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SAMTOOLS_DEPS = @SAMTOOLS_DEPS@
SAMTOOLS_LDFLAGS = @SAMTOOLS_LDFLAGS@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
VERSION = @VERSION@
abs_builddir = @abs_builddir@
abs_srcdir = @abs_srcdir@
abs_top_builddir = @abs_top_builddir@
abs_top_srcdir = @abs_top_srcdir@
ac_ct_CC = @ac_ct_CC@
am__include = @am__include@
am__leading_dot = @am__leading_dot@
am__quote = @am__quote@
am__tar = @am__tar@
am__untar = @am__untar@
bindir = @bindir@
build = @build@
build_alias = @build_alias@
build_cpu = @build_cpu@
build_os = @build_os@
build_vendor = @build_vendor@
builddir = @builddir@
datadir = @datadir@
datarootdir = @datarootdir@
docdir = @docdir@
dvidir = @dvidir@
exec_prefix = @exec_prefix@
host = @host@
host_alias = @host_alias@
host_cpu = @host_cpu@
host_os = @host_os@
host_vendor = @host_vendor@
htmldir = @htmldir@
includedir = @includedir@
infodir = @infodir@
install_sh = @install_sh@
libdir = @libdir@
libexecdir = @libexecdir@
localedir = @localedir@
localstatedir = @localstatedir@
mandir = @mandir@
mkdir_p = @mkdir_p@
oldincludedir = @oldincludedir@
pdfdir = @pdfdir@
pkgpyexecdir = @pkgpyexecdir@
pkgpythondir = @pkgpythondir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
pyexecdir = @pyexecdir@
pythondir = @pythondir@
samtoolsexec = @samtoolsexec@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
DIST_SUBDIRS = data
INCLUDE_PATTERN = -I%
LIBNAM_PATTERN = -l%
AM_CFLAGS = -I../src/ -I../test $(am__append_1) $(am__append_2) \
$(am__append_3) $(am__append_4)
@APPLE_64BIT_TRUE@APPLELDFLAGS = -pthread
@ICC_COMPILER_FALSE@@WITH_SIMD_TRUE@SIMD_INTRINS_FLAGS = -msse2
@ICC_COMPILER_TRUE@@WITH_SIMD_TRUE@SIMD_INTRINS_FLAGS =
@WITH_SIMD_FALSE@SIMD_INTRINS_FLAGS =
SEQ_LIB = ../src/libseq.a
SGM_LIB = ../src/libsgm.a ${SEQ_LIB}
SMIWAT_SRC = ../src/score.c ../src/score.h ../src/alibuffer.c \
../src/alibuffer.h ../src/alibuffer_struct.h $(am__append_5)
ALI_SRC = ../src/diffstr.c ../src/diffstr.h ${SMIWAT_SRC} \
../src/alignment.c ../src/alignment.h
HIT_SRC = ../src/sort.c ../src/sort.h \
../src/interval.c ../src/interval.h \
../src/hashidx.c ../src/hashidx.h \
../src/hashhit.c ../src/hashhit.h
SGM_SRC = ${HIT_SRC} ../src/array.c ../src/array.h ../src/vdef.h \
../src/segment.c ../src/segment.h
MAP_SRC = ../src/results.c ../src/results.h \
../src/resultpairs.c ../src/resultpairs.h \
../src/insert.c ../src/insert.h \
../src/report.c ../src/report.h ../src/rmap.c ../src/rmap.h
SMALT_SRC = ../src/smalt.c ../src/menu.c ../src/menu.h \
../src/threads.c ../src/threads.h \
../src/infmt.c ../src/infmt.h \
${MAP_SRC}
SMALT_TEST_SRC = ${SMALT_SRC} ${SGM_SRC} ${ALI_SRC} tracker.c tracker.h
TEST_DRIVERS = splitReads_test.py \
results_split_test.py \
ouform_cigar_test.py \
sample_test.py \
cigar_test.py \
