < $$f;                                            \
1544             case $$line in                                              \
1545               PASS:*|XFAIL:*);;                                         \
1546               *) echo; cat $$f;;                                        \
1547             esac;                                                       \
1548           done;                                                         \
1549         } >$(TEST_SUITE_LOG).tmp;                                       \
1550         mv $(TEST_SUITE_LOG).tmp $(TEST_SUITE_LOG);                     \
1551         if test "$$failures" -ne 0; then                                \
1552           msg="$${msg}See $(subdir)/$(TEST_SUITE_LOG).  ";              \
1553           if test -n "$(PACKAGE_BUGREPORT)"; then                       \
1554             msg="$${msg}Please report to $(PACKAGE_BUGREPORT).  ";      \
1555           fi;                                                           \
1556         fi;                                                             \
1557         test x"$$VERBOSE" = x || $$exit || cat $(TEST_SUITE_LOG);       \
1558         $(am__tty_colors);                                              \
1559         if $$exit; then                                                 \
1560           echo $(ECHO_N) "$$grn$(ECHO_C)";                              \
1561          else                                                           \
1562           echo $(ECHO_N) "$$red$(ECHO_C)";                              \
1563         fi;                                                             \
1564         echo "$$msg" | $(am__text_box);                                 \
1565         echo $(ECHO_N) "$$std$(ECHO_C)";                                \
1566         $$exit
1567
1568 # Run all the tests.
1569 check-TESTS:
1570         @list='$(RECHECK_LOGS)'; test -z "$$list" || rm -f $$list
1571         @test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
1572         @set_logs=; if test "X$(TEST_LOGS)" = X.log; then               \
1573           set_logs=TEST_LOGS=;                                          \
1574         fi;                                                             \
1575         $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) $$set_logs
1576
1577 .log.html:
1578         @list='$(RST2HTML) $$RST2HTML rst2html rst2html.py';            \
1579         for r2h in $$list; do                                           \
1580           if ($$r2h --version) >/dev/null 2>&1; then                    \
1581             R2H=$$r2h;                                                  \
1582           fi;                                                           \
1583         done;                                                           \
1584         if test -z "$$R2H"; then                                        \
1585           echo >&2 "cannot find rst2html, cannot create $@";            \
1586           exit 2;                                                       \
1587         fi;                                                             \
1588         $$R2H $< >$@.tmp
1589         @mv $@.tmp $@
1590
1591 # Be sure to run check first, and then to convert the result.
1592 # Beware of concurrent executions.  Run "check" not "check-TESTS", as
1593 # check-SCRIPTS and other dependencies are rebuilt by the former only.
1594 # And expect check to fail.
1595 check-html:
1596         @if $(MAKE) $(AM_MAKEFLAGS) check; then                 \
1597           rv=0; else rv=$$?;                                    \
1598         fi;                                                     \
1599         $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_HTML) || exit 4;   \
1600         exit $$rv
1601 recheck recheck-html:
1602         @target=`echo $@ | sed 's,^re,,'`;                              \
1603         list='$(TEST_LOGS)';                                            \
1604         list=`for f in $$list; do                                       \
1605                 test -f $$f || continue;                                \
1606                 if read line < $$f; then                                \
1607                   case $$line in FAIL*|XPASS*) echo $$f;; esac;         \
1608                 else echo $$f; fi;                                      \
1609               done | tr '\012\015' '  '`;                               \
1610         $(MAKE) $(AM_MAKEFLAGS) $$target AM_MAKEFLAGS='$(AM_MAKEFLAGS) TEST_LOGS="'"$$list"'"'
1611 .sh.log:
1612         @p='$<'; $(am__check_pre) $(SH_LOG_COMPILE) "$$tst" $(am__check_post)
1613 @am__EXEEXT_TRUE@.sh$(EXEEXT).log:
1614 @am__EXEEXT_TRUE@       @p='$<'; $(am__check_pre) $(SH_LOG_COMPILE) "$$tst" $(am__check_post)
1615
1616 distdir: $(DISTFILES)
1617         @list='$(MANS)'; if test -n "$$list"; then \
1618           list=`for p in $$list; do \
1619             if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
1620             if test -f "$$d$$p"; then echo "$$d$$p"; else :; fi; done`; \
1621           if test -n "$$list" && \
1622             grep 'ab help2man is required to generate this page' $$list >/dev/null; then \
1623             echo "error: found man pages containing the \`missing help2man' replacement text:" >&2; \
1624             grep -l 'ab help2man is required to generate this page' $$list | sed 's/^/         /' >&2; \
1625             echo "       to fix them, install help2man, remove and regenerate the man pages;" >&2; \
1626             echo "       typically \`make maintainer-clean' will remove them" >&2; \
1627             exit 1; \
1628           else :; fi; \
1629         else :; fi
1630         $(am__remove_distdir)
1631         test -d "$(distdir)" || mkdir "$(distdir)"
1632         @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
1633         topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
1634         list='$(DISTFILES)'; \
1635           dist_files=`for file in $$list; do echo $$file; done | \
1636           sed -e "s|^$$srcdirstrip/||;t" \
1637               -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
1638         case $$dist_files in \
1639           */*) $(MKDIR_P) `echo "$$dist_files" | \
1640                            sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
1641                            sort -u` ;; \
1642         esac; \
1643         for file in $$dist_files; do \
1644           if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
1645           if test -d $$d/$$file; then \
1646             dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
1647             if test -d "$(distdir)/$$file"; then \
1648               find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
1649             fi; \
1650             if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
1651               cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
1652               find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
1653             fi; \
1654             cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
1655           else \
1656             test -f "$(distdir)/$$file" \
1657             || cp -p $$d/$$file "$(distdir)/$$file" \
1658             || exit 1; \
1659           fi; \
1660         done
1661         -test -n "$(am__skip_mode_fix)" \
1662         || find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
1663           ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
1664           ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
1665           ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
1666         || chmod -R a+r "$(distdir)"
1667 dist-gzip: distdir
1668         tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
1669         $(am__remove_distdir)
1670
1671 dist-bzip2: distdir
1672         tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
1673         $(am__remove_distdir)
1674
1675 dist-lzma: distdir
1676         tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
1677         $(am__remove_distdir)
1678
1679 dist-xz: distdir
1680         tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
1681         $(am__remove_distdir)
1682
1683 dist-tarZ: distdir
1684         tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
1685         $(am__remove_distdir)
1686
1687 dist-shar: distdir
1688         shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
1689         $(am__remove_distdir)
1690
1691 dist-zip: distdir
1692         -rm -f $(distdir).zip
1693         zip -rq $(distdir).zip $(distdir)
1694         $(am__remove_distdir)
1695
1696 dist dist-all: distdir
1697         tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
1698         $(am__remove_distdir)
1699
1700 # This target untars the dist file and tries a VPATH configuration.  Then
1701 # it guarantees that the distribution is self-contained by making another
1702 # tarfile.
1703 distcheck: dist
1704         case '$(DIST_ARCHIVES)' in \
1705         *.tar.gz*) \
1706           GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
1707         *.tar.bz2*) \
1708           bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
1709         *.tar.lzma*) \
1710           unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
1711         *.tar.xz*) \
1712           xz -dc $(distdir).tar.xz | $(am__untar) ;;\
1713         *.tar.Z*) \
1714           uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
1715         *.shar.gz*) \
1716           GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
1717         *.zip*) \
1718           unzip $(distdir).zip ;;\
1719         esac
1720         chmod -R a-w $(distdir); chmod a+w $(distdir)
1721         mkdir $(distdir)/_build
1722         mkdir $(distdir)/_inst
1723         chmod a-w $(distdir)