mthread_test.py
@WITH_TESTDRIVER_TRUE@TESTS_ENVIRONMENT = $(PYTHON)
dist_data_DATA = ${TEST_DRIVERS} bam_cigar_test.py ioform_test.py xali_test.py \
formats.py testdata.py
@WITH_ZLIB_FALSE@ZLIB_LDFLAG =
@WITH_ZLIB_TRUE@ZLIB_LDFLAG = -lz
nodist_array_test_SOURCES = array_test.c
array_test_LDADD = $(SGM_LIB)
array_test_LDFLAGS = -lm $(ZLIB_LDFLAG)
nodist_diffstr_slice_test_SOURCES = diffstr_slice_test.c ../src/diffstr.c ../src/diffstr.h ../src/elib.c ../src/elib.h
diffstr_test_SOURCES = diffstr_test.c ../src/diffstr.c ../src/diffstr.h ../src/elib.c ../src/elib.h
#if WITH_SIMD
#nodist_mergesort_test_SOURCES = mergesort_test.c \
# ../src/elib.c ../src/elib.h ../src/randef.h ../src/sortdef.h \
# ../src/sort.c ../src/sort.h
#mergesort_test_CFLAGS = $(AM_CFLAGS) $(SIMD_INTRINS_FLAGS)
#endif
nodist_sequenceReadWrite_test_SOURCES = sequenceReadWrite_test.c
sequenceReadWrite_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
sequenceReverseComplement_test_SOURCES = sequenceReverseComplement_test.c
sequenceReverseComplement_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
nodist_sequenceCompress_test_SOURCES = sequenceCompress_test.c
sequenceCompress_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
nodist_sequenceDeCompress_test_SOURCES = sequenceDeCompress_test.c
sequenceDeCompress_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
nodist_seqSetIO_test_SOURCES = seqSetIO_test.c
seqSetIO_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
# test routines for hashing
nodist_hashhit_test_SOURCES = hashhit_test.c
hashhit_test_LDADD = $(SGM_LIB) -lm $(ZLIB_LDFLAG)
nodist_hashhit_track_test_SOURCES = hashhit_track_test.c ${HIT_SRC} \
tracker.c tracker.h \
../src/diffstr.c ../src/diffstr.h
hashhit_track_test_CFLAGS = $(AM_CFLAGS) -I
hashhit_track_test_CPPFLAGS = -DRESULTS_TRACKER
hashhit_track_test_LDADD = $(SEQ_LIB) -lm $(ZLIB_LDFLAG)
nodist_hashidx_test_SOURCES = hashidx_test.c
hashidx_test_LDADD = $(SGM_LIB) $(ZLIB_LDFLAG)
# tests for candidate segment selection
nodist_segment_test_SOURCES = segment_test.c
segment_test_LDADD = $(SGM_LIB) -lm $(ZLIB_LDFLAG)
nodist_segment_simple_test_SOURCES = segment_simple_test.c
segment_simple_test_LDADD = $(SGM_LIB) -lm $(ZLIB_LDFLAG)
# tests of alignment routines
nodist_alignment_test_SOURCES = alignment_test.c ${ALI_SRC}
alignment_test_CFLAGS = $(AM_CFLAGS) $(SIMD_INTRINS_FLAGS)
alignment_test_CPPFLAGS = -Dalignment_debug -Dalignment_timing
alignment_test_LDADD = $(SEQ_LIB) -lm $(ZLIB_LDFLAG)
# vectorised Smith-Waterman alignment
@WITH_SIMD_TRUE@nodist_swsimd_test_SOURCES = swsimd_test.c ${SMIWAT_SRC}
@WITH_SIMD_TRUE@swsimd_test_CFLAGS = $(AM_CFLAGS) $(SIMD_INTRINS_FLAGS)
@WITH_SIMD_TRUE@swsimd_test_CPPFLAGS = -Dalignment_matrix_debug
@WITH_SIMD_TRUE@swsimd_test_LDADD = $(SEQ_LIB) -lm $(ZLIB_LDFLAG)