1724         test -d $(distdir)/_build || exit 0; \
1725         dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
1726           && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
1727           && am__cwd=`pwd` \
1728           && $(am__cd) $(distdir)/_build \
1729           && ../configure --srcdir=.. --prefix="$$dc_install_base" \
1730             $(DISTCHECK_CONFIGURE_FLAGS) \
1731           && $(MAKE) $(AM_MAKEFLAGS) \
1732           && $(MAKE) $(AM_MAKEFLAGS) dvi \
1733           && $(MAKE) $(AM_MAKEFLAGS) check \
1734           && $(MAKE) $(AM_MAKEFLAGS) install \
1735           && $(MAKE) $(AM_MAKEFLAGS) installcheck \
1736           && $(MAKE) $(AM_MAKEFLAGS) uninstall \
1737           && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
1738                 distuninstallcheck \
1739           && chmod -R a-w "$$dc_install_base" \
1740           && ({ \
1741                (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
1742                && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
1743                && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
1744                && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
1745                     distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
1746               } || { rm -rf "$$dc_destdir"; exit 1; }) \
1747           && rm -rf "$$dc_destdir" \
1748           && $(MAKE) $(AM_MAKEFLAGS) dist \
1749           && rm -rf $(DIST_ARCHIVES) \
1750           && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
1751           && cd "$$am__cwd" \
1752           || exit 1
1753         $(am__remove_distdir)
1754         @(echo "$(distdir) archives ready for distribution: "; \
1755           list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
1756           sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
1757 distuninstallcheck:
1758         @$(am__cd) '$(distuninstallcheck_dir)' \
1759         && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
1760            || { echo "ERROR: files left after uninstall:" ; \
1761                 if test -n "$(DESTDIR)"; then \
1762                   echo "  (check DESTDIR support)"; \
1763                 fi ; \
1764                 $(distuninstallcheck_listfiles) ; \
1765                 exit 1; } >&2
1766 distcleancheck: distclean
1767         @if test '$(srcdir)' = . ; then \
1768           echo "ERROR: distcleancheck can only run from a VPATH build" ; \
1769           exit 1 ; \
1770         fi
1771         @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
1772           || { echo "ERROR: files left in build directory after distclean:" ; \
1773                $(distcleancheck_listfiles) ; \
1774                exit 1; } >&2
1775 check-am: all-am
1776         $(MAKE) $(AM_MAKEFLAGS) $(check_LTLIBRARIES) $(check_PROGRAMS)
1777         $(MAKE) $(AM_MAKEFLAGS) check-TESTS
1778 check: check-am
1779 all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) $(MANS) $(DATA) $(HEADERS) \
1780                 config.h
1781 install-binPROGRAMS: install-libLTLIBRARIES
1782
1783 installdirs:
1784         for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(pkgconfigdir)" "$(DESTDIR)$(library_includedir)"; do \
1785           test -z "$$dir" || $(MKDIR_P) "$$dir"; \
1786         done
1787 install: install-am
1788 install-exec: install-exec-am
1789 install-data: install-data-am
1790 uninstall: uninstall-am
1791
1792 install-am: all-am
1793         @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
1794
1795 installcheck: installcheck-am
1796 install-strip:
1797         $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
1798           install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
1799           `test -z '$(STRIP)' || \
1800             echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
1801 mostlyclean-generic:
1802         -test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
1803         -test -z "$(TEST_LOGS_TMP)" || rm -f $(TEST_LOGS_TMP)
1804         -test -z "$(TEST_SUITE_HTML)" || rm -f $(TEST_SUITE_HTML)
1805         -test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
1806
1807 clean-generic:
1808
1809 distclean-generic:
1810         -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
1811         -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
1812         -rm -f bin/$(am__dirstamp)
1813         -rm -f jellyfish/$(DEPDIR)/$(am__dirstamp)
1814         -rm -f jellyfish/$(am__dirstamp)
1815         -rm -f unit_tests/$(DEPDIR)/$(am__dirstamp)
1816         -rm -f unit_tests/$(am__dirstamp)
1817         -rm -f unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
1818         -rm -f unit_tests/gtest/src/$(am__dirstamp)
1819
1820 maintainer-clean-generic:
1821         @echo "This command is intended for maintainers to use"
1822         @echo "it deletes files that may require special tools to rebuild."