# test of mapping routines
nodist_rmap_test_SOURCES = rmap_test.c ${MAP_SRC}
#if WITH_BAMBAMC
# Dummy C++ source to trigger C++ linking.
#nodist_EXTRA_rmap_test_SOURCES = dummy.cxx
#endif
rmap_test_CFLAGS = $(AM_CFLAGS) $(BAMBAMC_INCL)
rmap_test_LDADD = $(SGM_LIB) $(BAMBAMC_DEPS) -lm $(ZLIB_LDFLAG)
rmap_test_LDFLAGS = $(BAMBAMC_LDFLG)
# test splitting of alignments across neighbouring reference sequences
@WITH_BAMBAMC_TRUE@smalt_Xali_test_SOURCES = ${SMALT_SRC}
@WITH_BAMBAMC_TRUE@smalt_Xali_test_CFLAGS = $(AM_CFLAGS) $(SIMD_INTRINS_FLAGS) $(BAMBAMC_INCL)
@WITH_BAMBAMC_TRUE@smalt_Xali_test_CPPFLAGS = -DSMALT_DEBUG_XALI
@WITH_BAMBAMC_TRUE@smalt_Xali_test_LDADD = $(SGM_LIB) $(BAMBAMC_DEPS) -lm -lpthread $(ZLIB_LDFLAG)
@WITH_BAMBAMC_TRUE@smalt_Xali_test_LDFLAGS = $(APPLELDFLAGS) $(BAMBAMC_LDFLG)
# testing smalt with simulated reads (not distributed)
nodist_smalt_test_SOURCES = ${SMALT_TEST_SRC}
smalt_test_CFLAGS = $(AM_CFLAGS) $(SIMD_INTRINS_FLAGS) -I../test $(BAMBAMC_INCL)
smalt_test_CPPFLAGS = -DRESULTS_TRACKER
smalt_test_LDADD = $(SEQ_LIB) $(BAMBAMC_DEPS) -lm -lpthread $(ZLIB_LDFLAG)
smalt_test_LDFLAGS = $(APPLELDFLAGS) $(BAMBAMC_LDFLG)
# output bas quality stats with smalt
nodist_smalt_basq_SOURCES = ../src/smalt.c ../src/menu.c ../src/menu.h \
../src/infmt.c ../src/infmt.h\
../src/threads.c ../src/threads.h ${MAP_SRC}
smalt_basq_CFLAGS = $(AM_CFLAGS) $(BAMBAMC_INCL)
smalt_basq_CPPFLAGS = -DRESULTS_BASQUAL
smalt_basq_LDADD = $(SGM_LIB) $(BAMBAMC_DEPS) -lm -lpthread $(ZLIB_LDFLAG)
smalt_basq_LDFLAGS = $(APPLELDFLAGS) $(BAMBAMC_LDFLG)
# extracting quality values for statistical analysis
nodist_basqual_test_SOURCES = basqual_test.c ../misc/basqual.c ../misc/basqual.h
basqual_test_CFLAGS = $(AM_CFLAGS) -I../misc
basqual_test_LDADD = $(SEQ_LIB) $(ZLIB_LDFLAG)
# generic interface to sequence input formats
nodist_infmt_test_SOURCES = infmt_test.c ../src/infmt.c ../src/infmt.h
# conditional dummy C++ source to cause C++ linking.
#if WITH_BAMBAMC
#nodist_EXTRA_infmt_test_SOURCES = dummy.cxx
#endif
infmt_test_CFLAGS = $(AM_CFLAGS) $(BAMBAMC_INCL)
infmt_test_LDFLAGS = $(BAMBAMC_LDFLG)
infmt_test_LDADD = $(SEQ_LIB) $(BAMBAMC_DEPS)
# optional samtools api
@WITH_SAMTOOLS_TRUE@nodist_samtools_api_test_SOURCES = samtools_api_test.c ../src/elib.c ../src/elib.h
@WITH_SAMTOOLS_TRUE@samtools_api_test_CFLAGS = $(AM_CFLAGS) $(SAMTOOLS_CFLAGS)
@WITH_SAMTOOLS_TRUE@samtools_api_test_LDFLAGS = $(SAMTOOLS_LDFLAGS)
@WITH_SAMTOOLS_TRUE@samtools_api_test_LDADD = $(SAMTOOLS_DEPS)
# optional libary for reading/writing BAM/SAM by German Tischler
# has to be linked with g++
@WITH_BAMBAMC_TRUE@nodist_bambam_test_SOURCES = bambam_test.c ../src/elib.c ../src/elib.h
# Dummy C++ source to cause C++ linking.
#nodist_EXTRA_bambam_test_SOURCES = dummy.cxx
@WITH_BAMBAMC_TRUE@bambam_test_CFLAGS = $(AM_CFLAGS) $(BAMBAMC_INCL)
@WITH_BAMBAMC_TRUE@bambam_test_CPPFLAGS = -DRESULTS_BASQUAL
@WITH_BAMBAMC_TRUE@bambam_test_LDFLAGS = $(BAMBAMC_LDFLG)
@WITH_BAMBAMC_TRUE@bambam_test_LDADD = $(BAMBAMC_DEPS)
all: all-recursive
.SUFFIXES:
.SUFFIXES: .c .o .obj
$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
&& { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign test/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --foreign test/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
esac;
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(top_srcdir)/configure: $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
clean-checkPROGRAMS:
-test -z "$(check_PROGRAMS)" || rm -f $(check_PROGRAMS)
alignment_test$(EXEEXT): $(alignment_test_OBJECTS) $(alignment_test_DEPENDENCIES)
@rm -f alignment_test$(EXEEXT)
$(alignment_test_LINK) $(alignment_test_OBJECTS) $(alignment_test_LDADD) $(LIBS)
array_test$(EXEEXT): $(array_test_OBJECTS) $(array_test_DEPENDENCIES)
@rm -f array_test$(EXEEXT)
$(array_test_LINK) $(array_test_OBJECTS) $(array_test_LDADD) $(LIBS)
bambam_test$(EXEEXT): $(bambam_test_OBJECTS) $(bambam_test_DEPENDENCIES)
@rm -f bambam_test$(EXEEXT)
$(bambam_test_LINK) $(bambam_test_OBJECTS) $(bambam_test_LDADD) $(LIBS)
basqual_test$(EXEEXT): $(basqual_test_OBJECTS) $(basqual_test_DEPENDENCIES)
@rm -f basqual_test$(EXEEXT)
$(basqual_test_LINK) $(basqual_test_OBJECTS) $(basqual_test_LDADD) $(LIBS)
diffstr_slice_test$(EXEEXT): $(diffstr_slice_test_OBJECTS) $(diffstr_slice_test_DEPENDENCIES)
@rm -f diffstr_slice_test$(EXEEXT)
$(LINK) $(diffstr_slice_test_OBJECTS) $(diffstr_slice_test_LDADD) $(LIBS)
diffstr_test$(EXEEXT): $(diffstr_test_OBJECTS) $(diffstr_test_DEPENDENCIES)
@rm -f diffstr_test$(EXEEXT)
$(LINK) $(diffstr_test_OBJECTS) $(diffstr_test_LDADD) $(LIBS)
hashhit_test$(EXEEXT): $(hashhit_test_OBJECTS) $(hashhit_test_DEPENDENCIES)
@rm -f hashhit_test$(EXEEXT)
$(LINK) $(hashhit_test_OBJECTS) $(hashhit_test_LDADD) $(LIBS)
hashhit_track_test$(EXEEXT): $(hashhit_track_test_OBJECTS) $(hashhit_track_test_DEPENDENCIES)
@rm -f hashhit_track_test$(EXEEXT)
$(hashhit_track_test_LINK) $(hashhit_track_test_OBJECTS) $(hashhit_track_test_LDADD) $(LIBS)
hashidx_test$(EXEEXT): $(hashidx_test_OBJECTS) $(hashidx_test_DEPENDENCIES)
@rm -f hashidx_test$(EXEEXT)
$(LINK) $(hashidx_test_OBJECTS) $(hashidx_test_LDADD) $(LIBS)
infmt_test$(EXEEXT): $(infmt_test_OBJECTS) $(infmt_test_DEPENDENCIES)
@rm -f infmt_test$(EXEEXT)
$(infmt_test_LINK) $(infmt_test_OBJECTS) $(infmt_test_LDADD) $(LIBS)
rmap_test$(EXEEXT): $(rmap_test_OBJECTS) $(rmap_test_DEPENDENCIES)
@rm -f rmap_test$(EXEEXT)
$(rmap_test_LINK) $(rmap_test_OBJECTS) $(rmap_test_LDADD) $(LIBS)
samtools_api_test$(EXEEXT): $(samtools_api_test_OBJECTS) $(samtools_api_test_DEPENDENCIES)
@rm -f samtools_api_test$(EXEEXT)
$(samtools_api_test_LINK) $(samtools_api_test_OBJECTS) $(samtools_api_test_LDADD) $(LIBS)
segment_simple_test$(EXEEXT): $(segment_simple_test_OBJECTS) $(segment_simple_test_DEPENDENCIES)
@rm -f segment_simple_test$(EXEEXT)
$(LINK) $(segment_simple_test_OBJECTS) $(segment_simple_test_LDADD) $(LIBS)
segment_test$(EXEEXT): $(segment_test_OBJECTS) $(segment_test_DEPENDENCIES)
@rm -f segment_test$(EXEEXT)
$(LINK) $(segment_test_OBJECTS) $(segment_test_LDADD) $(LIBS)
seqSetIO_test$(EXEEXT): $(seqSetIO_test_OBJECTS) $(seqSetIO_test_DEPENDENCIES)
@rm -f seqSetIO_test$(EXEEXT)
$(LINK) $(seqSetIO_test_OBJECTS) $(seqSetIO_test_LDADD) $(LIBS)
sequenceCompress_test$(EXEEXT): $(sequenceCompress_test_OBJECTS) $(sequenceCompress_test_DEPENDENCIES)
@rm -f sequenceCompress_test$(EXEEXT)
$(LINK) $(sequenceCompress_test_OBJECTS) $(sequenceCompress_test_LDADD) $(LIBS)
sequenceDeCompress_test$(EXEEXT): $(sequenceDeCompress_test_OBJECTS) $(sequenceDeCompress_test_DEPENDENCIES)
@rm -f sequenceDeCompress_test$(EXEEXT)
$(LINK) $(sequenceDeCompress_test_OBJECTS) $(sequenceDeCompress_test_LDADD) $(LIBS)
sequenceReadWrite_test$(EXEEXT): $(sequenceReadWrite_test_OBJECTS) $(sequenceReadWrite_test_DEPENDENCIES)
@rm -f sequenceReadWrite_test$(EXEEXT)
$(LINK) $(sequenceReadWrite_test_OBJECTS) $(sequenceReadWrite_test_LDADD) $(LIBS)
sequenceReverseComplement_test$(EXEEXT): $(sequenceReverseComplement_test_OBJECTS) $(sequenceReverseComplement_test_DEPENDENCIES)
@rm -f sequenceReverseComplement_test$(EXEEXT)
$(LINK) $(sequenceReverseComplement_test_OBJECTS) $(sequenceReverseComplement_test_LDADD) $(LIBS)
smalt_Xali_test$(EXEEXT): $(smalt_Xali_test_OBJECTS) $(smalt_Xali_test_DEPENDENCIES)
@rm -f smalt_Xali_test$(EXEEXT)
$(smalt_Xali_test_LINK) $(smalt_Xali_test_OBJECTS) $(smalt_Xali_test_LDADD) $(LIBS)
smalt_basq$(EXEEXT): $(smalt_basq_OBJECTS) $(smalt_basq_DEPENDENCIES)
@rm -f smalt_basq$(EXEEXT)
$(smalt_basq_LINK) $(smalt_basq_OBJECTS) $(smalt_basq_LDADD) $(LIBS)
smalt_test$(EXEEXT): $(smalt_test_OBJECTS) $(smalt_test_DEPENDENCIES)
@rm -f smalt_test$(EXEEXT)
$(smalt_test_LINK) $(smalt_test_OBJECTS) $(smalt_test_LDADD) $(LIBS)
swsimd_test$(EXEEXT): $(swsimd_test_OBJECTS) $(swsimd_test_DEPENDENCIES)
@rm -f swsimd_test$(EXEEXT)
$(swsimd_test_LINK) $(swsimd_test_OBJECTS) $(swsimd_test_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-alibuffer.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-alignment.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-alignment_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-diffstr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-score.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/alignment_test-swsimd.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/array_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bambam_test-bambam_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bambam_test-elib.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/basqual_test-basqual.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/basqual_test-basqual_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffstr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffstr_slice_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffstr_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/elib.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-diffstr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-hashhit.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-hashhit_track_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-hashidx.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-interval.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-sort.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashhit_track_test-tracker.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hashidx_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/infmt_test-infmt.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/infmt_test-infmt_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-insert.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-report.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-resultpairs.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-results.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-rmap.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rmap_test-rmap_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/samtools_api_test-elib.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/samtools_api_test-samtools_api_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/segment_simple_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/segment_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seqSetIO_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sequenceCompress_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sequenceDeCompress_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sequenceReadWrite_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sequenceReverseComplement_test.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-infmt.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-insert.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-menu.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-report.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-resultpairs.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/smalt_Xali_test-results.Po@am__quote@
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dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
if test -d "$(distdir)/$$file"; then \
find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
test -f "$(distdir)/$$file" \
|| cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
test -d "$(distdir)/$$subdir" \
|| $(MKDIR_P) "$(distdir)/$$subdir" \
|| exit 1; \
fi; \
done
@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
$(am__relativize); \
new_distdir=$$reldir; \
dir1=$$subdir; dir2="$(top_distdir)"; \
$(am__relativize); \
new_top_distdir=$$reldir; \
echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
($(am__cd) $$subdir && \
$(MAKE) $(AM_MAKEFLAGS) \
top_distdir="$$new_top_distdir" \
distdir="$$new_distdir" \
am__remove_distdir=: \
am__skip_length_check=: \
am__skip_mode_fix=: \
distdir) \
|| exit 1; \
fi; \
done
check-am: all-am
$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-recursive
all-am: Makefile $(DATA)
installdirs: installdirs-recursive
installdirs-am:
for dir in "$(DESTDIR)$(datadir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-recursive
install-exec: install-exec-recursive
install-data: install-data-recursive
uninstall: uninstall-recursive
install-am: all-am
@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
installcheck: installcheck-recursive
install-strip:
$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
`test -z '$(STRIP)' || \
echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
mostlyclean-generic:
clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@echo "it deletes files that may require special tools to rebuild."
clean: clean-recursive
clean-am: clean-checkPROGRAMS clean-generic mostlyclean-am
distclean: distclean-recursive
-rm -rf ./$(DEPDIR)
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
dvi: dvi-recursive
dvi-am:
html: html-recursive
html-am:
info: info-recursive
info-am:
install-data-am: install-dist_dataDATA
install-dvi: install-dvi-recursive
install-dvi-am:
install-exec-am:
install-html: install-html-recursive
install-html-am:
install-info: install-info-recursive
install-info-am:
install-man:
install-pdf: install-pdf-recursive
install-pdf-am:
install-ps: install-ps-recursive
install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-recursive
-rm -rf ./$(DEPDIR)
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
mostlyclean: mostlyclean-recursive
mostlyclean-am: mostlyclean-compile mostlyclean-generic
pdf: pdf-recursive
pdf-am:
ps: ps-recursive
ps-am:
uninstall-am: uninstall-dist_dataDATA
.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) check-am \
ctags-recursive install-am install-strip tags-recursive
.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
all all-am check check-TESTS check-am clean \
clean-checkPROGRAMS clean-generic ctags ctags-recursive \
distclean distclean-compile distclean-generic distclean-tags \
distdir dvi dvi-am html html-am info info-am install \
install-am install-data install-data-am install-dist_dataDATA \
install-dvi install-dvi-am install-exec install-exec-am \
install-html install-html-am install-info install-info-am \
install-man install-pdf install-pdf-am install-ps \
install-ps-am install-strip installcheck installcheck-am \
installdirs installdirs-am maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
uninstall uninstall-am uninstall-dist_dataDATA
#
#bambam_test_CFLAGS = -I../src $(filter-out -std=%, $(BAMBAMC_CFLAGS))
#bambam_test_LDFLAGS = $(BAMBAMC_LIBS)
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
|