1823 clean: clean-am
1824
1825 clean-am: clean-binPROGRAMS clean-checkLTLIBRARIES clean-checkPROGRAMS \
1826         clean-generic clean-libLTLIBRARIES clean-libtool clean-local \
1827         mostlyclean-am
1828
1829 distclean: distclean-am
1830         -rm -f $(am__CONFIG_DISTCLEAN_FILES)
1831         -rm -rf jellyfish/$(DEPDIR) unit_tests/$(DEPDIR) unit_tests/gtest/src/$(DEPDIR)
1832         -rm -f Makefile
1833 distclean-am: clean-am distclean-compile distclean-generic \
1834         distclean-hdr distclean-libtool distclean-tags
1835
1836 dvi: dvi-am
1837
1838 dvi-am:
1839
1840 html: html-am
1841
1842 html-am:
1843
1844 info: info-am
1845
1846 info-am:
1847
1848 install-data-am: install-library_includeHEADERS install-man \
1849         install-pkgconfigDATA
1850
1851 install-dvi: install-dvi-am
1852
1853 install-dvi-am:
1854
1855 install-exec-am: install-binPROGRAMS install-libLTLIBRARIES
1856
1857 install-html: install-html-am
1858
1859 install-html-am:
1860
1861 install-info: install-info-am
1862
1863 install-info-am:
1864
1865 install-man: install-man1
1866
1867 install-pdf: install-pdf-am
1868
1869 install-pdf-am:
1870
1871 install-ps: install-ps-am
1872
1873 install-ps-am:
1874
1875 installcheck-am:
1876
1877 maintainer-clean: maintainer-clean-am
1878         -rm -f $(am__CONFIG_DISTCLEAN_FILES)
1879         -rm -rf $(top_srcdir)/autom4te.cache
1880         -rm -rf jellyfish/$(DEPDIR) unit_tests/$(DEPDIR) unit_tests/gtest/src/$(DEPDIR)
1881         -rm -f Makefile
1882 maintainer-clean-am: distclean-am maintainer-clean-generic
1883
1884 mostlyclean: mostlyclean-am
1885
1886 mostlyclean-am: mostlyclean-compile mostlyclean-generic \
1887         mostlyclean-libtool
1888
1889 pdf: pdf-am
1890
1891 pdf-am:
1892
1893 ps: ps-am
1894
1895 ps-am:
1896
1897 uninstall-am: uninstall-binPROGRAMS uninstall-libLTLIBRARIES \
1898         uninstall-library_includeHEADERS uninstall-man \
1899         uninstall-pkgconfigDATA
1900
1901 uninstall-man: uninstall-man1
1902
1903 .MAKE: all check-am check-html install-am install-strip recheck \
1904         recheck-html
1905
1906 .PHONY: CTAGS GTAGS all all-am am--refresh check check-TESTS check-am \
1907         check-html clean clean-binPROGRAMS clean-checkLTLIBRARIES \
1908         clean-checkPROGRAMS clean-generic clean-libLTLIBRARIES \
1909         clean-libtool clean-local ctags dist dist-all dist-bzip2 \
1910         dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
1911         distcheck distclean distclean-compile distclean-generic \
1912         distclean-hdr distclean-libtool distclean-tags distcleancheck \
1913         distdir distuninstallcheck dvi dvi-am html html-am info \
1914         info-am install install-am install-binPROGRAMS install-data \
1915         install-data-am install-dvi install-dvi-am install-exec \
1916         install-exec-am install-html install-html-am install-info \
1917         install-info-am install-libLTLIBRARIES \
1918         install-library_includeHEADERS install-man install-man1 \
1919         install-pdf install-pdf-am install-pkgconfigDATA install-ps \
1920         install-ps-am install-strip installcheck installcheck-am \
1921         installdirs maintainer-clean maintainer-clean-generic \
1922         mostlyclean mostlyclean-compile mostlyclean-generic \
1923         mostlyclean-libtool pdf pdf-am ps ps-am recheck recheck-html \
1924         tags uninstall uninstall-am uninstall-binPROGRAMS \
1925         uninstall-libLTLIBRARIES uninstall-library_includeHEADERS \
1926         uninstall-man uninstall-man1 uninstall-pkgconfigDATA
1927
1928 clean-local: clean-local-check
1929 .PHONY: clean-local-check
1930 clean-local-check:
1931         -cd tests; rm -f seq10m* seq1m* *_0 *_1 *_2 *.md5sum *.histo *.stats *.timing *.query *.dump *.fa
1932
1933 tests/serial_hashing.log: tests/generate_sequence.log
1934 tests/parallel_hashing.log: tests/generate_sequence.log
1935 tests/serial_direct_indexing.log: tests/generate_sequence.log
1936 tests/parallel_direct_indexing.log: tests/generate_sequence.log
1937 tests/multi_file.log: tests/generate_sequence.log
1938 tests/raw_hash.log: tests/generate_sequence.log
1939 tests/from_stream.log: tests/generate_sequence.log
1940 tests/parallel_fastq_hashing.log: tests/generate_fastq_sequence.log
1941 tests/parallel_fastq_sequence_hashing.log: tests/generate_fastq_sequence.log
1942 tests/multi_file_fastq.log: tests/generate_fastq_sequence.log
1943 tests/from_stream_fastq.log: tests/generate_fastq_sequence.log
1944 tests/merge.log: tests/generate_fastq_sequence.log
1945 tests/min_qual.log: tests/generate_fastq_sequence.log
1946 tests/parsers.log: tests/generate_sequence.log
1947
1948 # Tell versions [3.59,3.63) of GNU make to not export all variables.
1949 # Otherwise a system limit (for SysV at least) may be exceeded.
1950 .NOEXPORT: