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	gmap_ssse3-block.$(OBJEXT) gmap_ssse3-chrom.$(OBJEXT) \
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	gmap_ssse3-uinttable.$(OBJEXT) gmap_ssse3-gregion.$(OBJEXT) \
	gmap_ssse3-match.$(OBJEXT) gmap_ssse3-matchpool.$(OBJEXT) \
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	gmap_ssse3-orderstat.$(OBJEXT) \
	gmap_ssse3-oligoindex_hr.$(OBJEXT) gmap_ssse3-intron.$(OBJEXT) \
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	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_ssse3_CFLAGS) \
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	$(am__DEPENDENCIES_1)
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	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapindex_CFLAGS) \
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	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_CFLAGS) $(CFLAGS) \
	$(gmapl_LDFLAGS) $(LDFLAGS) -o $@
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	gmapl_avx2-bzip2.$(OBJEXT) gmapl_avx2-sequence.$(OBJEXT) \
	gmapl_avx2-reader.$(OBJEXT) gmapl_avx2-genomicpos.$(OBJEXT) \
	gmapl_avx2-compress.$(OBJEXT) \
	gmapl_avx2-compress-write.$(OBJEXT) \
	gmapl_avx2-gbuffer.$(OBJEXT) gmapl_avx2-genome.$(OBJEXT) \
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	gmapl_avx2-genome128_hr.$(OBJEXT) \
	gmapl_avx2-genome_sites.$(OBJEXT) \
	gmapl_avx2-genome-write.$(OBJEXT) \
	gmapl_avx2-bitpack64-read.$(OBJEXT) \
	gmapl_avx2-bitpack64-readtwo.$(OBJEXT) \
	gmapl_avx2-merge.$(OBJEXT) gmapl_avx2-indexdb.$(OBJEXT) \
	gmapl_avx2-indexdb_hr.$(OBJEXT) gmapl_avx2-oligo.$(OBJEXT) \
	gmapl_avx2-block.$(OBJEXT) gmapl_avx2-chrom.$(OBJEXT) \
	gmapl_avx2-segmentpos.$(OBJEXT) gmapl_avx2-chrnum.$(OBJEXT) \
	gmapl_avx2-uinttable.$(OBJEXT) gmapl_avx2-gregion.$(OBJEXT) \
	gmapl_avx2-match.$(OBJEXT) gmapl_avx2-matchpool.$(OBJEXT) \
	gmapl_avx2-diagnostic.$(OBJEXT) gmapl_avx2-stage1.$(OBJEXT) \
	gmapl_avx2-diag.$(OBJEXT) gmapl_avx2-diagpool.$(OBJEXT) \
	gmapl_avx2-cmet.$(OBJEXT) gmapl_avx2-atoi.$(OBJEXT) \
	gmapl_avx2-orderstat.$(OBJEXT) \
	gmapl_avx2-oligoindex_hr.$(OBJEXT) gmapl_avx2-intron.$(OBJEXT) \
	gmapl_avx2-maxent.$(OBJEXT) gmapl_avx2-maxent_hr.$(OBJEXT) \
	gmapl_avx2-pair.$(OBJEXT) gmapl_avx2-pairpool.$(OBJEXT) \
	gmapl_avx2-cellpool.$(OBJEXT) gmapl_avx2-stage2.$(OBJEXT) \
	gmapl_avx2-doublelist.$(OBJEXT) gmapl_avx2-smooth.$(OBJEXT) \
	gmapl_avx2-splicestringpool.$(OBJEXT) \
	gmapl_avx2-splicetrie_build.$(OBJEXT) \
	gmapl_avx2-splicetrie.$(OBJEXT) \
	gmapl_avx2-boyer-moore.$(OBJEXT) gmapl_avx2-dynprog.$(OBJEXT) \
	gmapl_avx2-dynprog_simd.$(OBJEXT) \
	gmapl_avx2-dynprog_single.$(OBJEXT) \
	gmapl_avx2-dynprog_genome.$(OBJEXT) \
	gmapl_avx2-dynprog_cdna.$(OBJEXT) \
	gmapl_avx2-dynprog_end.$(OBJEXT) \
	gmapl_avx2-translation.$(OBJEXT) gmapl_avx2-pbinom.$(OBJEXT) \
	gmapl_avx2-changepoint.$(OBJEXT) gmapl_avx2-stage3.$(OBJEXT) \
	gmapl_avx2-request.$(OBJEXT) gmapl_avx2-result.$(OBJEXT) \
	gmapl_avx2-output.$(OBJEXT) gmapl_avx2-inbuffer.$(OBJEXT) \
	gmapl_avx2-samheader.$(OBJEXT) gmapl_avx2-outbuffer.$(OBJEXT) \
	gmapl_avx2-chimera.$(OBJEXT) gmapl_avx2-datadir.$(OBJEXT) \
	gmapl_avx2-parserange.$(OBJEXT) gmapl_avx2-getopt.$(OBJEXT) \
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	$(am__DEPENDENCIES_1)
gmapl_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_avx2_CFLAGS) \
	$(CFLAGS) $(gmapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
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	gmapl_avx512-assert.$(OBJEXT) gmapl_avx512-mem.$(OBJEXT) \
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	gmapl_avx512-bigendian.$(OBJEXT) \
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	gmapl_avx512-iit-read-univ.$(OBJEXT) \
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	gmapl_avx512-bzip2.$(OBJEXT) gmapl_avx512-sequence.$(OBJEXT) \
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	gmapl_avx512-compress-write.$(OBJEXT) \
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	gmapl_avx512-genome_sites.$(OBJEXT) \
	gmapl_avx512-genome-write.$(OBJEXT) \
	gmapl_avx512-bitpack64-read.$(OBJEXT) \
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	gmapl_avx512-block.$(OBJEXT) gmapl_avx512-chrom.$(OBJEXT) \
	gmapl_avx512-segmentpos.$(OBJEXT) \
	gmapl_avx512-chrnum.$(OBJEXT) gmapl_avx512-uinttable.$(OBJEXT) \
	gmapl_avx512-gregion.$(OBJEXT) gmapl_avx512-match.$(OBJEXT) \
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	gmapl_avx512-atoi.$(OBJEXT) gmapl_avx512-orderstat.$(OBJEXT) \
	gmapl_avx512-oligoindex_hr.$(OBJEXT) \
	gmapl_avx512-intron.$(OBJEXT) gmapl_avx512-maxent.$(OBJEXT) \
	gmapl_avx512-maxent_hr.$(OBJEXT) gmapl_avx512-pair.$(OBJEXT) \
	gmapl_avx512-pairpool.$(OBJEXT) \
	gmapl_avx512-cellpool.$(OBJEXT) gmapl_avx512-stage2.$(OBJEXT) \
	gmapl_avx512-doublelist.$(OBJEXT) \
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	gmapl_avx512-dynprog.$(OBJEXT) \
	gmapl_avx512-dynprog_simd.$(OBJEXT) \
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	gmapl_avx512-dynprog_genome.$(OBJEXT) \
	gmapl_avx512-dynprog_cdna.$(OBJEXT) \
	gmapl_avx512-dynprog_end.$(OBJEXT) \
	gmapl_avx512-translation.$(OBJEXT) \
	gmapl_avx512-pbinom.$(OBJEXT) \
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	gmapl_avx512-stage3.$(OBJEXT) gmapl_avx512-request.$(OBJEXT) \
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	gmapl_avx512-inbuffer.$(OBJEXT) \
	gmapl_avx512-samheader.$(OBJEXT) \
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	gmapl_avx512-chimera.$(OBJEXT) gmapl_avx512-datadir.$(OBJEXT) \
	gmapl_avx512-parserange.$(OBJEXT) \
	gmapl_avx512-getopt.$(OBJEXT) gmapl_avx512-getopt1.$(OBJEXT) \
	gmapl_avx512-gmap.$(OBJEXT)
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	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gmapl_avx512_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_avx512_CFLAGS) \
	$(CFLAGS) $(gmapl_avx512_LDFLAGS) $(LDFLAGS) -o $@
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	gmapl_nosimd-genome_sites.$(OBJEXT) \
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	gmapl_nosimd-indexdb_hr.$(OBJEXT) gmapl_nosimd-oligo.$(OBJEXT) \
	gmapl_nosimd-block.$(OBJEXT) gmapl_nosimd-chrom.$(OBJEXT) \
	gmapl_nosimd-segmentpos.$(OBJEXT) \
	gmapl_nosimd-chrnum.$(OBJEXT) gmapl_nosimd-uinttable.$(OBJEXT) \
	gmapl_nosimd-gregion.$(OBJEXT) gmapl_nosimd-match.$(OBJEXT) \
	gmapl_nosimd-matchpool.$(OBJEXT) \
	gmapl_nosimd-diagnostic.$(OBJEXT) \
	gmapl_nosimd-stage1.$(OBJEXT) gmapl_nosimd-diag.$(OBJEXT) \
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	gmapl_nosimd-atoi.$(OBJEXT) gmapl_nosimd-orderstat.$(OBJEXT) \
	gmapl_nosimd-oligoindex_hr.$(OBJEXT) \
	gmapl_nosimd-intron.$(OBJEXT) gmapl_nosimd-maxent.$(OBJEXT) \
	gmapl_nosimd-maxent_hr.$(OBJEXT) gmapl_nosimd-pair.$(OBJEXT) \
	gmapl_nosimd-pairpool.$(OBJEXT) \
	gmapl_nosimd-cellpool.$(OBJEXT) gmapl_nosimd-stage2.$(OBJEXT) \
	gmapl_nosimd-doublelist.$(OBJEXT) \
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	gmapl_nosimd-splicestringpool.$(OBJEXT) \
	gmapl_nosimd-splicetrie_build.$(OBJEXT) \
	gmapl_nosimd-splicetrie.$(OBJEXT) \
	gmapl_nosimd-boyer-moore.$(OBJEXT) \
	gmapl_nosimd-dynprog.$(OBJEXT) \
	gmapl_nosimd-dynprog_simd.$(OBJEXT) \
	gmapl_nosimd-dynprog_single.$(OBJEXT) \
	gmapl_nosimd-dynprog_genome.$(OBJEXT) \
	gmapl_nosimd-dynprog_cdna.$(OBJEXT) \
	gmapl_nosimd-dynprog_end.$(OBJEXT) \
	gmapl_nosimd-translation.$(OBJEXT) \
	gmapl_nosimd-pbinom.$(OBJEXT) \
	gmapl_nosimd-changepoint.$(OBJEXT) \
	gmapl_nosimd-stage3.$(OBJEXT) gmapl_nosimd-request.$(OBJEXT) \
	gmapl_nosimd-result.$(OBJEXT) gmapl_nosimd-output.$(OBJEXT) \
	gmapl_nosimd-inbuffer.$(OBJEXT) \
	gmapl_nosimd-samheader.$(OBJEXT) \
	gmapl_nosimd-outbuffer.$(OBJEXT) \
	gmapl_nosimd-chimera.$(OBJEXT) gmapl_nosimd-datadir.$(OBJEXT) \
	gmapl_nosimd-parserange.$(OBJEXT) \
	gmapl_nosimd-getopt.$(OBJEXT) gmapl_nosimd-getopt1.$(OBJEXT) \
	gmapl_nosimd-gmap.$(OBJEXT)
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	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_nosimd_CFLAGS) \
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	gmapl_sse2-gbuffer.$(OBJEXT) gmapl_sse2-genome.$(OBJEXT) \
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	gmapl_sse2-bitpack64-read.$(OBJEXT) \
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	$(am__DEPENDENCIES_1)
gmapl_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse2_CFLAGS) \
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	$(am__DEPENDENCIES_1)
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	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse42_CFLAGS) \
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	$(am__DEPENDENCIES_1)
gmapl_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_ssse3_CFLAGS) \
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	gsnap_avx2-chrnum.$(OBJEXT) gsnap_avx2-maxent_hr.$(OBJEXT) \
	gsnap_avx2-cigar.$(OBJEXT) gsnap_avx2-samprint.$(OBJEXT) \
	gsnap_avx2-mapq.$(OBJEXT) gsnap_avx2-shortread.$(OBJEXT) \
	gsnap_avx2-substring.$(OBJEXT) gsnap_avx2-junction.$(OBJEXT) \
	gsnap_avx2-stage3hr.$(OBJEXT) gsnap_avx2-spanningelt.$(OBJEXT) \
	gsnap_avx2-cmet.$(OBJEXT) gsnap_avx2-atoi.$(OBJEXT) \
	gsnap_avx2-maxent.$(OBJEXT) gsnap_avx2-pair.$(OBJEXT) \
	gsnap_avx2-pairpool.$(OBJEXT) gsnap_avx2-diag.$(OBJEXT) \
	gsnap_avx2-diagpool.$(OBJEXT) gsnap_avx2-orderstat.$(OBJEXT) \
	gsnap_avx2-oligoindex_hr.$(OBJEXT) \
	gsnap_avx2-cellpool.$(OBJEXT) gsnap_avx2-stage2.$(OBJEXT) \
	gsnap_avx2-intron.$(OBJEXT) gsnap_avx2-boyer-moore.$(OBJEXT) \
	gsnap_avx2-changepoint.$(OBJEXT) gsnap_avx2-pbinom.$(OBJEXT) \
	gsnap_avx2-dynprog.$(OBJEXT) gsnap_avx2-dynprog_simd.$(OBJEXT) \
	gsnap_avx2-dynprog_single.$(OBJEXT) \
	gsnap_avx2-dynprog_genome.$(OBJEXT) \
	gsnap_avx2-dynprog_cdna.$(OBJEXT) \
	gsnap_avx2-dynprog_end.$(OBJEXT) gsnap_avx2-gbuffer.$(OBJEXT) \
	gsnap_avx2-doublelist.$(OBJEXT) gsnap_avx2-smooth.$(OBJEXT) \
	gsnap_avx2-chimera.$(OBJEXT) gsnap_avx2-stage3.$(OBJEXT) \
	gsnap_avx2-splicestringpool.$(OBJEXT) \
	gsnap_avx2-splicetrie_build.$(OBJEXT) \
	gsnap_avx2-splicetrie.$(OBJEXT) gsnap_avx2-splice.$(OBJEXT) \
	gsnap_avx2-indel.$(OBJEXT) \
	gsnap_avx2-bitpack64-access.$(OBJEXT) \
	gsnap_avx2-bytecoding.$(OBJEXT) gsnap_avx2-univdiag.$(OBJEXT) \
	gsnap_avx2-sedgesort.$(OBJEXT) \
	gsnap_avx2-sarray-read.$(OBJEXT) \
	gsnap_avx2-sarray-search.$(OBJEXT) \
	gsnap_avx2-merge-heap.$(OBJEXT) gsnap_avx2-stage1hr.$(OBJEXT) \
	gsnap_avx2-request.$(OBJEXT) gsnap_avx2-resulthr.$(OBJEXT) \
	gsnap_avx2-output.$(OBJEXT) gsnap_avx2-inbuffer.$(OBJEXT) \
	gsnap_avx2-samheader.$(OBJEXT) gsnap_avx2-outbuffer.$(OBJEXT) \
	gsnap_avx2-datadir.$(OBJEXT) gsnap_avx2-parserange.$(OBJEXT) \
	gsnap_avx2-getopt.$(OBJEXT) gsnap_avx2-getopt1.$(OBJEXT) \
	gsnap_avx2-gsnap.$(OBJEXT)
dist_gsnap_avx2_OBJECTS = $(am__objects_24)
gsnap_avx2_OBJECTS = $(dist_gsnap_avx2_OBJECTS)
gsnap_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnap_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_avx2_CFLAGS) \
	$(CFLAGS) $(gsnap_avx2_LDFLAGS) $(LDFLAGS) -o $@
am__objects_25 = gsnap_avx512-except.$(OBJEXT) \
	gsnap_avx512-assert.$(OBJEXT) gsnap_avx512-mem.$(OBJEXT) \
	gsnap_avx512-intlist.$(OBJEXT) gsnap_avx512-list.$(OBJEXT) \
	gsnap_avx512-littleendian.$(OBJEXT) \
	gsnap_avx512-bigendian.$(OBJEXT) \
	gsnap_avx512-univinterval.$(OBJEXT) \
	gsnap_avx512-interval.$(OBJEXT) \
	gsnap_avx512-uintlist.$(OBJEXT) \
	gsnap_avx512-stopwatch.$(OBJEXT) \
	gsnap_avx512-semaphore.$(OBJEXT) gsnap_avx512-access.$(OBJEXT) \
	gsnap_avx512-filestring.$(OBJEXT) \
	gsnap_avx512-iit-read-univ.$(OBJEXT) \
	gsnap_avx512-iit-read.$(OBJEXT) gsnap_avx512-md5.$(OBJEXT) \
	gsnap_avx512-bzip2.$(OBJEXT) gsnap_avx512-sequence.$(OBJEXT) \
	gsnap_avx512-reader.$(OBJEXT) \
	gsnap_avx512-genomicpos.$(OBJEXT) \
	gsnap_avx512-compress.$(OBJEXT) gsnap_avx512-genome.$(OBJEXT) \
	gsnap_avx512-popcount.$(OBJEXT) \
	gsnap_avx512-genome128_hr.$(OBJEXT) \
	gsnap_avx512-genome_sites.$(OBJEXT) \
	gsnap_avx512-bitpack64-read.$(OBJEXT) \
	gsnap_avx512-bitpack64-readtwo.$(OBJEXT) \
	gsnap_avx512-merge.$(OBJEXT) gsnap_avx512-indexdb.$(OBJEXT) \
	gsnap_avx512-indexdb_hr.$(OBJEXT) gsnap_avx512-oligo.$(OBJEXT) \
	gsnap_avx512-chrom.$(OBJEXT) gsnap_avx512-segmentpos.$(OBJEXT) \
	gsnap_avx512-chrnum.$(OBJEXT) gsnap_avx512-maxent_hr.$(OBJEXT) \
	gsnap_avx512-cigar.$(OBJEXT) gsnap_avx512-samprint.$(OBJEXT) \
	gsnap_avx512-mapq.$(OBJEXT) gsnap_avx512-shortread.$(OBJEXT) \
	gsnap_avx512-substring.$(OBJEXT) \
	gsnap_avx512-junction.$(OBJEXT) \
	gsnap_avx512-stage3hr.$(OBJEXT) \
	gsnap_avx512-spanningelt.$(OBJEXT) gsnap_avx512-cmet.$(OBJEXT) \
	gsnap_avx512-atoi.$(OBJEXT) gsnap_avx512-maxent.$(OBJEXT) \
	gsnap_avx512-pair.$(OBJEXT) gsnap_avx512-pairpool.$(OBJEXT) \
	gsnap_avx512-diag.$(OBJEXT) gsnap_avx512-diagpool.$(OBJEXT) \
	gsnap_avx512-orderstat.$(OBJEXT) \
	gsnap_avx512-oligoindex_hr.$(OBJEXT) \
	gsnap_avx512-cellpool.$(OBJEXT) gsnap_avx512-stage2.$(OBJEXT) \
	gsnap_avx512-intron.$(OBJEXT) \
	gsnap_avx512-boyer-moore.$(OBJEXT) \
	gsnap_avx512-changepoint.$(OBJEXT) \
	gsnap_avx512-pbinom.$(OBJEXT) gsnap_avx512-dynprog.$(OBJEXT) \
	gsnap_avx512-dynprog_simd.$(OBJEXT) \
	gsnap_avx512-dynprog_single.$(OBJEXT) \
	gsnap_avx512-dynprog_genome.$(OBJEXT) \
	gsnap_avx512-dynprog_cdna.$(OBJEXT) \
	gsnap_avx512-dynprog_end.$(OBJEXT) \
	gsnap_avx512-gbuffer.$(OBJEXT) \
	gsnap_avx512-doublelist.$(OBJEXT) \
	gsnap_avx512-smooth.$(OBJEXT) gsnap_avx512-chimera.$(OBJEXT) \
	gsnap_avx512-stage3.$(OBJEXT) \
	gsnap_avx512-splicestringpool.$(OBJEXT) \
	gsnap_avx512-splicetrie_build.$(OBJEXT) \
	gsnap_avx512-splicetrie.$(OBJEXT) \
	gsnap_avx512-splice.$(OBJEXT) gsnap_avx512-indel.$(OBJEXT) \
	gsnap_avx512-bitpack64-access.$(OBJEXT) \
	gsnap_avx512-bytecoding.$(OBJEXT) \
	gsnap_avx512-univdiag.$(OBJEXT) \
	gsnap_avx512-sedgesort.$(OBJEXT) \
	gsnap_avx512-sarray-read.$(OBJEXT) \
	gsnap_avx512-sarray-search.$(OBJEXT) \
	gsnap_avx512-merge-heap.$(OBJEXT) \
	gsnap_avx512-stage1hr.$(OBJEXT) gsnap_avx512-request.$(OBJEXT) \
	gsnap_avx512-resulthr.$(OBJEXT) gsnap_avx512-output.$(OBJEXT) \
	gsnap_avx512-inbuffer.$(OBJEXT) \
	gsnap_avx512-samheader.$(OBJEXT) \
	gsnap_avx512-outbuffer.$(OBJEXT) \
	gsnap_avx512-datadir.$(OBJEXT) \
	gsnap_avx512-parserange.$(OBJEXT) \
	gsnap_avx512-getopt.$(OBJEXT) gsnap_avx512-getopt1.$(OBJEXT) \
	gsnap_avx512-gsnap.$(OBJEXT)
dist_gsnap_avx512_OBJECTS = $(am__objects_25)
gsnap_avx512_OBJECTS = $(dist_gsnap_avx512_OBJECTS)
gsnap_avx512_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnap_avx512_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_avx512_CFLAGS) \
	$(CFLAGS) $(gsnap_avx512_LDFLAGS) $(LDFLAGS) -o $@
am__objects_26 = gsnap_nosimd-except.$(OBJEXT) \
	gsnap_nosimd-assert.$(OBJEXT) gsnap_nosimd-mem.$(OBJEXT) \
	gsnap_nosimd-intlist.$(OBJEXT) gsnap_nosimd-list.$(OBJEXT) \
	gsnap_nosimd-littleendian.$(OBJEXT) \
	gsnap_nosimd-bigendian.$(OBJEXT) \
	gsnap_nosimd-univinterval.$(OBJEXT) \
	gsnap_nosimd-interval.$(OBJEXT) \
	gsnap_nosimd-uintlist.$(OBJEXT) \
	gsnap_nosimd-stopwatch.$(OBJEXT) \
	gsnap_nosimd-semaphore.$(OBJEXT) gsnap_nosimd-access.$(OBJEXT) \
	gsnap_nosimd-filestring.$(OBJEXT) \
	gsnap_nosimd-iit-read-univ.$(OBJEXT) \
	gsnap_nosimd-iit-read.$(OBJEXT) gsnap_nosimd-md5.$(OBJEXT) \
	gsnap_nosimd-bzip2.$(OBJEXT) gsnap_nosimd-sequence.$(OBJEXT) \
	gsnap_nosimd-reader.$(OBJEXT) \
	gsnap_nosimd-genomicpos.$(OBJEXT) \
	gsnap_nosimd-compress.$(OBJEXT) gsnap_nosimd-genome.$(OBJEXT) \
	gsnap_nosimd-popcount.$(OBJEXT) \
	gsnap_nosimd-genome128_hr.$(OBJEXT) \
	gsnap_nosimd-genome_sites.$(OBJEXT) \
	gsnap_nosimd-bitpack64-read.$(OBJEXT) \
	gsnap_nosimd-bitpack64-readtwo.$(OBJEXT) \
	gsnap_nosimd-merge.$(OBJEXT) gsnap_nosimd-indexdb.$(OBJEXT) \
	gsnap_nosimd-indexdb_hr.$(OBJEXT) gsnap_nosimd-oligo.$(OBJEXT) \
	gsnap_nosimd-chrom.$(OBJEXT) gsnap_nosimd-segmentpos.$(OBJEXT) \
	gsnap_nosimd-chrnum.$(OBJEXT) gsnap_nosimd-maxent_hr.$(OBJEXT) \
	gsnap_nosimd-cigar.$(OBJEXT) gsnap_nosimd-samprint.$(OBJEXT) \
	gsnap_nosimd-mapq.$(OBJEXT) gsnap_nosimd-shortread.$(OBJEXT) \
	gsnap_nosimd-substring.$(OBJEXT) \
	gsnap_nosimd-junction.$(OBJEXT) \
	gsnap_nosimd-stage3hr.$(OBJEXT) \
	gsnap_nosimd-spanningelt.$(OBJEXT) gsnap_nosimd-cmet.$(OBJEXT) \
	gsnap_nosimd-atoi.$(OBJEXT) gsnap_nosimd-maxent.$(OBJEXT) \
	gsnap_nosimd-pair.$(OBJEXT) gsnap_nosimd-pairpool.$(OBJEXT) \
	gsnap_nosimd-diag.$(OBJEXT) gsnap_nosimd-diagpool.$(OBJEXT) \
	gsnap_nosimd-orderstat.$(OBJEXT) \
	gsnap_nosimd-oligoindex_hr.$(OBJEXT) \
	gsnap_nosimd-cellpool.$(OBJEXT) gsnap_nosimd-stage2.$(OBJEXT) \
	gsnap_nosimd-intron.$(OBJEXT) \
	gsnap_nosimd-boyer-moore.$(OBJEXT) \
	gsnap_nosimd-changepoint.$(OBJEXT) \
	gsnap_nosimd-pbinom.$(OBJEXT) gsnap_nosimd-dynprog.$(OBJEXT) \
	gsnap_nosimd-dynprog_simd.$(OBJEXT) \
	gsnap_nosimd-dynprog_single.$(OBJEXT) \
	gsnap_nosimd-dynprog_genome.$(OBJEXT) \
	gsnap_nosimd-dynprog_cdna.$(OBJEXT) \
	gsnap_nosimd-dynprog_end.$(OBJEXT) \
	gsnap_nosimd-gbuffer.$(OBJEXT) \
	gsnap_nosimd-doublelist.$(OBJEXT) \
	gsnap_nosimd-smooth.$(OBJEXT) gsnap_nosimd-chimera.$(OBJEXT) \
	gsnap_nosimd-stage3.$(OBJEXT) \
	gsnap_nosimd-splicestringpool.$(OBJEXT) \
	gsnap_nosimd-splicetrie_build.$(OBJEXT) \
	gsnap_nosimd-splicetrie.$(OBJEXT) \
	gsnap_nosimd-splice.$(OBJEXT) gsnap_nosimd-indel.$(OBJEXT) \
	gsnap_nosimd-bitpack64-access.$(OBJEXT) \
	gsnap_nosimd-bytecoding.$(OBJEXT) \
	gsnap_nosimd-univdiag.$(OBJEXT) \
	gsnap_nosimd-sedgesort.$(OBJEXT) \
	gsnap_nosimd-sarray-read.$(OBJEXT) \
	gsnap_nosimd-sarray-search.$(OBJEXT) \
	gsnap_nosimd-merge-heap.$(OBJEXT) \
	gsnap_nosimd-stage1hr.$(OBJEXT) gsnap_nosimd-request.$(OBJEXT) \
	gsnap_nosimd-resulthr.$(OBJEXT) gsnap_nosimd-output.$(OBJEXT) \
	gsnap_nosimd-inbuffer.$(OBJEXT) \
	gsnap_nosimd-samheader.$(OBJEXT) \
	gsnap_nosimd-outbuffer.$(OBJEXT) \
	gsnap_nosimd-datadir.$(OBJEXT) \
	gsnap_nosimd-parserange.$(OBJEXT) \
	gsnap_nosimd-getopt.$(OBJEXT) gsnap_nosimd-getopt1.$(OBJEXT) \
	gsnap_nosimd-gsnap.$(OBJEXT)
dist_gsnap_nosimd_OBJECTS = $(am__objects_26)
gsnap_nosimd_OBJECTS = $(dist_gsnap_nosimd_OBJECTS)
gsnap_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnap_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_nosimd_CFLAGS) \
	$(CFLAGS) $(gsnap_nosimd_LDFLAGS) $(LDFLAGS) -o $@
am__objects_27 = gsnap_sse2-except.$(OBJEXT) \
	gsnap_sse2-assert.$(OBJEXT) gsnap_sse2-mem.$(OBJEXT) \
	gsnap_sse2-intlist.$(OBJEXT) gsnap_sse2-list.$(OBJEXT) \
	gsnap_sse2-littleendian.$(OBJEXT) \
	gsnap_sse2-bigendian.$(OBJEXT) \
	gsnap_sse2-univinterval.$(OBJEXT) \
	gsnap_sse2-interval.$(OBJEXT) gsnap_sse2-uintlist.$(OBJEXT) \
	gsnap_sse2-stopwatch.$(OBJEXT) gsnap_sse2-semaphore.$(OBJEXT) \
	gsnap_sse2-access.$(OBJEXT) gsnap_sse2-filestring.$(OBJEXT) \
	gsnap_sse2-iit-read-univ.$(OBJEXT) \
	gsnap_sse2-iit-read.$(OBJEXT) gsnap_sse2-md5.$(OBJEXT) \
	gsnap_sse2-bzip2.$(OBJEXT) gsnap_sse2-sequence.$(OBJEXT) \
	gsnap_sse2-reader.$(OBJEXT) gsnap_sse2-genomicpos.$(OBJEXT) \
	gsnap_sse2-compress.$(OBJEXT) gsnap_sse2-genome.$(OBJEXT) \
	gsnap_sse2-popcount.$(OBJEXT) \
	gsnap_sse2-genome128_hr.$(OBJEXT) \
	gsnap_sse2-genome_sites.$(OBJEXT) \
	gsnap_sse2-bitpack64-read.$(OBJEXT) \
	gsnap_sse2-bitpack64-readtwo.$(OBJEXT) \
	gsnap_sse2-merge.$(OBJEXT) gsnap_sse2-indexdb.$(OBJEXT) \
	gsnap_sse2-indexdb_hr.$(OBJEXT) gsnap_sse2-oligo.$(OBJEXT) \
	gsnap_sse2-chrom.$(OBJEXT) gsnap_sse2-segmentpos.$(OBJEXT) \
	gsnap_sse2-chrnum.$(OBJEXT) gsnap_sse2-maxent_hr.$(OBJEXT) \
	gsnap_sse2-cigar.$(OBJEXT) gsnap_sse2-samprint.$(OBJEXT) \
	gsnap_sse2-mapq.$(OBJEXT) gsnap_sse2-shortread.$(OBJEXT) \
	gsnap_sse2-substring.$(OBJEXT) gsnap_sse2-junction.$(OBJEXT) \
	gsnap_sse2-stage3hr.$(OBJEXT) gsnap_sse2-spanningelt.$(OBJEXT) \
	gsnap_sse2-cmet.$(OBJEXT) gsnap_sse2-atoi.$(OBJEXT) \
	gsnap_sse2-maxent.$(OBJEXT) gsnap_sse2-pair.$(OBJEXT) \
	gsnap_sse2-pairpool.$(OBJEXT) gsnap_sse2-diag.$(OBJEXT) \
	gsnap_sse2-diagpool.$(OBJEXT) gsnap_sse2-orderstat.$(OBJEXT) \
	gsnap_sse2-oligoindex_hr.$(OBJEXT) \
	gsnap_sse2-cellpool.$(OBJEXT) gsnap_sse2-stage2.$(OBJEXT) \
	gsnap_sse2-intron.$(OBJEXT) gsnap_sse2-boyer-moore.$(OBJEXT) \
	gsnap_sse2-changepoint.$(OBJEXT) gsnap_sse2-pbinom.$(OBJEXT) \
	gsnap_sse2-dynprog.$(OBJEXT) gsnap_sse2-dynprog_simd.$(OBJEXT) \
	gsnap_sse2-dynprog_single.$(OBJEXT) \
	gsnap_sse2-dynprog_genome.$(OBJEXT) \
	gsnap_sse2-dynprog_cdna.$(OBJEXT) \
	gsnap_sse2-dynprog_end.$(OBJEXT) gsnap_sse2-gbuffer.$(OBJEXT) \
	gsnap_sse2-doublelist.$(OBJEXT) gsnap_sse2-smooth.$(OBJEXT) \
	gsnap_sse2-chimera.$(OBJEXT) gsnap_sse2-stage3.$(OBJEXT) \
	gsnap_sse2-splicestringpool.$(OBJEXT) \
	gsnap_sse2-splicetrie_build.$(OBJEXT) \
	gsnap_sse2-splicetrie.$(OBJEXT) gsnap_sse2-splice.$(OBJEXT) \
	gsnap_sse2-indel.$(OBJEXT) \
	gsnap_sse2-bitpack64-access.$(OBJEXT) \
	gsnap_sse2-bytecoding.$(OBJEXT) gsnap_sse2-univdiag.$(OBJEXT) \
	gsnap_sse2-sedgesort.$(OBJEXT) \
	gsnap_sse2-sarray-read.$(OBJEXT) \
	gsnap_sse2-sarray-search.$(OBJEXT) \
	gsnap_sse2-merge-heap.$(OBJEXT) gsnap_sse2-stage1hr.$(OBJEXT) \
	gsnap_sse2-request.$(OBJEXT) gsnap_sse2-resulthr.$(OBJEXT) \
	gsnap_sse2-output.$(OBJEXT) gsnap_sse2-inbuffer.$(OBJEXT) \
	gsnap_sse2-samheader.$(OBJEXT) gsnap_sse2-outbuffer.$(OBJEXT) \
	gsnap_sse2-datadir.$(OBJEXT) gsnap_sse2-parserange.$(OBJEXT) \
	gsnap_sse2-getopt.$(OBJEXT) gsnap_sse2-getopt1.$(OBJEXT) \
	gsnap_sse2-gsnap.$(OBJEXT)
dist_gsnap_sse2_OBJECTS = $(am__objects_27)
gsnap_sse2_OBJECTS = $(dist_gsnap_sse2_OBJECTS)
gsnap_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnap_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse2_CFLAGS) \
	$(CFLAGS) $(gsnap_sse2_LDFLAGS) $(LDFLAGS) -o $@
am__objects_28 = gsnap_sse41-except.$(OBJEXT) \
	gsnap_sse41-assert.$(OBJEXT) gsnap_sse41-mem.$(OBJEXT) \
	gsnap_sse41-intlist.$(OBJEXT) gsnap_sse41-list.$(OBJEXT) \
	gsnap_sse41-littleendian.$(OBJEXT) \
	gsnap_sse41-bigendian.$(OBJEXT) \
	gsnap_sse41-univinterval.$(OBJEXT) \
	gsnap_sse41-interval.$(OBJEXT) gsnap_sse41-uintlist.$(OBJEXT) \
	gsnap_sse41-stopwatch.$(OBJEXT) \
	gsnap_sse41-semaphore.$(OBJEXT) gsnap_sse41-access.$(OBJEXT) \
	gsnap_sse41-filestring.$(OBJEXT) \
	gsnap_sse41-iit-read-univ.$(OBJEXT) \
	gsnap_sse41-iit-read.$(OBJEXT) gsnap_sse41-md5.$(OBJEXT) \
	gsnap_sse41-bzip2.$(OBJEXT) gsnap_sse41-sequence.$(OBJEXT) \
	gsnap_sse41-reader.$(OBJEXT) gsnap_sse41-genomicpos.$(OBJEXT) \
	gsnap_sse41-compress.$(OBJEXT) gsnap_sse41-genome.$(OBJEXT) \
	gsnap_sse41-popcount.$(OBJEXT) \
	gsnap_sse41-genome128_hr.$(OBJEXT) \
	gsnap_sse41-genome_sites.$(OBJEXT) \
	gsnap_sse41-bitpack64-read.$(OBJEXT) \
	gsnap_sse41-bitpack64-readtwo.$(OBJEXT) \
	gsnap_sse41-merge.$(OBJEXT) gsnap_sse41-indexdb.$(OBJEXT) \
	gsnap_sse41-indexdb_hr.$(OBJEXT) gsnap_sse41-oligo.$(OBJEXT) \
	gsnap_sse41-chrom.$(OBJEXT) gsnap_sse41-segmentpos.$(OBJEXT) \
	gsnap_sse41-chrnum.$(OBJEXT) gsnap_sse41-maxent_hr.$(OBJEXT) \
	gsnap_sse41-cigar.$(OBJEXT) gsnap_sse41-samprint.$(OBJEXT) \
	gsnap_sse41-mapq.$(OBJEXT) gsnap_sse41-shortread.$(OBJEXT) \
	gsnap_sse41-substring.$(OBJEXT) gsnap_sse41-junction.$(OBJEXT) \
	gsnap_sse41-stage3hr.$(OBJEXT) \
	gsnap_sse41-spanningelt.$(OBJEXT) gsnap_sse41-cmet.$(OBJEXT) \
	gsnap_sse41-atoi.$(OBJEXT) gsnap_sse41-maxent.$(OBJEXT) \
	gsnap_sse41-pair.$(OBJEXT) gsnap_sse41-pairpool.$(OBJEXT) \
	gsnap_sse41-diag.$(OBJEXT) gsnap_sse41-diagpool.$(OBJEXT) \
	gsnap_sse41-orderstat.$(OBJEXT) \
	gsnap_sse41-oligoindex_hr.$(OBJEXT) \
	gsnap_sse41-cellpool.$(OBJEXT) gsnap_sse41-stage2.$(OBJEXT) \
	gsnap_sse41-intron.$(OBJEXT) gsnap_sse41-boyer-moore.$(OBJEXT) \
	gsnap_sse41-changepoint.$(OBJEXT) gsnap_sse41-pbinom.$(OBJEXT) \
	gsnap_sse41-dynprog.$(OBJEXT) \
	gsnap_sse41-dynprog_simd.$(OBJEXT) \
	gsnap_sse41-dynprog_single.$(OBJEXT) \
	gsnap_sse41-dynprog_genome.$(OBJEXT) \
	gsnap_sse41-dynprog_cdna.$(OBJEXT) \
	gsnap_sse41-dynprog_end.$(OBJEXT) \
	gsnap_sse41-gbuffer.$(OBJEXT) gsnap_sse41-doublelist.$(OBJEXT) \
	gsnap_sse41-smooth.$(OBJEXT) gsnap_sse41-chimera.$(OBJEXT) \
	gsnap_sse41-stage3.$(OBJEXT) \
	gsnap_sse41-splicestringpool.$(OBJEXT) \
	gsnap_sse41-splicetrie_build.$(OBJEXT) \
	gsnap_sse41-splicetrie.$(OBJEXT) gsnap_sse41-splice.$(OBJEXT) \
	gsnap_sse41-indel.$(OBJEXT) \
	gsnap_sse41-bitpack64-access.$(OBJEXT) \
	gsnap_sse41-bytecoding.$(OBJEXT) \
	gsnap_sse41-univdiag.$(OBJEXT) gsnap_sse41-sedgesort.$(OBJEXT) \
	gsnap_sse41-sarray-read.$(OBJEXT) \
	gsnap_sse41-sarray-search.$(OBJEXT) \
	gsnap_sse41-merge-heap.$(OBJEXT) \
	gsnap_sse41-stage1hr.$(OBJEXT) gsnap_sse41-request.$(OBJEXT) \
	gsnap_sse41-resulthr.$(OBJEXT) gsnap_sse41-output.$(OBJEXT) \
	gsnap_sse41-inbuffer.$(OBJEXT) gsnap_sse41-samheader.$(OBJEXT) \
	gsnap_sse41-outbuffer.$(OBJEXT) gsnap_sse41-datadir.$(OBJEXT) \
	gsnap_sse41-parserange.$(OBJEXT) gsnap_sse41-getopt.$(OBJEXT) \
	gsnap_sse41-getopt1.$(OBJEXT) gsnap_sse41-gsnap.$(OBJEXT)
dist_gsnap_sse41_OBJECTS = $(am__objects_28)
gsnap_sse41_OBJECTS = $(dist_gsnap_sse41_OBJECTS)
gsnap_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnap_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse41_CFLAGS) \
	$(CFLAGS) $(gsnap_sse41_LDFLAGS) $(LDFLAGS) -o $@
am__objects_29 = gsnap_sse42-except.$(OBJEXT) \
	gsnap_sse42-assert.$(OBJEXT) gsnap_sse42-mem.$(OBJEXT) \
	gsnap_sse42-intlist.$(OBJEXT) gsnap_sse42-list.$(OBJEXT) \
	gsnap_sse42-littleendian.$(OBJEXT) \
	gsnap_sse42-bigendian.$(OBJEXT) \
	gsnap_sse42-univinterval.$(OBJEXT) \
	gsnap_sse42-interval.$(OBJEXT) gsnap_sse42-uintlist.$(OBJEXT) \
	gsnap_sse42-stopwatch.$(OBJEXT) \
	gsnap_sse42-semaphore.$(OBJEXT) gsnap_sse42-access.$(OBJEXT) \
	gsnap_sse42-filestring.$(OBJEXT) \
	gsnap_sse42-iit-read-univ.$(OBJEXT) \
	gsnap_sse42-iit-read.$(OBJEXT) gsnap_sse42-md5.$(OBJEXT) \
	gsnap_sse42-bzip2.$(OBJEXT) gsnap_sse42-sequence.$(OBJEXT) \
	gsnap_sse42-reader.$(OBJEXT) gsnap_sse42-genomicpos.$(OBJEXT) \
	gsnap_sse42-compress.$(OBJEXT) gsnap_sse42-genome.$(OBJEXT) \
	gsnap_sse42-popcount.$(OBJEXT) \
	gsnap_sse42-genome128_hr.$(OBJEXT) \
	gsnap_sse42-genome_sites.$(OBJEXT) \
	gsnap_sse42-bitpack64-read.$(OBJEXT) \
	gsnap_sse42-bitpack64-readtwo.$(OBJEXT) \
	gsnap_sse42-merge.$(OBJEXT) gsnap_sse42-indexdb.$(OBJEXT) \
	gsnap_sse42-indexdb_hr.$(OBJEXT) gsnap_sse42-oligo.$(OBJEXT) \
	gsnap_sse42-chrom.$(OBJEXT) gsnap_sse42-segmentpos.$(OBJEXT) \
	gsnap_sse42-chrnum.$(OBJEXT) gsnap_sse42-maxent_hr.$(OBJEXT) \
	gsnap_sse42-cigar.$(OBJEXT) gsnap_sse42-samprint.$(OBJEXT) \
	gsnap_sse42-mapq.$(OBJEXT) gsnap_sse42-shortread.$(OBJEXT) \
	gsnap_sse42-substring.$(OBJEXT) gsnap_sse42-junction.$(OBJEXT) \
	gsnap_sse42-stage3hr.$(OBJEXT) \
	gsnap_sse42-spanningelt.$(OBJEXT) gsnap_sse42-cmet.$(OBJEXT) \
	gsnap_sse42-atoi.$(OBJEXT) gsnap_sse42-maxent.$(OBJEXT) \
	gsnap_sse42-pair.$(OBJEXT) gsnap_sse42-pairpool.$(OBJEXT) \
	gsnap_sse42-diag.$(OBJEXT) gsnap_sse42-diagpool.$(OBJEXT) \
	gsnap_sse42-orderstat.$(OBJEXT) \
	gsnap_sse42-oligoindex_hr.$(OBJEXT) \
	gsnap_sse42-cellpool.$(OBJEXT) gsnap_sse42-stage2.$(OBJEXT) \
	gsnap_sse42-intron.$(OBJEXT) gsnap_sse42-boyer-moore.$(OBJEXT) \
	gsnap_sse42-changepoint.$(OBJEXT) gsnap_sse42-pbinom.$(OBJEXT) \
	gsnap_sse42-dynprog.$(OBJEXT) \
	gsnap_sse42-dynprog_simd.$(OBJEXT) \
	gsnap_sse42-dynprog_single.$(OBJEXT) \
	gsnap_sse42-dynprog_genome.$(OBJEXT) \
	gsnap_sse42-dynprog_cdna.$(OBJEXT) \
	gsnap_sse42-dynprog_end.$(OBJEXT) \
	gsnap_sse42-gbuffer.$(OBJEXT) gsnap_sse42-doublelist.$(OBJEXT) \
	gsnap_sse42-smooth.$(OBJEXT) gsnap_sse42-chimera.$(OBJEXT) \
	gsnap_sse42-stage3.$(OBJEXT) \
	gsnap_sse42-splicestringpool.$(OBJEXT) \
	gsnap_sse42-splicetrie_build.$(OBJEXT) \
	gsnap_sse42-splicetrie.$(OBJEXT) gsnap_sse42-splice.$(OBJEXT) \
	gsnap_sse42-indel.$(OBJEXT) \
	gsnap_sse42-bitpack64-access.$(OBJEXT) \
	gsnap_sse42-bytecoding.$(OBJEXT) \
	gsnap_sse42-univdiag.$(OBJEXT) gsnap_sse42-sedgesort.$(OBJEXT) \
	gsnap_sse42-sarray-read.$(OBJEXT) \
	gsnap_sse42-sarray-search.$(OBJEXT) \
	gsnap_sse42-merge-heap.$(OBJEXT) \
	gsnap_sse42-stage1hr.$(OBJEXT) gsnap_sse42-request.$(OBJEXT) \
	gsnap_sse42-resulthr.$(OBJEXT) gsnap_sse42-output.$(OBJEXT) \
	gsnap_sse42-inbuffer.$(OBJEXT) gsnap_sse42-samheader.$(OBJEXT) \
	gsnap_sse42-outbuffer.$(OBJEXT) gsnap_sse42-datadir.$(OBJEXT) \
	gsnap_sse42-parserange.$(OBJEXT) gsnap_sse42-getopt.$(OBJEXT) \
	gsnap_sse42-getopt1.$(OBJEXT) gsnap_sse42-gsnap.$(OBJEXT)
dist_gsnap_sse42_OBJECTS = $(am__objects_29)
gsnap_sse42_OBJECTS = $(dist_gsnap_sse42_OBJECTS)
gsnap_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnap_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse42_CFLAGS) \
	$(CFLAGS) $(gsnap_sse42_LDFLAGS) $(LDFLAGS) -o $@
am__objects_30 = gsnap_ssse3-except.$(OBJEXT) \
	gsnap_ssse3-assert.$(OBJEXT) gsnap_ssse3-mem.$(OBJEXT) \
	gsnap_ssse3-intlist.$(OBJEXT) gsnap_ssse3-list.$(OBJEXT) \
	gsnap_ssse3-littleendian.$(OBJEXT) \
	gsnap_ssse3-bigendian.$(OBJEXT) \
	gsnap_ssse3-univinterval.$(OBJEXT) \
	gsnap_ssse3-interval.$(OBJEXT) gsnap_ssse3-uintlist.$(OBJEXT) \
	gsnap_ssse3-stopwatch.$(OBJEXT) \
	gsnap_ssse3-semaphore.$(OBJEXT) gsnap_ssse3-access.$(OBJEXT) \
	gsnap_ssse3-filestring.$(OBJEXT) \
	gsnap_ssse3-iit-read-univ.$(OBJEXT) \
	gsnap_ssse3-iit-read.$(OBJEXT) gsnap_ssse3-md5.$(OBJEXT) \
	gsnap_ssse3-bzip2.$(OBJEXT) gsnap_ssse3-sequence.$(OBJEXT) \
	gsnap_ssse3-reader.$(OBJEXT) gsnap_ssse3-genomicpos.$(OBJEXT) \
	gsnap_ssse3-compress.$(OBJEXT) gsnap_ssse3-genome.$(OBJEXT) \
	gsnap_ssse3-popcount.$(OBJEXT) \
	gsnap_ssse3-genome128_hr.$(OBJEXT) \
	gsnap_ssse3-genome_sites.$(OBJEXT) \
	gsnap_ssse3-bitpack64-read.$(OBJEXT) \
	gsnap_ssse3-bitpack64-readtwo.$(OBJEXT) \
	gsnap_ssse3-merge.$(OBJEXT) gsnap_ssse3-indexdb.$(OBJEXT) \
	gsnap_ssse3-indexdb_hr.$(OBJEXT) gsnap_ssse3-oligo.$(OBJEXT) \
	gsnap_ssse3-chrom.$(OBJEXT) gsnap_ssse3-segmentpos.$(OBJEXT) \
	gsnap_ssse3-chrnum.$(OBJEXT) gsnap_ssse3-maxent_hr.$(OBJEXT) \
	gsnap_ssse3-cigar.$(OBJEXT) gsnap_ssse3-samprint.$(OBJEXT) \
	gsnap_ssse3-mapq.$(OBJEXT) gsnap_ssse3-shortread.$(OBJEXT) \
	gsnap_ssse3-substring.$(OBJEXT) gsnap_ssse3-junction.$(OBJEXT) \
	gsnap_ssse3-stage3hr.$(OBJEXT) \
	gsnap_ssse3-spanningelt.$(OBJEXT) gsnap_ssse3-cmet.$(OBJEXT) \
	gsnap_ssse3-atoi.$(OBJEXT) gsnap_ssse3-maxent.$(OBJEXT) \
	gsnap_ssse3-pair.$(OBJEXT) gsnap_ssse3-pairpool.$(OBJEXT) \
	gsnap_ssse3-diag.$(OBJEXT) gsnap_ssse3-diagpool.$(OBJEXT) \
	gsnap_ssse3-orderstat.$(OBJEXT) \
	gsnap_ssse3-oligoindex_hr.$(OBJEXT) \
	gsnap_ssse3-cellpool.$(OBJEXT) gsnap_ssse3-stage2.$(OBJEXT) \
	gsnap_ssse3-intron.$(OBJEXT) gsnap_ssse3-boyer-moore.$(OBJEXT) \
	gsnap_ssse3-changepoint.$(OBJEXT) gsnap_ssse3-pbinom.$(OBJEXT) \
	gsnap_ssse3-dynprog.$(OBJEXT) \
	gsnap_ssse3-dynprog_simd.$(OBJEXT) \
	gsnap_ssse3-dynprog_single.$(OBJEXT) \
	gsnap_ssse3-dynprog_genome.$(OBJEXT) \
	gsnap_ssse3-dynprog_cdna.$(OBJEXT) \
	gsnap_ssse3-dynprog_end.$(OBJEXT) \
	gsnap_ssse3-gbuffer.$(OBJEXT) gsnap_ssse3-doublelist.$(OBJEXT) \
	gsnap_ssse3-smooth.$(OBJEXT) gsnap_ssse3-chimera.$(OBJEXT) \
	gsnap_ssse3-stage3.$(OBJEXT) \
	gsnap_ssse3-splicestringpool.$(OBJEXT) \
	gsnap_ssse3-splicetrie_build.$(OBJEXT) \
	gsnap_ssse3-splicetrie.$(OBJEXT) gsnap_ssse3-splice.$(OBJEXT) \
	gsnap_ssse3-indel.$(OBJEXT) \
	gsnap_ssse3-bitpack64-access.$(OBJEXT) \
	gsnap_ssse3-bytecoding.$(OBJEXT) \
	gsnap_ssse3-univdiag.$(OBJEXT) gsnap_ssse3-sedgesort.$(OBJEXT) \
	gsnap_ssse3-sarray-read.$(OBJEXT) \
	gsnap_ssse3-sarray-search.$(OBJEXT) \
	gsnap_ssse3-merge-heap.$(OBJEXT) \
	gsnap_ssse3-stage1hr.$(OBJEXT) gsnap_ssse3-request.$(OBJEXT) \
	gsnap_ssse3-resulthr.$(OBJEXT) gsnap_ssse3-output.$(OBJEXT) \
	gsnap_ssse3-inbuffer.$(OBJEXT) gsnap_ssse3-samheader.$(OBJEXT) \
	gsnap_ssse3-outbuffer.$(OBJEXT) gsnap_ssse3-datadir.$(OBJEXT) \
	gsnap_ssse3-parserange.$(OBJEXT) gsnap_ssse3-getopt.$(OBJEXT) \
	gsnap_ssse3-getopt1.$(OBJEXT) gsnap_ssse3-gsnap.$(OBJEXT)
dist_gsnap_ssse3_OBJECTS = $(am__objects_30)
gsnap_ssse3_OBJECTS = $(dist_gsnap_ssse3_OBJECTS)
gsnap_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnap_ssse3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_ssse3_CFLAGS) \
	$(CFLAGS) $(gsnap_ssse3_LDFLAGS) $(LDFLAGS) -o $@
am__objects_31 = gsnapl-cpuid.$(OBJEXT) gsnapl-gsnapl_select.$(OBJEXT)
dist_gsnapl_OBJECTS = $(am__objects_31)
gsnapl_OBJECTS = $(dist_gsnapl_OBJECTS)
gsnapl_DEPENDENCIES =
gsnapl_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_CFLAGS) $(CFLAGS) \
	$(gsnapl_LDFLAGS) $(LDFLAGS) -o $@
am__objects_32 = gsnapl_avx2-except.$(OBJEXT) \
	gsnapl_avx2-assert.$(OBJEXT) gsnapl_avx2-mem.$(OBJEXT) \
	gsnapl_avx2-intlist.$(OBJEXT) gsnapl_avx2-list.$(OBJEXT) \
	gsnapl_avx2-littleendian.$(OBJEXT) \
	gsnapl_avx2-bigendian.$(OBJEXT) \
	gsnapl_avx2-univinterval.$(OBJEXT) \
	gsnapl_avx2-interval.$(OBJEXT) gsnapl_avx2-uintlist.$(OBJEXT) \
	gsnapl_avx2-uint8list.$(OBJEXT) \
	gsnapl_avx2-stopwatch.$(OBJEXT) \
	gsnapl_avx2-semaphore.$(OBJEXT) gsnapl_avx2-access.$(OBJEXT) \
	gsnapl_avx2-filestring.$(OBJEXT) \
	gsnapl_avx2-iit-read-univ.$(OBJEXT) \
	gsnapl_avx2-iit-read.$(OBJEXT) gsnapl_avx2-md5.$(OBJEXT) \
	gsnapl_avx2-bzip2.$(OBJEXT) gsnapl_avx2-sequence.$(OBJEXT) \
	gsnapl_avx2-reader.$(OBJEXT) gsnapl_avx2-genomicpos.$(OBJEXT) \
	gsnapl_avx2-compress.$(OBJEXT) gsnapl_avx2-genome.$(OBJEXT) \
	gsnapl_avx2-popcount.$(OBJEXT) \
	gsnapl_avx2-genome128_hr.$(OBJEXT) \
	gsnapl_avx2-genome_sites.$(OBJEXT) \
	gsnapl_avx2-bitpack64-read.$(OBJEXT) \
	gsnapl_avx2-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_avx2-merge.$(OBJEXT) gsnapl_avx2-indexdb.$(OBJEXT) \
	gsnapl_avx2-indexdb_hr.$(OBJEXT) gsnapl_avx2-oligo.$(OBJEXT) \
	gsnapl_avx2-chrom.$(OBJEXT) gsnapl_avx2-segmentpos.$(OBJEXT) \
	gsnapl_avx2-chrnum.$(OBJEXT) gsnapl_avx2-maxent_hr.$(OBJEXT) \
	gsnapl_avx2-cigar.$(OBJEXT) gsnapl_avx2-samprint.$(OBJEXT) \
	gsnapl_avx2-mapq.$(OBJEXT) gsnapl_avx2-shortread.$(OBJEXT) \
	gsnapl_avx2-substring.$(OBJEXT) gsnapl_avx2-junction.$(OBJEXT) \
	gsnapl_avx2-stage3hr.$(OBJEXT) \
	gsnapl_avx2-spanningelt.$(OBJEXT) gsnapl_avx2-cmet.$(OBJEXT) \
	gsnapl_avx2-atoi.$(OBJEXT) gsnapl_avx2-maxent.$(OBJEXT) \
	gsnapl_avx2-pair.$(OBJEXT) gsnapl_avx2-pairpool.$(OBJEXT) \
	gsnapl_avx2-diag.$(OBJEXT) gsnapl_avx2-diagpool.$(OBJEXT) \
	gsnapl_avx2-orderstat.$(OBJEXT) \
	gsnapl_avx2-oligoindex_hr.$(OBJEXT) \
	gsnapl_avx2-cellpool.$(OBJEXT) gsnapl_avx2-stage2.$(OBJEXT) \
	gsnapl_avx2-intron.$(OBJEXT) gsnapl_avx2-boyer-moore.$(OBJEXT) \
	gsnapl_avx2-changepoint.$(OBJEXT) gsnapl_avx2-pbinom.$(OBJEXT) \
	gsnapl_avx2-dynprog.$(OBJEXT) \
	gsnapl_avx2-dynprog_simd.$(OBJEXT) \
	gsnapl_avx2-dynprog_single.$(OBJEXT) \
	gsnapl_avx2-dynprog_genome.$(OBJEXT) \
	gsnapl_avx2-dynprog_cdna.$(OBJEXT) \
	gsnapl_avx2-dynprog_end.$(OBJEXT) \
	gsnapl_avx2-gbuffer.$(OBJEXT) gsnapl_avx2-doublelist.$(OBJEXT) \
	gsnapl_avx2-smooth.$(OBJEXT) gsnapl_avx2-chimera.$(OBJEXT) \
	gsnapl_avx2-stage3.$(OBJEXT) \
	gsnapl_avx2-splicestringpool.$(OBJEXT) \
	gsnapl_avx2-splicetrie_build.$(OBJEXT) \
	gsnapl_avx2-splicetrie.$(OBJEXT) gsnapl_avx2-splice.$(OBJEXT) \
	gsnapl_avx2-indel.$(OBJEXT) \
	gsnapl_avx2-bitpack64-access.$(OBJEXT) \
	gsnapl_avx2-merge-heap.$(OBJEXT) \
	gsnapl_avx2-stage1hr.$(OBJEXT) gsnapl_avx2-request.$(OBJEXT) \
	gsnapl_avx2-resulthr.$(OBJEXT) gsnapl_avx2-output.$(OBJEXT) \
	gsnapl_avx2-inbuffer.$(OBJEXT) gsnapl_avx2-samheader.$(OBJEXT) \
	gsnapl_avx2-outbuffer.$(OBJEXT) gsnapl_avx2-datadir.$(OBJEXT) \
	gsnapl_avx2-parserange.$(OBJEXT) gsnapl_avx2-getopt.$(OBJEXT) \
	gsnapl_avx2-getopt1.$(OBJEXT) gsnapl_avx2-gsnap.$(OBJEXT)
dist_gsnapl_avx2_OBJECTS = $(am__objects_32)
gsnapl_avx2_OBJECTS = $(dist_gsnapl_avx2_OBJECTS)
gsnapl_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnapl_avx2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_avx2_CFLAGS) \
	$(CFLAGS) $(gsnapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
am__objects_33 = gsnapl_avx512-except.$(OBJEXT) \
	gsnapl_avx512-assert.$(OBJEXT) gsnapl_avx512-mem.$(OBJEXT) \
	gsnapl_avx512-intlist.$(OBJEXT) gsnapl_avx512-list.$(OBJEXT) \
	gsnapl_avx512-littleendian.$(OBJEXT) \
	gsnapl_avx512-bigendian.$(OBJEXT) \
	gsnapl_avx512-univinterval.$(OBJEXT) \
	gsnapl_avx512-interval.$(OBJEXT) \
	gsnapl_avx512-uintlist.$(OBJEXT) \
	gsnapl_avx512-uint8list.$(OBJEXT) \
	gsnapl_avx512-stopwatch.$(OBJEXT) \
	gsnapl_avx512-semaphore.$(OBJEXT) \
	gsnapl_avx512-access.$(OBJEXT) \
	gsnapl_avx512-filestring.$(OBJEXT) \
	gsnapl_avx512-iit-read-univ.$(OBJEXT) \
	gsnapl_avx512-iit-read.$(OBJEXT) gsnapl_avx512-md5.$(OBJEXT) \
	gsnapl_avx512-bzip2.$(OBJEXT) gsnapl_avx512-sequence.$(OBJEXT) \
	gsnapl_avx512-reader.$(OBJEXT) \
	gsnapl_avx512-genomicpos.$(OBJEXT) \
	gsnapl_avx512-compress.$(OBJEXT) \
	gsnapl_avx512-genome.$(OBJEXT) \
	gsnapl_avx512-popcount.$(OBJEXT) \
	gsnapl_avx512-genome128_hr.$(OBJEXT) \
	gsnapl_avx512-genome_sites.$(OBJEXT) \
	gsnapl_avx512-bitpack64-read.$(OBJEXT) \
	gsnapl_avx512-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_avx512-merge.$(OBJEXT) gsnapl_avx512-indexdb.$(OBJEXT) \
	gsnapl_avx512-indexdb_hr.$(OBJEXT) \
	gsnapl_avx512-oligo.$(OBJEXT) gsnapl_avx512-chrom.$(OBJEXT) \
	gsnapl_avx512-segmentpos.$(OBJEXT) \
	gsnapl_avx512-chrnum.$(OBJEXT) \
	gsnapl_avx512-maxent_hr.$(OBJEXT) \
	gsnapl_avx512-cigar.$(OBJEXT) gsnapl_avx512-samprint.$(OBJEXT) \
	gsnapl_avx512-mapq.$(OBJEXT) gsnapl_avx512-shortread.$(OBJEXT) \
	gsnapl_avx512-substring.$(OBJEXT) \
	gsnapl_avx512-junction.$(OBJEXT) \
	gsnapl_avx512-stage3hr.$(OBJEXT) \
	gsnapl_avx512-spanningelt.$(OBJEXT) \
	gsnapl_avx512-cmet.$(OBJEXT) gsnapl_avx512-atoi.$(OBJEXT) \
	gsnapl_avx512-maxent.$(OBJEXT) gsnapl_avx512-pair.$(OBJEXT) \
	gsnapl_avx512-pairpool.$(OBJEXT) gsnapl_avx512-diag.$(OBJEXT) \
	gsnapl_avx512-diagpool.$(OBJEXT) \
	gsnapl_avx512-orderstat.$(OBJEXT) \
	gsnapl_avx512-oligoindex_hr.$(OBJEXT) \
	gsnapl_avx512-cellpool.$(OBJEXT) \
	gsnapl_avx512-stage2.$(OBJEXT) gsnapl_avx512-intron.$(OBJEXT) \
	gsnapl_avx512-boyer-moore.$(OBJEXT) \
	gsnapl_avx512-changepoint.$(OBJEXT) \
	gsnapl_avx512-pbinom.$(OBJEXT) gsnapl_avx512-dynprog.$(OBJEXT) \
	gsnapl_avx512-dynprog_simd.$(OBJEXT) \
	gsnapl_avx512-dynprog_single.$(OBJEXT) \
	gsnapl_avx512-dynprog_genome.$(OBJEXT) \
	gsnapl_avx512-dynprog_cdna.$(OBJEXT) \
	gsnapl_avx512-dynprog_end.$(OBJEXT) \
	gsnapl_avx512-gbuffer.$(OBJEXT) \
	gsnapl_avx512-doublelist.$(OBJEXT) \
	gsnapl_avx512-smooth.$(OBJEXT) gsnapl_avx512-chimera.$(OBJEXT) \
	gsnapl_avx512-stage3.$(OBJEXT) \
	gsnapl_avx512-splicestringpool.$(OBJEXT) \
	gsnapl_avx512-splicetrie_build.$(OBJEXT) \
	gsnapl_avx512-splicetrie.$(OBJEXT) \
	gsnapl_avx512-splice.$(OBJEXT) gsnapl_avx512-indel.$(OBJEXT) \
	gsnapl_avx512-bitpack64-access.$(OBJEXT) \
	gsnapl_avx512-merge-heap.$(OBJEXT) \
	gsnapl_avx512-stage1hr.$(OBJEXT) \
	gsnapl_avx512-request.$(OBJEXT) \
	gsnapl_avx512-resulthr.$(OBJEXT) \
	gsnapl_avx512-output.$(OBJEXT) \
	gsnapl_avx512-inbuffer.$(OBJEXT) \
	gsnapl_avx512-samheader.$(OBJEXT) \
	gsnapl_avx512-outbuffer.$(OBJEXT) \
	gsnapl_avx512-datadir.$(OBJEXT) \
	gsnapl_avx512-parserange.$(OBJEXT) \
	gsnapl_avx512-getopt.$(OBJEXT) gsnapl_avx512-getopt1.$(OBJEXT) \
	gsnapl_avx512-gsnap.$(OBJEXT)
dist_gsnapl_avx512_OBJECTS = $(am__objects_33)
gsnapl_avx512_OBJECTS = $(dist_gsnapl_avx512_OBJECTS)
gsnapl_avx512_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_avx512_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_avx512_CFLAGS) \
	$(CFLAGS) $(gsnapl_avx512_LDFLAGS) $(LDFLAGS) -o $@
am__objects_34 = gsnapl_nosimd-except.$(OBJEXT) \
	gsnapl_nosimd-assert.$(OBJEXT) gsnapl_nosimd-mem.$(OBJEXT) \
	gsnapl_nosimd-intlist.$(OBJEXT) gsnapl_nosimd-list.$(OBJEXT) \
	gsnapl_nosimd-littleendian.$(OBJEXT) \
	gsnapl_nosimd-bigendian.$(OBJEXT) \
	gsnapl_nosimd-univinterval.$(OBJEXT) \
	gsnapl_nosimd-interval.$(OBJEXT) \
	gsnapl_nosimd-uintlist.$(OBJEXT) \
	gsnapl_nosimd-uint8list.$(OBJEXT) \
	gsnapl_nosimd-stopwatch.$(OBJEXT) \
	gsnapl_nosimd-semaphore.$(OBJEXT) \
	gsnapl_nosimd-access.$(OBJEXT) \
	gsnapl_nosimd-filestring.$(OBJEXT) \
	gsnapl_nosimd-iit-read-univ.$(OBJEXT) \
	gsnapl_nosimd-iit-read.$(OBJEXT) gsnapl_nosimd-md5.$(OBJEXT) \
	gsnapl_nosimd-bzip2.$(OBJEXT) gsnapl_nosimd-sequence.$(OBJEXT) \
	gsnapl_nosimd-reader.$(OBJEXT) \
	gsnapl_nosimd-genomicpos.$(OBJEXT) \
	gsnapl_nosimd-compress.$(OBJEXT) \
	gsnapl_nosimd-genome.$(OBJEXT) \
	gsnapl_nosimd-popcount.$(OBJEXT) \
	gsnapl_nosimd-genome128_hr.$(OBJEXT) \
	gsnapl_nosimd-genome_sites.$(OBJEXT) \
	gsnapl_nosimd-bitpack64-read.$(OBJEXT) \
	gsnapl_nosimd-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_nosimd-merge.$(OBJEXT) gsnapl_nosimd-indexdb.$(OBJEXT) \
	gsnapl_nosimd-indexdb_hr.$(OBJEXT) \
	gsnapl_nosimd-oligo.$(OBJEXT) gsnapl_nosimd-chrom.$(OBJEXT) \
	gsnapl_nosimd-segmentpos.$(OBJEXT) \
	gsnapl_nosimd-chrnum.$(OBJEXT) \
	gsnapl_nosimd-maxent_hr.$(OBJEXT) \
	gsnapl_nosimd-cigar.$(OBJEXT) gsnapl_nosimd-samprint.$(OBJEXT) \
	gsnapl_nosimd-mapq.$(OBJEXT) gsnapl_nosimd-shortread.$(OBJEXT) \
	gsnapl_nosimd-substring.$(OBJEXT) \
	gsnapl_nosimd-junction.$(OBJEXT) \
	gsnapl_nosimd-stage3hr.$(OBJEXT) \
	gsnapl_nosimd-spanningelt.$(OBJEXT) \
	gsnapl_nosimd-cmet.$(OBJEXT) gsnapl_nosimd-atoi.$(OBJEXT) \
	gsnapl_nosimd-maxent.$(OBJEXT) gsnapl_nosimd-pair.$(OBJEXT) \
	gsnapl_nosimd-pairpool.$(OBJEXT) gsnapl_nosimd-diag.$(OBJEXT) \
	gsnapl_nosimd-diagpool.$(OBJEXT) \
	gsnapl_nosimd-orderstat.$(OBJEXT) \
	gsnapl_nosimd-oligoindex_hr.$(OBJEXT) \
	gsnapl_nosimd-cellpool.$(OBJEXT) \
	gsnapl_nosimd-stage2.$(OBJEXT) gsnapl_nosimd-intron.$(OBJEXT) \
	gsnapl_nosimd-boyer-moore.$(OBJEXT) \
	gsnapl_nosimd-changepoint.$(OBJEXT) \
	gsnapl_nosimd-pbinom.$(OBJEXT) gsnapl_nosimd-dynprog.$(OBJEXT) \
	gsnapl_nosimd-dynprog_simd.$(OBJEXT) \
	gsnapl_nosimd-dynprog_single.$(OBJEXT) \
	gsnapl_nosimd-dynprog_genome.$(OBJEXT) \
	gsnapl_nosimd-dynprog_cdna.$(OBJEXT) \
	gsnapl_nosimd-dynprog_end.$(OBJEXT) \
	gsnapl_nosimd-gbuffer.$(OBJEXT) \
	gsnapl_nosimd-doublelist.$(OBJEXT) \
	gsnapl_nosimd-smooth.$(OBJEXT) gsnapl_nosimd-chimera.$(OBJEXT) \
	gsnapl_nosimd-stage3.$(OBJEXT) \
	gsnapl_nosimd-splicestringpool.$(OBJEXT) \
	gsnapl_nosimd-splicetrie_build.$(OBJEXT) \
	gsnapl_nosimd-splicetrie.$(OBJEXT) \
	gsnapl_nosimd-splice.$(OBJEXT) gsnapl_nosimd-indel.$(OBJEXT) \
	gsnapl_nosimd-bitpack64-access.$(OBJEXT) \
	gsnapl_nosimd-merge-heap.$(OBJEXT) \
	gsnapl_nosimd-stage1hr.$(OBJEXT) \
	gsnapl_nosimd-request.$(OBJEXT) \
	gsnapl_nosimd-resulthr.$(OBJEXT) \
	gsnapl_nosimd-output.$(OBJEXT) \
	gsnapl_nosimd-inbuffer.$(OBJEXT) \
	gsnapl_nosimd-samheader.$(OBJEXT) \
	gsnapl_nosimd-outbuffer.$(OBJEXT) \
	gsnapl_nosimd-datadir.$(OBJEXT) \
	gsnapl_nosimd-parserange.$(OBJEXT) \
	gsnapl_nosimd-getopt.$(OBJEXT) gsnapl_nosimd-getopt1.$(OBJEXT) \
	gsnapl_nosimd-gsnap.$(OBJEXT)
dist_gsnapl_nosimd_OBJECTS = $(am__objects_34)
gsnapl_nosimd_OBJECTS = $(dist_gsnapl_nosimd_OBJECTS)
gsnapl_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_nosimd_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_nosimd_CFLAGS) \
	$(CFLAGS) $(gsnapl_nosimd_LDFLAGS) $(LDFLAGS) -o $@
am__objects_35 = gsnapl_sse2-except.$(OBJEXT) \
	gsnapl_sse2-assert.$(OBJEXT) gsnapl_sse2-mem.$(OBJEXT) \
	gsnapl_sse2-intlist.$(OBJEXT) gsnapl_sse2-list.$(OBJEXT) \
	gsnapl_sse2-littleendian.$(OBJEXT) \
	gsnapl_sse2-bigendian.$(OBJEXT) \
	gsnapl_sse2-univinterval.$(OBJEXT) \
	gsnapl_sse2-interval.$(OBJEXT) gsnapl_sse2-uintlist.$(OBJEXT) \
	gsnapl_sse2-uint8list.$(OBJEXT) \
	gsnapl_sse2-stopwatch.$(OBJEXT) \
	gsnapl_sse2-semaphore.$(OBJEXT) gsnapl_sse2-access.$(OBJEXT) \
	gsnapl_sse2-filestring.$(OBJEXT) \
	gsnapl_sse2-iit-read-univ.$(OBJEXT) \
	gsnapl_sse2-iit-read.$(OBJEXT) gsnapl_sse2-md5.$(OBJEXT) \
	gsnapl_sse2-bzip2.$(OBJEXT) gsnapl_sse2-sequence.$(OBJEXT) \
	gsnapl_sse2-reader.$(OBJEXT) gsnapl_sse2-genomicpos.$(OBJEXT) \
	gsnapl_sse2-compress.$(OBJEXT) gsnapl_sse2-genome.$(OBJEXT) \
	gsnapl_sse2-popcount.$(OBJEXT) \
	gsnapl_sse2-genome128_hr.$(OBJEXT) \
	gsnapl_sse2-genome_sites.$(OBJEXT) \
	gsnapl_sse2-bitpack64-read.$(OBJEXT) \
	gsnapl_sse2-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_sse2-merge.$(OBJEXT) gsnapl_sse2-indexdb.$(OBJEXT) \
	gsnapl_sse2-indexdb_hr.$(OBJEXT) gsnapl_sse2-oligo.$(OBJEXT) \
	gsnapl_sse2-chrom.$(OBJEXT) gsnapl_sse2-segmentpos.$(OBJEXT) \
	gsnapl_sse2-chrnum.$(OBJEXT) gsnapl_sse2-maxent_hr.$(OBJEXT) \
	gsnapl_sse2-cigar.$(OBJEXT) gsnapl_sse2-samprint.$(OBJEXT) \
	gsnapl_sse2-mapq.$(OBJEXT) gsnapl_sse2-shortread.$(OBJEXT) \
	gsnapl_sse2-substring.$(OBJEXT) gsnapl_sse2-junction.$(OBJEXT) \
	gsnapl_sse2-stage3hr.$(OBJEXT) \
	gsnapl_sse2-spanningelt.$(OBJEXT) gsnapl_sse2-cmet.$(OBJEXT) \
	gsnapl_sse2-atoi.$(OBJEXT) gsnapl_sse2-maxent.$(OBJEXT) \
	gsnapl_sse2-pair.$(OBJEXT) gsnapl_sse2-pairpool.$(OBJEXT) \
	gsnapl_sse2-diag.$(OBJEXT) gsnapl_sse2-diagpool.$(OBJEXT) \
	gsnapl_sse2-orderstat.$(OBJEXT) \
	gsnapl_sse2-oligoindex_hr.$(OBJEXT) \
	gsnapl_sse2-cellpool.$(OBJEXT) gsnapl_sse2-stage2.$(OBJEXT) \
	gsnapl_sse2-intron.$(OBJEXT) gsnapl_sse2-boyer-moore.$(OBJEXT) \
	gsnapl_sse2-changepoint.$(OBJEXT) gsnapl_sse2-pbinom.$(OBJEXT) \
	gsnapl_sse2-dynprog.$(OBJEXT) \
	gsnapl_sse2-dynprog_simd.$(OBJEXT) \
	gsnapl_sse2-dynprog_single.$(OBJEXT) \
	gsnapl_sse2-dynprog_genome.$(OBJEXT) \
	gsnapl_sse2-dynprog_cdna.$(OBJEXT) \
	gsnapl_sse2-dynprog_end.$(OBJEXT) \
	gsnapl_sse2-gbuffer.$(OBJEXT) gsnapl_sse2-doublelist.$(OBJEXT) \
	gsnapl_sse2-smooth.$(OBJEXT) gsnapl_sse2-chimera.$(OBJEXT) \
	gsnapl_sse2-stage3.$(OBJEXT) \
	gsnapl_sse2-splicestringpool.$(OBJEXT) \
	gsnapl_sse2-splicetrie_build.$(OBJEXT) \
	gsnapl_sse2-splicetrie.$(OBJEXT) gsnapl_sse2-splice.$(OBJEXT) \
	gsnapl_sse2-indel.$(OBJEXT) \
	gsnapl_sse2-bitpack64-access.$(OBJEXT) \
	gsnapl_sse2-merge-heap.$(OBJEXT) \
	gsnapl_sse2-stage1hr.$(OBJEXT) gsnapl_sse2-request.$(OBJEXT) \
	gsnapl_sse2-resulthr.$(OBJEXT) gsnapl_sse2-output.$(OBJEXT) \
	gsnapl_sse2-inbuffer.$(OBJEXT) gsnapl_sse2-samheader.$(OBJEXT) \
	gsnapl_sse2-outbuffer.$(OBJEXT) gsnapl_sse2-datadir.$(OBJEXT) \
	gsnapl_sse2-parserange.$(OBJEXT) gsnapl_sse2-getopt.$(OBJEXT) \
	gsnapl_sse2-getopt1.$(OBJEXT) gsnapl_sse2-gsnap.$(OBJEXT)
dist_gsnapl_sse2_OBJECTS = $(am__objects_35)
gsnapl_sse2_OBJECTS = $(dist_gsnapl_sse2_OBJECTS)
gsnapl_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
gsnapl_sse2_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse2_CFLAGS) \
	$(CFLAGS) $(gsnapl_sse2_LDFLAGS) $(LDFLAGS) -o $@
am__objects_36 = gsnapl_sse41-except.$(OBJEXT) \
	gsnapl_sse41-assert.$(OBJEXT) gsnapl_sse41-mem.$(OBJEXT) \
	gsnapl_sse41-intlist.$(OBJEXT) gsnapl_sse41-list.$(OBJEXT) \
	gsnapl_sse41-littleendian.$(OBJEXT) \
	gsnapl_sse41-bigendian.$(OBJEXT) \
	gsnapl_sse41-univinterval.$(OBJEXT) \
	gsnapl_sse41-interval.$(OBJEXT) \
	gsnapl_sse41-uintlist.$(OBJEXT) \
	gsnapl_sse41-uint8list.$(OBJEXT) \
	gsnapl_sse41-stopwatch.$(OBJEXT) \
	gsnapl_sse41-semaphore.$(OBJEXT) gsnapl_sse41-access.$(OBJEXT) \
	gsnapl_sse41-filestring.$(OBJEXT) \
	gsnapl_sse41-iit-read-univ.$(OBJEXT) \
	gsnapl_sse41-iit-read.$(OBJEXT) gsnapl_sse41-md5.$(OBJEXT) \
	gsnapl_sse41-bzip2.$(OBJEXT) gsnapl_sse41-sequence.$(OBJEXT) \
	gsnapl_sse41-reader.$(OBJEXT) \
	gsnapl_sse41-genomicpos.$(OBJEXT) \
	gsnapl_sse41-compress.$(OBJEXT) gsnapl_sse41-genome.$(OBJEXT) \
	gsnapl_sse41-popcount.$(OBJEXT) \
	gsnapl_sse41-genome128_hr.$(OBJEXT) \
	gsnapl_sse41-genome_sites.$(OBJEXT) \
	gsnapl_sse41-bitpack64-read.$(OBJEXT) \
	gsnapl_sse41-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_sse41-merge.$(OBJEXT) gsnapl_sse41-indexdb.$(OBJEXT) \
	gsnapl_sse41-indexdb_hr.$(OBJEXT) gsnapl_sse41-oligo.$(OBJEXT) \
	gsnapl_sse41-chrom.$(OBJEXT) gsnapl_sse41-segmentpos.$(OBJEXT) \
	gsnapl_sse41-chrnum.$(OBJEXT) gsnapl_sse41-maxent_hr.$(OBJEXT) \
	gsnapl_sse41-cigar.$(OBJEXT) gsnapl_sse41-samprint.$(OBJEXT) \
	gsnapl_sse41-mapq.$(OBJEXT) gsnapl_sse41-shortread.$(OBJEXT) \
	gsnapl_sse41-substring.$(OBJEXT) \
	gsnapl_sse41-junction.$(OBJEXT) \
	gsnapl_sse41-stage3hr.$(OBJEXT) \
	gsnapl_sse41-spanningelt.$(OBJEXT) gsnapl_sse41-cmet.$(OBJEXT) \
	gsnapl_sse41-atoi.$(OBJEXT) gsnapl_sse41-maxent.$(OBJEXT) \
	gsnapl_sse41-pair.$(OBJEXT) gsnapl_sse41-pairpool.$(OBJEXT) \
	gsnapl_sse41-diag.$(OBJEXT) gsnapl_sse41-diagpool.$(OBJEXT) \
	gsnapl_sse41-orderstat.$(OBJEXT) \
	gsnapl_sse41-oligoindex_hr.$(OBJEXT) \
	gsnapl_sse41-cellpool.$(OBJEXT) gsnapl_sse41-stage2.$(OBJEXT) \
	gsnapl_sse41-intron.$(OBJEXT) \
	gsnapl_sse41-boyer-moore.$(OBJEXT) \
	gsnapl_sse41-changepoint.$(OBJEXT) \
	gsnapl_sse41-pbinom.$(OBJEXT) gsnapl_sse41-dynprog.$(OBJEXT) \
	gsnapl_sse41-dynprog_simd.$(OBJEXT) \
	gsnapl_sse41-dynprog_single.$(OBJEXT) \
	gsnapl_sse41-dynprog_genome.$(OBJEXT) \
	gsnapl_sse41-dynprog_cdna.$(OBJEXT) \
	gsnapl_sse41-dynprog_end.$(OBJEXT) \
	gsnapl_sse41-gbuffer.$(OBJEXT) \
	gsnapl_sse41-doublelist.$(OBJEXT) \
	gsnapl_sse41-smooth.$(OBJEXT) gsnapl_sse41-chimera.$(OBJEXT) \
	gsnapl_sse41-stage3.$(OBJEXT) \
	gsnapl_sse41-splicestringpool.$(OBJEXT) \
	gsnapl_sse41-splicetrie_build.$(OBJEXT) \
	gsnapl_sse41-splicetrie.$(OBJEXT) \
	gsnapl_sse41-splice.$(OBJEXT) gsnapl_sse41-indel.$(OBJEXT) \
	gsnapl_sse41-bitpack64-access.$(OBJEXT) \
	gsnapl_sse41-merge-heap.$(OBJEXT) \
	gsnapl_sse41-stage1hr.$(OBJEXT) gsnapl_sse41-request.$(OBJEXT) \
	gsnapl_sse41-resulthr.$(OBJEXT) gsnapl_sse41-output.$(OBJEXT) \
	gsnapl_sse41-inbuffer.$(OBJEXT) \
	gsnapl_sse41-samheader.$(OBJEXT) \
	gsnapl_sse41-outbuffer.$(OBJEXT) \
	gsnapl_sse41-datadir.$(OBJEXT) \
	gsnapl_sse41-parserange.$(OBJEXT) \
	gsnapl_sse41-getopt.$(OBJEXT) gsnapl_sse41-getopt1.$(OBJEXT) \
	gsnapl_sse41-gsnap.$(OBJEXT)
dist_gsnapl_sse41_OBJECTS = $(am__objects_36)
gsnapl_sse41_OBJECTS = $(dist_gsnapl_sse41_OBJECTS)
gsnapl_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_sse41_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse41_CFLAGS) \
	$(CFLAGS) $(gsnapl_sse41_LDFLAGS) $(LDFLAGS) -o $@
am__objects_37 = gsnapl_sse42-except.$(OBJEXT) \
	gsnapl_sse42-assert.$(OBJEXT) gsnapl_sse42-mem.$(OBJEXT) \
	gsnapl_sse42-intlist.$(OBJEXT) gsnapl_sse42-list.$(OBJEXT) \
	gsnapl_sse42-littleendian.$(OBJEXT) \
	gsnapl_sse42-bigendian.$(OBJEXT) \
	gsnapl_sse42-univinterval.$(OBJEXT) \
	gsnapl_sse42-interval.$(OBJEXT) \
	gsnapl_sse42-uintlist.$(OBJEXT) \
	gsnapl_sse42-uint8list.$(OBJEXT) \
	gsnapl_sse42-stopwatch.$(OBJEXT) \
	gsnapl_sse42-semaphore.$(OBJEXT) gsnapl_sse42-access.$(OBJEXT) \
	gsnapl_sse42-filestring.$(OBJEXT) \
	gsnapl_sse42-iit-read-univ.$(OBJEXT) \
	gsnapl_sse42-iit-read.$(OBJEXT) gsnapl_sse42-md5.$(OBJEXT) \
	gsnapl_sse42-bzip2.$(OBJEXT) gsnapl_sse42-sequence.$(OBJEXT) \
	gsnapl_sse42-reader.$(OBJEXT) \
	gsnapl_sse42-genomicpos.$(OBJEXT) \
	gsnapl_sse42-compress.$(OBJEXT) gsnapl_sse42-genome.$(OBJEXT) \
	gsnapl_sse42-popcount.$(OBJEXT) \
	gsnapl_sse42-genome128_hr.$(OBJEXT) \
	gsnapl_sse42-genome_sites.$(OBJEXT) \
	gsnapl_sse42-bitpack64-read.$(OBJEXT) \
	gsnapl_sse42-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_sse42-merge.$(OBJEXT) gsnapl_sse42-indexdb.$(OBJEXT) \
	gsnapl_sse42-indexdb_hr.$(OBJEXT) gsnapl_sse42-oligo.$(OBJEXT) \
	gsnapl_sse42-chrom.$(OBJEXT) gsnapl_sse42-segmentpos.$(OBJEXT) \
	gsnapl_sse42-chrnum.$(OBJEXT) gsnapl_sse42-maxent_hr.$(OBJEXT) \
	gsnapl_sse42-cigar.$(OBJEXT) gsnapl_sse42-samprint.$(OBJEXT) \
	gsnapl_sse42-mapq.$(OBJEXT) gsnapl_sse42-shortread.$(OBJEXT) \
	gsnapl_sse42-substring.$(OBJEXT) \
	gsnapl_sse42-junction.$(OBJEXT) \
	gsnapl_sse42-stage3hr.$(OBJEXT) \
	gsnapl_sse42-spanningelt.$(OBJEXT) gsnapl_sse42-cmet.$(OBJEXT) \
	gsnapl_sse42-atoi.$(OBJEXT) gsnapl_sse42-maxent.$(OBJEXT) \
	gsnapl_sse42-pair.$(OBJEXT) gsnapl_sse42-pairpool.$(OBJEXT) \
	gsnapl_sse42-diag.$(OBJEXT) gsnapl_sse42-diagpool.$(OBJEXT) \
	gsnapl_sse42-orderstat.$(OBJEXT) \
	gsnapl_sse42-oligoindex_hr.$(OBJEXT) \
	gsnapl_sse42-cellpool.$(OBJEXT) gsnapl_sse42-stage2.$(OBJEXT) \
	gsnapl_sse42-intron.$(OBJEXT) \
	gsnapl_sse42-boyer-moore.$(OBJEXT) \
	gsnapl_sse42-changepoint.$(OBJEXT) \
	gsnapl_sse42-pbinom.$(OBJEXT) gsnapl_sse42-dynprog.$(OBJEXT) \
	gsnapl_sse42-dynprog_simd.$(OBJEXT) \
	gsnapl_sse42-dynprog_single.$(OBJEXT) \
	gsnapl_sse42-dynprog_genome.$(OBJEXT) \
	gsnapl_sse42-dynprog_cdna.$(OBJEXT) \
	gsnapl_sse42-dynprog_end.$(OBJEXT) \
	gsnapl_sse42-gbuffer.$(OBJEXT) \
	gsnapl_sse42-doublelist.$(OBJEXT) \
	gsnapl_sse42-smooth.$(OBJEXT) gsnapl_sse42-chimera.$(OBJEXT) \
	gsnapl_sse42-stage3.$(OBJEXT) \
	gsnapl_sse42-splicestringpool.$(OBJEXT) \
	gsnapl_sse42-splicetrie_build.$(OBJEXT) \
	gsnapl_sse42-splicetrie.$(OBJEXT) \
	gsnapl_sse42-splice.$(OBJEXT) gsnapl_sse42-indel.$(OBJEXT) \
	gsnapl_sse42-bitpack64-access.$(OBJEXT) \
	gsnapl_sse42-merge-heap.$(OBJEXT) \
	gsnapl_sse42-stage1hr.$(OBJEXT) gsnapl_sse42-request.$(OBJEXT) \
	gsnapl_sse42-resulthr.$(OBJEXT) gsnapl_sse42-output.$(OBJEXT) \
	gsnapl_sse42-inbuffer.$(OBJEXT) \
	gsnapl_sse42-samheader.$(OBJEXT) \
	gsnapl_sse42-outbuffer.$(OBJEXT) \
	gsnapl_sse42-datadir.$(OBJEXT) \
	gsnapl_sse42-parserange.$(OBJEXT) \
	gsnapl_sse42-getopt.$(OBJEXT) gsnapl_sse42-getopt1.$(OBJEXT) \
	gsnapl_sse42-gsnap.$(OBJEXT)
dist_gsnapl_sse42_OBJECTS = $(am__objects_37)
gsnapl_sse42_OBJECTS = $(dist_gsnapl_sse42_OBJECTS)
gsnapl_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
gsnapl_sse42_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse42_CFLAGS) \
	$(CFLAGS) $(gsnapl_sse42_LDFLAGS) $(LDFLAGS) -o $@
am__objects_38 = gsnapl_ssse3-except.$(OBJEXT) \
	gsnapl_ssse3-assert.$(OBJEXT) gsnapl_ssse3-mem.$(OBJEXT) \
	gsnapl_ssse3-intlist.$(OBJEXT) gsnapl_ssse3-list.$(OBJEXT) \
	gsnapl_ssse3-littleendian.$(OBJEXT) \
	gsnapl_ssse3-bigendian.$(OBJEXT) \
	gsnapl_ssse3-univinterval.$(OBJEXT) \
	gsnapl_ssse3-interval.$(OBJEXT) \
	gsnapl_ssse3-uintlist.$(OBJEXT) \
	gsnapl_ssse3-uint8list.$(OBJEXT) \
	gsnapl_ssse3-stopwatch.$(OBJEXT) \
	gsnapl_ssse3-semaphore.$(OBJEXT) gsnapl_ssse3-access.$(OBJEXT) \
	gsnapl_ssse3-filestring.$(OBJEXT) \
	gsnapl_ssse3-iit-read-univ.$(OBJEXT) \
	gsnapl_ssse3-iit-read.$(OBJEXT) gsnapl_ssse3-md5.$(OBJEXT) \
	gsnapl_ssse3-bzip2.$(OBJEXT) gsnapl_ssse3-sequence.$(OBJEXT) \
	gsnapl_ssse3-reader.$(OBJEXT) \
	gsnapl_ssse3-genomicpos.$(OBJEXT) \
	gsnapl_ssse3-compress.$(OBJEXT) gsnapl_ssse3-genome.$(OBJEXT) \
	gsnapl_ssse3-popcount.$(OBJEXT) \
	gsnapl_ssse3-genome128_hr.$(OBJEXT) \
	gsnapl_ssse3-genome_sites.$(OBJEXT) \
	gsnapl_ssse3-bitpack64-read.$(OBJEXT) \
	gsnapl_ssse3-bitpack64-readtwo.$(OBJEXT) \
	gsnapl_ssse3-merge.$(OBJEXT) gsnapl_ssse3-indexdb.$(OBJEXT) \
	gsnapl_ssse3-indexdb_hr.$(OBJEXT) gsnapl_ssse3-oligo.$(OBJEXT) \
	gsnapl_ssse3-chrom.$(OBJEXT) gsnapl_ssse3-segmentpos.$(OBJEXT) \
	gsnapl_ssse3-chrnum.$(OBJEXT) gsnapl_ssse3-maxent_hr.$(OBJEXT) \
	gsnapl_ssse3-cigar.$(OBJEXT) gsnapl_ssse3-samprint.$(OBJEXT) \
	gsnapl_ssse3-mapq.$(OBJEXT) gsnapl_ssse3-shortread.$(OBJEXT) \
	gsnapl_ssse3-substring.$(OBJEXT) \
	gsnapl_ssse3-junction.$(OBJEXT) \
	gsnapl_ssse3-stage3hr.$(OBJEXT) \
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	$(dist_gsnapl_sse42_SOURCES) $(dist_gsnapl_ssse3_SOURCES) \
	$(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
	$(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
	$(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
	$(dist_uniqscanl_SOURCES)
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ALLOCA = @ALLOCA@
AMTAR = @AMTAR@
AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AR = @AR@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
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BINDIR = @BINDIR@
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CCDEPMODE = @CCDEPMODE@
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PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
POPCNT_CFLAGS = @POPCNT_CFLAGS@
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# Copied from ../util so "gmap_setup -B src" works during "make check"
CLEANFILES = fa_coords gmap_process

# Include master.c and master.h, so they get included in distribution
EXTRA_DIST = mpidebug.c mpidebug.h master.c master.h

# -DUTILITYP=1 needed for iit_store, iit_dump, iit_get, gmapindex, and
# get-genome so they can handle both small and large genomes at run
# time

#lib_LTLIBRARIES = libgmap-@LIBGMAP_API_VERSION@.la
lib_LTLIBRARIES = libgmap.la
include_HEADERS = fopen.h bool.h types.h separator.h comp.h \
 except.h assert.h mem.h \
 intlistdef.h intlist.h listdef.h list.h \
 doublelist.h \
 littleendian.h bigendian.h \
 interval.h uintlist.h uint8list.h \
 iitdef.h iit-read.h iit-write.h parserange.h \
 univinterval.h iit-read-univ.h \
 table.h tableuint.h uinttable.h uinttableuint.h \
 stopwatch.h semaphore.h access.h \
 chrom.h filestring.h \
 md5.h complement.h bzip2.h sequence.h \
 genomicpos.h \
 bitpack64-read.h bitpack64-readtwo.h \
 maxent_hr.h \
 popcount.h genome128_hr.h \
 compress.h bytecoding.h sarray-read.h \
 mode.h chrnum.h genome.h samflags.h \
 datadir.h

LIBGMAP_LA_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 doublelist.c doublelist.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 interval.c interval.h uintlist.c uintlist.h uint8list.c uint8list.h \
 iit-read.c iit-read.h iit-write.c iit-write.h parserange.c parserange.h \
 univinterval.c univinterval.h iit-read-univ.c iit-read-univ.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 table.c table.h tableuint.c tableuint.h uinttable.c uinttable.h uinttableuint.c uinttableuint.h\
 chrom.c chrom.h filestring.c filestring.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
 genomicpos.c genomicpos.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 maxent_hr.c maxent_hr.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h \
 compress.c compress.h bytecoding.c bytecoding.h sarray-read.c sarray-read.h \
 mode.h chrnum.c chrnum.h genome.c genome.h \
 datadir.c datadir.h

libgmap_CC = $(PTHREAD_CC)
libgmap_la_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) -fPIC -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
libgmap_la_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) -version-info $(LIBGMAP_SO_VERSION)
libgmap_la_LIBADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_libgmap_la_SOURCES = $(LIBGMAP_LA_FILES)
CPUID_FILES = bool.h cpuid.c cpuid.h
cpuid_CC = $(CC)
cpuid_CFLAGS = $(AM_CFLAGS) -DMAIN=1
cpuid_LDFLAGS = $(AM_LDFLAGS)
cpuid_LDADD = 
dist_cpuid_SOURCES = $(CPUID_FILES)
GMAP_SELECT_FILES = bool.h cpuid.c cpuid.h gmap_select.c
gmap_CC = $(CC)
gmap_CFLAGS = $(AM_CFLAGS)
gmap_LDFLAGS = $(AM_LDFLAGS)
gmap_LDADD = 
dist_gmap_SOURCES = $(GMAP_SELECT_FILES)
GMAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gmapl_select.c
gmapl_CC = $(CC)
gmapl_CFLAGS = $(AM_CFLAGS)
gmapl_LDFLAGS = $(AM_LDFLAGS)
gmapl_LDADD = 
dist_gmapl_SOURCES = $(GMAPL_SELECT_FILES)
GSNAP_SELECT_FILES = bool.h cpuid.c cpuid.h gsnap_select.c
gsnap_CC = $(CC)
gsnap_CFLAGS = $(AM_CFLAGS)
gsnap_LDFLAGS = $(AM_LDFLAGS)
gsnap_LDADD = 
dist_gsnap_SOURCES = $(GSNAP_SELECT_FILES)
GSNAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gsnapl_select.c
gsnapl_CC = $(CC)
gsnapl_CFLAGS = $(AM_CFLAGS)
gsnapl_LDFLAGS = $(AM_LDFLAGS)
gsnapl_LDADD = 
dist_gsnapl_SOURCES = $(GSNAPL_SELECT_FILES)
GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h compress-write.c compress-write.h \
 gbuffer.c gbuffer.h genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 genome-write.c genome-write.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h block.c block.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h uinttable.c uinttable.h gregion.c gregion.h \
 matchdef.h match.c match.h matchpool.c matchpool.h \
 diagnostic.c diagnostic.h stage1.c stage1.h \
 diagdef.h diag.c diag.h diagpool.c diagpool.h \
 cmet.c cmet.h atoi.c atoi.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h \
 scores.h intron.c intron.h maxent.c maxent.h maxent_hr.c maxent_hr.h samflags.h pairdef.h pair.c pair.h \
 pairpool.c pairpool.h cellpool.c cellpool.h stage2.c stage2.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 boyer-moore.c boyer-moore.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 translation.c translation.h \
 pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
 request.c request.h result.c result.h output.c output.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h gmap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmap_nosimd_CC = $(PTHREAD_CC)
gmap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS)
gmap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_nosimd_SOURCES = $(GMAP_FILES)
gmap_sse2_CC = $(PTHREAD_CC)
gmap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
gmap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_sse2_SOURCES = $(GMAP_FILES)
gmap_ssse3_CC = $(PTHREAD_CC)
gmap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
gmap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_ssse3_SOURCES = $(GMAP_FILES)
gmap_sse41_CC = $(PTHREAD_CC)
gmap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
gmap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_sse41_SOURCES = $(GMAP_FILES)
gmap_sse42_CC = $(PTHREAD_CC)
gmap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
gmap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_sse42_SOURCES = $(GMAP_FILES)
gmap_avx2_CC = $(PTHREAD_CC)
gmap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
gmap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_avx2_SOURCES = $(GMAP_FILES)
gmap_avx512_CC = $(PTHREAD_CC)
gmap_avx512_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 $(SIMD_AVX512_CFLAGS)
gmap_avx512_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_avx512_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_avx512_SOURCES = $(GMAP_FILES)
GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h uint8list.c uint8list.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h compress-write.c compress-write.h \
 gbuffer.c gbuffer.h genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 genome-write.c genome-write.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h block.c block.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h uinttable.c uinttable.h gregion.c gregion.h \
 matchdef.h match.c match.h matchpool.c matchpool.h \
 diagnostic.c diagnostic.h stage1.c stage1.h \
 diagdef.h diag.c diag.h diagpool.c diagpool.h \
 cmet.c cmet.h atoi.c atoi.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h \
 scores.h intron.c intron.h maxent.c maxent.h maxent_hr.c maxent_hr.h samflags.h pairdef.h pair.c pair.h \
 pairpool.c pairpool.h cellpool.c cellpool.h stage2.c stage2.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 boyer-moore.c boyer-moore.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 translation.c translation.h \
 pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
 request.c request.h result.c result.h output.c output.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h gmap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmapl_nosimd_CC = $(PTHREAD_CC)
gmapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS)
gmapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_nosimd_SOURCES = $(GMAPL_FILES)
gmapl_sse2_CC = $(PTHREAD_CC)
gmapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
gmapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_sse2_SOURCES = $(GMAPL_FILES)
gmapl_ssse3_CC = $(PTHREAD_CC)
gmapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
gmapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_ssse3_SOURCES = $(GMAPL_FILES)
gmapl_sse41_CC = $(PTHREAD_CC)
gmapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
gmapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_sse41_SOURCES = $(GMAPL_FILES)
gmapl_sse42_CC = $(PTHREAD_CC)
gmapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
gmapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_sse42_SOURCES = $(GMAPL_FILES)
gmapl_avx2_CC = $(PTHREAD_CC)
gmapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
gmapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_avx2_SOURCES = $(GMAPL_FILES)
gmapl_avx512_CC = $(PTHREAD_CC)
gmapl_avx512_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 $(SIMD_AVX512_CFLAGS)
gmapl_avx512_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_avx512_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_avx512_SOURCES = $(GMAPL_FILES)
GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h \
 uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h \
 genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h \
 maxent_hr.c maxent_hr.h cigar.c cigar.h samflags.h samprint.c samprint.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h junction.c junction.h stage3hr.c stage3hr.h \
 spanningelt.c spanningelt.h cmet.c cmet.h atoi.c atoi.h \
 comp.h maxent.c maxent.h pairdef.h pair.c pair.h pairpool.c pairpool.h diag.c diag.h diagpool.c diagpool.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h cellpool.c cellpool.h stage2.c stage2.h \
 intron.c intron.h boyer-moore.c boyer-moore.h changepoint.c changepoint.h pbinom.c pbinom.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 gbuffer.c gbuffer.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
 bytecoding.c bytecoding.h \
 univdiagdef.h univdiag.c univdiag.h sedgesort.c sedgesort.h sarray-read.c sarray-read.h \
 sarray-search.c sarray-search.h \
 merge-heap.c merge-heap.h stage1hr.c stage1hr.h \
 request.c request.h resulthr.c resulthr.h output.c output.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 datadir.c datadir.h mode.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h gsnap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
# Previously included -lrt for shm_open, but we are not calling that
gsnap_nosimd_CC = $(PTHREAD_CC)
gsnap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS)
gsnap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_nosimd_SOURCES = $(GSNAP_FILES)
gsnap_sse2_CC = $(PTHREAD_CC)
gsnap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
gsnap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_sse2_SOURCES = $(GSNAP_FILES)
gsnap_ssse3_CC = $(PTHREAD_CC)
gsnap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
gsnap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_ssse3_SOURCES = $(GSNAP_FILES)
gsnap_sse41_CC = $(PTHREAD_CC)
gsnap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
gsnap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_sse41_SOURCES = $(GSNAP_FILES)
gsnap_sse42_CC = $(PTHREAD_CC)
gsnap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
gsnap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_sse42_SOURCES = $(GSNAP_FILES)
gsnap_avx2_CC = $(PTHREAD_CC)
gsnap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
gsnap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_avx2_SOURCES = $(GSNAP_FILES)
gsnap_avx512_CC = $(PTHREAD_CC)
gsnap_avx512_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 $(SIMD_AVX512_CFLAGS)
gsnap_avx512_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnap_avx512_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnap_avx512_SOURCES = $(GSNAP_FILES)
GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h \
 uintlist.c uintlist.h uint8list.c uint8list.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h \
 genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h \
 maxent_hr.c maxent_hr.h cigar.c cigar.h samflags.h samprint.c samprint.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h junction.c junction.h stage3hr.c stage3hr.h \
 spanningelt.c spanningelt.h cmet.c cmet.h atoi.c atoi.h \
 comp.h maxent.c maxent.h pairdef.h pair.c pair.h pairpool.c pairpool.h diag.c diag.h diagpool.c diagpool.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h cellpool.c cellpool.h stage2.c stage2.h \
 intron.c intron.h boyer-moore.c boyer-moore.h changepoint.c changepoint.h pbinom.c pbinom.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 gbuffer.c gbuffer.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
 merge-heap.c merge-heap.h stage1hr.c stage1hr.h \
 request.c request.h resulthr.c resulthr.h output.c output.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 datadir.c datadir.h mode.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h gsnap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnapl_nosimd_CC = $(PTHREAD_CC)
gsnapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS)
gsnapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_nosimd_SOURCES = $(GSNAPL_FILES)
gsnapl_sse2_CC = $(PTHREAD_CC)
gsnapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
gsnapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_sse2_SOURCES = $(GSNAPL_FILES)
gsnapl_ssse3_CC = $(PTHREAD_CC)
gsnapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
gsnapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_ssse3_SOURCES = $(GSNAPL_FILES)
gsnapl_sse41_CC = $(PTHREAD_CC)
gsnapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
gsnapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_sse41_SOURCES = $(GSNAPL_FILES)
gsnapl_sse42_CC = $(PTHREAD_CC)
gsnapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
gsnapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_sse42_SOURCES = $(GSNAPL_FILES)
gsnapl_avx2_CC = $(PTHREAD_CC)
gsnapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
gsnapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_avx2_SOURCES = $(GSNAPL_FILES)
gsnapl_avx512_CC = $(PTHREAD_CC)
gsnapl_avx512_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS) -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 $(SIMD_AVX512_CFLAGS)
gsnapl_avx512_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gsnapl_avx512_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gsnapl_avx512_SOURCES = $(GSNAPL_FILES)

# Build as a non-SIMD program
UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h \
 genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h \
 maxent_hr.c maxent_hr.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h junction.c junction.h stage3hr.c stage3hr.h \
 spanningelt.c spanningelt.h cmet.c cmet.h atoi.c atoi.h \
 cigar.c cigar.h \
 comp.h maxent.c maxent.h pairdef.h pair.c pair.h pairpool.c pairpool.h diag.c diag.h diagpool.c diagpool.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h cellpool.c cellpool.h stage2.c stage2.h \
 intron.c intron.h boyer-moore.c boyer-moore.h changepoint.c changepoint.h pbinom.c pbinom.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 translation.c translation.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
 bytecoding.c bytecoding.h \
 univdiagdef.h univdiag.c univdiag.h sedgesort.c sedgesort.h sarray-read.c sarray-read.h \
 sarray-search.c sarray-search.h \
 merge-heap.c merge-heap.h stage1hr.c stage1hr.h resulthr.c resulthr.h \
 datadir.c datadir.h mode.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h uniqscan.c

uniqscan_CC = $(PTHREAD_CC)
uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS)
uniqscan_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscan_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscan_SOURCES = $(UNIQSCAN_FILES)
UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h uint8list.c uint8list.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
 genomicpos.c genomicpos.h compress.c compress.h \
 genome.c genome.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 merge.c merge.h \
 indexdbdef.h indexdb.c indexdb.h indexdb_hr.c indexdb_hr.h \
 oligo.c oligo.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 chrnum.c chrnum.h \
 maxent_hr.c maxent_hr.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h junction.c junction.h stage3hr.c stage3hr.h \
 spanningelt.c spanningelt.h cmet.c cmet.h atoi.c atoi.h \
 cigar.c cigar.h \
 comp.h maxent.c maxent.h pairdef.h pair.c pair.h pairpool.c pairpool.h diag.c diag.h diagpool.c diagpool.h \
 orderstat.c orderstat.h oligoindex_hr.c oligoindex_hr.h cellpool.c cellpool.h stage2.c stage2.h \
 intron.c intron.h boyer-moore.c boyer-moore.h changepoint.c changepoint.h pbinom.c pbinom.h \
 dynprog.c dynprog.h dynprog_simd.c dynprog_simd.h \
 dynprog_single.c dynprog_single.h dynprog_genome.c dynprog_genome.h dynprog_cdna.c dynprog_cdna.h dynprog_end.c dynprog_end.h \
 translation.c translation.h \
 doublelist.c doublelist.h smooth.c smooth.h \
 chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
 splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
 splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
 merge-heap.c merge-heap.h stage1hr.c stage1hr.h resulthr.c resulthr.h \
 datadir.c datadir.h mode.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h uniqscan.c

uniqscanl_CC = $(PTHREAD_CC)
uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS)
uniqscanl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscanl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscanl_SOURCES = $(UNIQSCANL_FILES)

# Build utility programs as non-SIMD programs
GMAPINDEX_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iit-write-univ.c iit-write-univ.h \
 iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
 genomicpos.c genomicpos.h compress-write.c compress-write.h genome-write.c genome-write.h \
 compress.c compress.h popcount.c popcount.h genome128_hr.c genome128_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.c indexdb.h \
 indexdb-write.c indexdb-write.h \
 table.c table.h tableuint.c tableuint.h tableuint8.c tableuint8.h tableint.c tableint.h \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 saca-k.c saca-k.h uint8list.c uint8list.h \
 bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
 parserange.c parserange.h \
 gmapindex.c

gmapindex_CC = $(PTHREAD_CC)
gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
gmapindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapindex_SOURCES = $(GMAPINDEX_FILES)
SNPINDEX_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 genomicpos.c genomicpos.h compress.c compress.h compress-write.c compress-write.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.c indexdb.h \
 indexdb-write.c indexdb-write.h \
 chrom.c chrom.h \
 complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
 datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h snpindex.c

snpindex_CC = $(PTHREAD_CC)
snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
snpindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
snpindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_snpindex_SOURCES = $(SNPINDEX_FILES)
CMETINDEX_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 genomicpos.c genomicpos.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 univinterval.c univinterval.h interval.h interval.c \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
 complement.h compress.c compress.h compress-write.c compress-write.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.h indexdb.c \
 indexdb-write.c indexdb-write.h \
 cmet.c cmet.h \
 complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
 uintlist.c uintlist.h intlist.c intlist.h \
 saca-k.c saca-k.h uint8list.c uint8list.h \
 bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
 list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h cmetindex.c

cmetindex_CC = $(PTHREAD_CC)
cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
cmetindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
cmetindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_cmetindex_SOURCES = $(CMETINDEX_FILES)
ATOIINDEX_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 genomicpos.c genomicpos.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 univinterval.c univinterval.h interval.h interval.c \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
 complement.h compress.c compress.h compress-write.c compress-write.h \
 popcount.c popcount.h genome128_hr.c genome128_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
 bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.h indexdb.c \
 indexdb-write.c indexdb-write.h \
 atoi.c atoi.h \
 complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
 uintlist.c uintlist.h intlist.c intlist.h \
 saca-k.c saca-k.h uint8list.c uint8list.h \
 bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
 list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h atoiindex.c

atoiindex_CC = $(PTHREAD_CC)
atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
atoiindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
atoiindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_atoiindex_SOURCES = $(ATOIINDEX_FILES)
GET_GENOME_FILES = fopen.h bool.h types.h separator.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
 genome.c genome.h \
 genomicpos.c genomicpos.h chrom.c chrom.h \
 chrnum.c chrnum.h \
 datadir.c datadir.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h get-genome.c

get_genome_CC = $(PTHREAD_CC)
get_genome_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
get_genome_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
get_genome_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_get_genome_SOURCES = $(GET_GENOME_FILES)
IIT_STORE_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h \
 uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 doublelist.c doublelist.h \
 iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
 tableint.c tableint.h table.c table.h chrom.c chrom.h \
 getopt.c getopt1.c getopt.h iit_store.c

iit_store_CC = $(PTHREAD_CC)
iit_store_CFLAGS = $(AM_CFLAGS)  $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_store_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_store_LDADD = $(PTHREAD_LIBS)
dist_iit_store_SOURCES = $(IIT_STORE_FILES)
IIT_GET_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 univinterval.c univinterval.h interval.c interval.h \
 uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 complement.h parserange.c parserange.h getopt.c getopt1.c getopt.h iit_get.c

iit_get_CC = $(PTHREAD_CC)
iit_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_get_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_get_LDADD = $(PTHREAD_LIBS)
dist_iit_get_SOURCES = $(IIT_GET_FILES)
IIT_DUMP_FILES = fopen.h bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 intlistdef.h intlist.c intlist.h list.c list.h \
 univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 filestring.c filestring.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h parserange.c parserange.h \
 getopt.c getopt1.c getopt.h iit_dump.c

iit_dump_CC = $(PTHREAD_CC)
iit_dump_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_dump_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_dump_LDADD = $(PTHREAD_LIBS)
dist_iit_dump_SOURCES = $(IIT_DUMP_FILES)
SAM_SORT_FILES = bool.h types.h \
 except.c except.h assert.c assert.h mem.c mem.h \
 littleendian.c littleendian.h bigendian.c bigendian.h \
 genomicpos.h chrnum.h \
 intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
 stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
 univinterval.c univinterval.h interval.c interval.h \
 uintlist.c uintlist.h \
 filestring.c filestring.h \
 parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
 samflags.h samheader.c samheader.h samread.c samread.h \
 datadir.c datadir.h \
 getopt.c getopt1.c getopt.h sam_sort.c

sam_sort_CC = $(PTHREAD_CC)
sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
sam_sort_LDADD = $(PTHREAD_LIBS)
dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
all: config.h
	$(MAKE) $(AM_MAKEFLAGS) all-am

.SUFFIXES:
.SUFFIXES: .c .lo .o .obj
$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(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) --gnu src/Makefile'; \
	$(am__cd) $(top_srcdir) && \
	  $(AUTOMAKE) --gnu src/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: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):

config.h: stamp-h1
	@test -f $@ || rm -f stamp-h1
	@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1

stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
	@rm -f stamp-h1
	cd $(top_builddir) && $(SHELL) ./config.status src/config.h
$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 
	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
	rm -f stamp-h1
	touch $@

distclean-hdr:
	-rm -f config.h stamp-h1

install-libLTLIBRARIES: $(lib_LTLIBRARIES)
	@$(NORMAL_INSTALL)
	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
	list2=; for p in $$list; do \
	  if test -f $$p; then \
	    list2="$$list2 $$p"; \
	  else :; fi; \
	done; \
	test -z "$$list2" || { \
	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
	}

uninstall-libLTLIBRARIES:
	@$(NORMAL_UNINSTALL)
	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
	for p in $$list; do \
	  $(am__strip_dir) \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
	done

clean-libLTLIBRARIES:
	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
	@list='$(lib_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
	}

libgmap.la: $(libgmap_la_OBJECTS) $(libgmap_la_DEPENDENCIES) $(EXTRA_libgmap_la_DEPENDENCIES) 
	$(AM_V_CCLD)$(libgmap_la_LINK) -rpath $(libdir) $(libgmap_la_OBJECTS) $(libgmap_la_LIBADD) $(LIBS)
install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
	if test -n "$$list"; then \
	  echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
	fi; \
	for p in $$list; do echo "$$p $$p"; done | \
	sed 's/$(EXEEXT)$$//' | \
	while read p p1; do if test -f $$p \
	 || test -f $$p1 \
	  ; then echo "$$p"; echo "$$p"; else :; fi; \
	done | \
	sed -e 'p;s,.*/,,;n;h' \
	    -e 's|.*|.|' \
	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
	sed 'N;N;N;s,\n, ,g' | \
	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
	    else { print "f", $$3 "/" $$4, $$1; } } \
	  END { for (d in files) print "f", d, files[d] }' | \
	while read type dir files; do \
	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
	    test -z "$$files" || { \
	    echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
	    $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
	    } \
	; done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
	files=`for p in $$list; do echo "$$p"; done | \
	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
	      -e 's/$$/$(EXEEXT)/' \
	`; \
	test -n "$$list" || exit 0; \
	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
	cd "$(DESTDIR)$(bindir)" && rm -f $$files

clean-binPROGRAMS:
	@list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
	echo " rm -f" $$list; \
	rm -f $$list || exit $$?; \
	test -n "$(EXEEXT)" || exit 0; \
	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
	echo " rm -f" $$list; \
	rm -f $$list

atoiindex$(EXEEXT): $(atoiindex_OBJECTS) $(atoiindex_DEPENDENCIES) $(EXTRA_atoiindex_DEPENDENCIES) 
	@rm -f atoiindex$(EXEEXT)
	$(AM_V_CCLD)$(atoiindex_LINK) $(atoiindex_OBJECTS) $(atoiindex_LDADD) $(LIBS)

cmetindex$(EXEEXT): $(cmetindex_OBJECTS) $(cmetindex_DEPENDENCIES) $(EXTRA_cmetindex_DEPENDENCIES) 
	@rm -f cmetindex$(EXEEXT)
	$(AM_V_CCLD)$(cmetindex_LINK) $(cmetindex_OBJECTS) $(cmetindex_LDADD) $(LIBS)

cpuid$(EXEEXT): $(cpuid_OBJECTS) $(cpuid_DEPENDENCIES) $(EXTRA_cpuid_DEPENDENCIES) 
	@rm -f cpuid$(EXEEXT)
	$(AM_V_CCLD)$(cpuid_LINK) $(cpuid_OBJECTS) $(cpuid_LDADD) $(LIBS)

get-genome$(EXEEXT): $(get_genome_OBJECTS) $(get_genome_DEPENDENCIES) $(EXTRA_get_genome_DEPENDENCIES) 
	@rm -f get-genome$(EXEEXT)
	$(AM_V_CCLD)$(get_genome_LINK) $(get_genome_OBJECTS) $(get_genome_LDADD) $(LIBS)

gmap$(EXEEXT): $(gmap_OBJECTS) $(gmap_DEPENDENCIES) $(EXTRA_gmap_DEPENDENCIES) 
	@rm -f gmap$(EXEEXT)
	$(AM_V_CCLD)$(gmap_LINK) $(gmap_OBJECTS) $(gmap_LDADD) $(LIBS)

gmap.avx2$(EXEEXT): $(gmap_avx2_OBJECTS) $(gmap_avx2_DEPENDENCIES) $(EXTRA_gmap_avx2_DEPENDENCIES) 
	@rm -f gmap.avx2$(EXEEXT)
	$(AM_V_CCLD)$(gmap_avx2_LINK) $(gmap_avx2_OBJECTS) $(gmap_avx2_LDADD) $(LIBS)

gmap.avx512$(EXEEXT): $(gmap_avx512_OBJECTS) $(gmap_avx512_DEPENDENCIES) $(EXTRA_gmap_avx512_DEPENDENCIES) 
	@rm -f gmap.avx512$(EXEEXT)
	$(AM_V_CCLD)$(gmap_avx512_LINK) $(gmap_avx512_OBJECTS) $(gmap_avx512_LDADD) $(LIBS)

gmap.nosimd$(EXEEXT): $(gmap_nosimd_OBJECTS) $(gmap_nosimd_DEPENDENCIES) $(EXTRA_gmap_nosimd_DEPENDENCIES) 
	@rm -f gmap.nosimd$(EXEEXT)
	$(AM_V_CCLD)$(gmap_nosimd_LINK) $(gmap_nosimd_OBJECTS) $(gmap_nosimd_LDADD) $(LIBS)

gmap.sse2$(EXEEXT): $(gmap_sse2_OBJECTS) $(gmap_sse2_DEPENDENCIES) $(EXTRA_gmap_sse2_DEPENDENCIES) 
	@rm -f gmap.sse2$(EXEEXT)
	$(AM_V_CCLD)$(gmap_sse2_LINK) $(gmap_sse2_OBJECTS) $(gmap_sse2_LDADD) $(LIBS)

gmap.sse41$(EXEEXT): $(gmap_sse41_OBJECTS) $(gmap_sse41_DEPENDENCIES) $(EXTRA_gmap_sse41_DEPENDENCIES) 
	@rm -f gmap.sse41$(EXEEXT)
	$(AM_V_CCLD)$(gmap_sse41_LINK) $(gmap_sse41_OBJECTS) $(gmap_sse41_LDADD) $(LIBS)

gmap.sse42$(EXEEXT): $(gmap_sse42_OBJECTS) $(gmap_sse42_DEPENDENCIES) $(EXTRA_gmap_sse42_DEPENDENCIES) 
	@rm -f gmap.sse42$(EXEEXT)
	$(AM_V_CCLD)$(gmap_sse42_LINK) $(gmap_sse42_OBJECTS) $(gmap_sse42_LDADD) $(LIBS)

gmap.ssse3$(EXEEXT): $(gmap_ssse3_OBJECTS) $(gmap_ssse3_DEPENDENCIES) $(EXTRA_gmap_ssse3_DEPENDENCIES) 
	@rm -f gmap.ssse3$(EXEEXT)
	$(AM_V_CCLD)$(gmap_ssse3_LINK) $(gmap_ssse3_OBJECTS) $(gmap_ssse3_LDADD) $(LIBS)

gmapindex$(EXEEXT): $(gmapindex_OBJECTS) $(gmapindex_DEPENDENCIES) $(EXTRA_gmapindex_DEPENDENCIES) 
	@rm -f gmapindex$(EXEEXT)
	$(AM_V_CCLD)$(gmapindex_LINK) $(gmapindex_OBJECTS) $(gmapindex_LDADD) $(LIBS)

gmapl$(EXEEXT): $(gmapl_OBJECTS) $(gmapl_DEPENDENCIES) $(EXTRA_gmapl_DEPENDENCIES) 
	@rm -f gmapl$(EXEEXT)
	$(AM_V_CCLD)$(gmapl_LINK) $(gmapl_OBJECTS) $(gmapl_LDADD) $(LIBS)

gmapl.avx2$(EXEEXT): $(gmapl_avx2_OBJECTS) $(gmapl_avx2_DEPENDENCIES) $(EXTRA_gmapl_avx2_DEPENDENCIES) 
	@rm -f gmapl.avx2$(EXEEXT)
	$(AM_V_CCLD)$(gmapl_avx2_LINK) $(gmapl_avx2_OBJECTS) $(gmapl_avx2_LDADD) $(LIBS)

gmapl.avx512$(EXEEXT): $(gmapl_avx512_OBJECTS) $(gmapl_avx512_DEPENDENCIES) $(EXTRA_gmapl_avx512_DEPENDENCIES) 
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libgmap_la-mem.lo: mem.c
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libgmap_la-intlist.lo: intlist.c
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libgmap_la-list.lo: list.c
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libgmap_la-doublelist.lo: doublelist.c
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libgmap_la-littleendian.lo: littleendian.c
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libgmap_la-interval.lo: interval.c
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libgmap_la-uintlist.lo: uintlist.c
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libgmap_la-uint8list.lo: uint8list.c
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libgmap_la-iit-read.lo: iit-read.c
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libgmap_la-iit-write.lo: iit-write.c
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libgmap_la-parserange.lo: parserange.c
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libgmap_la-univinterval.lo: univinterval.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-univinterval.lo -MD -MP -MF $(DEPDIR)/libgmap_la-univinterval.Tpo -c -o libgmap_la-univinterval.lo `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgmap_la-univinterval.Tpo $(DEPDIR)/libgmap_la-univinterval.Plo
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libgmap_la-iit-read-univ.lo: iit-read-univ.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-iit-read-univ.lo -MD -MP -MF $(DEPDIR)/libgmap_la-iit-read-univ.Tpo -c -o libgmap_la-iit-read-univ.lo `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgmap_la-iit-read-univ.Tpo $(DEPDIR)/libgmap_la-iit-read-univ.Plo
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libgmap_la-stopwatch.lo: stopwatch.c
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@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgmap_la-stopwatch.Tpo $(DEPDIR)/libgmap_la-stopwatch.Plo
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libgmap_la-semaphore.lo: semaphore.c
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@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgmap_la-semaphore.Tpo $(DEPDIR)/libgmap_la-semaphore.Plo
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libgmap_la-access.lo: access.c
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libgmap_la-table.lo: table.c
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libgmap_la-tableuint.lo: tableuint.c
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libgmap_la-uinttable.lo: uinttable.c
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libgmap_la-uinttableuint.lo: uinttableuint.c
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libgmap_la-chrom.lo: chrom.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-chrom.lo -MD -MP -MF $(DEPDIR)/libgmap_la-chrom.Tpo -c -o libgmap_la-chrom.lo `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
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libgmap_la-filestring.lo: filestring.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-filestring.lo -MD -MP -MF $(DEPDIR)/libgmap_la-filestring.Tpo -c -o libgmap_la-filestring.lo `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
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libgmap_la-md5.lo: md5.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-md5.lo -MD -MP -MF $(DEPDIR)/libgmap_la-md5.Tpo -c -o libgmap_la-md5.lo `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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libgmap_la-bzip2.lo: bzip2.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-bzip2.lo -MD -MP -MF $(DEPDIR)/libgmap_la-bzip2.Tpo -c -o libgmap_la-bzip2.lo `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
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libgmap_la-sequence.lo: sequence.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-sequence.lo -MD -MP -MF $(DEPDIR)/libgmap_la-sequence.Tpo -c -o libgmap_la-sequence.lo `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
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libgmap_la-genomicpos.lo: genomicpos.c
@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgmap_la_CFLAGS) $(CFLAGS) -MT libgmap_la-genomicpos.lo -MD -MP -MF $(DEPDIR)/libgmap_la-genomicpos.Tpo -c -o libgmap_la-genomicpos.lo `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
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libgmap_la-bitpack64-read.lo: bitpack64-read.c
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libgmap_la-bitpack64-readtwo.lo: bitpack64-readtwo.c
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libgmap_la-maxent_hr.lo: maxent_hr.c
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libgmap_la-popcount.lo: popcount.c
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libgmap_la-genome128_hr.lo: genome128_hr.c
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libgmap_la-compress.lo: compress.c
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libgmap_la-bytecoding.lo: bytecoding.c
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libgmap_la-sarray-read.lo: sarray-read.c
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libgmap_la-chrnum.lo: chrnum.c
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libgmap_la-genome.lo: genome.c
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libgmap_la-datadir.lo: datadir.c
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atoiindex-except.o: except.c
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atoiindex-except.obj: except.c
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atoiindex-assert.o: assert.c
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atoiindex-assert.obj: assert.c
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atoiindex-mem.o: mem.c
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atoiindex-mem.obj: mem.c
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atoiindex-littleendian.o: littleendian.c
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atoiindex-littleendian.obj: littleendian.c
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atoiindex-bigendian.o: bigendian.c
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get_genome-iit-read-univ.obj: iit-read-univ.c
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get_genome-iit-read.o: iit-read.c
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get_genome-iit-read.obj: iit-read.c
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get_genome-md5.o: md5.c
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get_genome-md5.obj: md5.c
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get_genome-bzip2.o: bzip2.c
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get_genome-bzip2.obj: bzip2.c
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get_genome-sequence.o: sequence.c
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get_genome-sequence.obj: sequence.c
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get_genome-genome.o: genome.c
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get_genome-genome.obj: genome.c
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get_genome-genomicpos.o: genomicpos.c
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get_genome-genomicpos.obj: genomicpos.c
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get_genome-chrom.o: chrom.c
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get_genome-chrom.obj: chrom.c
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get_genome-chrnum.o: chrnum.c
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get_genome-chrnum.obj: chrnum.c
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get_genome-datadir.o: datadir.c
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gmap_avx2-iit-read-univ.o: iit-read-univ.c
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gmap_avx2-md5.o: md5.c
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gmap_avx2-bzip2.o: bzip2.c
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gmap_avx2-sequence.o: sequence.c
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gmap_avx2-reader.o: reader.c
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gmap_nosimd-semaphore.o: semaphore.c
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gmap_nosimd-md5.o: md5.c
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gmap_nosimd-bzip2.o: bzip2.c
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gmap_sse42-orderstat.o: orderstat.c
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gmap_sse42-oligoindex_hr.o: oligoindex_hr.c
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gmap_sse42-intron.o: intron.c
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gmap_sse42-maxent.o: maxent.c
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gmap_sse42-maxent_hr.o: maxent_hr.c
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gmap_sse42-pair.o: pair.c
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gmap_sse42-pairpool.o: pairpool.c
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gmap_sse42-cellpool.o: cellpool.c
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gmap_sse42-dynprog_single.o: dynprog_single.c
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gmap_sse42-dynprog_single.obj: dynprog_single.c
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gmap_sse42-dynprog_genome.o: dynprog_genome.c
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gmap_sse42-dynprog_cdna.o: dynprog_cdna.c
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gmap_sse42-dynprog_end.o: dynprog_end.c
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gmap_sse42-translation.o: translation.c
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gmap_sse42-pbinom.o: pbinom.c
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gmap_sse42-changepoint.o: changepoint.c
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gmapl_sse2-semaphore.o: semaphore.c
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gmapl_sse2-semaphore.obj: semaphore.c
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gmapl_sse2-md5.o: md5.c
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gmapl_sse2-bzip2.o: bzip2.c
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gmapl_sse42-samheader.o: samheader.c
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gmapl_ssse3-gbuffer.o: gbuffer.c
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gmapl_ssse3-genome.o: genome.c
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gsnap_avx512-md5.o: md5.c
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gsnap_avx512-bzip2.o: bzip2.c
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gsnap_avx512-bzip2.obj: bzip2.c
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gsnap_avx512-sequence.o: sequence.c
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gsnap_avx512-reader.o: reader.c
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gsnap_avx512-genomicpos.obj: genomicpos.c
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gsnap_avx512-compress.o: compress.c
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gsnap_avx512-genome.o: genome.c
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gsnap_avx512-genome.obj: genome.c
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gsnap_avx512-popcount.o: popcount.c
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gsnap_avx512-maxent_hr.o: maxent_hr.c
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gsnap_avx512-cigar.o: cigar.c
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gsnap_avx512-samprint.o: samprint.c
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gsnap_avx512-mapq.o: mapq.c
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gsnap_avx512-shortread.o: shortread.c
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gsnap_avx512-substring.o: substring.c
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gsnap_avx512-junction.o: junction.c
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gsnap_avx512-stage3hr.o: stage3hr.c
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gsnap_avx512-sarray-read.o: sarray-read.c
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gsnap_avx512-sarray-search.o: sarray-search.c
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gsnap_nosimd-access.o: access.c
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gsnap_nosimd-iit-read-univ.o: iit-read-univ.c
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gsnap_nosimd-md5.o: md5.c
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gsnap_nosimd-bzip2.o: bzip2.c
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gsnap_nosimd-sequence.o: sequence.c
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gsnap_sse2-maxent_hr.o: maxent_hr.c
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gsnap_sse2-cigar.o: cigar.c
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gsnap_sse2-mapq.o: mapq.c
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gsnap_sse2-shortread.o: shortread.c
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gsnap_sse2-junction.o: junction.c
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gsnap_sse42-chrom.o: chrom.c
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gsnap_sse42-segmentpos.o: segmentpos.c
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gsnap_sse42-chrnum.o: chrnum.c
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gsnap_sse42-maxent_hr.o: maxent_hr.c
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gsnap_sse42-samprint.o: samprint.c
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gsnap_sse42-mapq.o: mapq.c
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gsnap_sse42-shortread.o: shortread.c
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gsnapl_avx2-stage3hr.o: stage3hr.c
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gsnapl_sse2-maxent_hr.o: maxent_hr.c
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gsnapl_sse2-cigar.o: cigar.c
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gsnapl_sse2-samprint.o: samprint.c
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gsnapl_sse2-mapq.o: mapq.c
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gsnapl_sse2-shortread.o: shortread.c
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gsnapl_sse2-substring.o: substring.c
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gsnapl_sse2-junction.o: junction.c
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gsnapl_sse2-stage3hr.o: stage3hr.c
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gsnapl_sse41-maxent_hr.o: maxent_hr.c
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gsnapl_sse41-cigar.o: cigar.c
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gsnapl_sse42-cigar.o: cigar.c
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gsnapl_sse42-cigar.obj: cigar.c
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gsnapl_sse42-samprint.o: samprint.c
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gsnapl_sse42-samprint.obj: samprint.c
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gsnapl_sse42-mapq.o: mapq.c
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gsnapl_sse42-mapq.obj: mapq.c
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gsnapl_sse42-shortread.o: shortread.c
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gsnapl_sse42-shortread.obj: shortread.c
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gsnapl_sse42-substring.o: substring.c
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gsnapl_sse42-substring.obj: substring.c
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gsnapl_sse42-junction.o: junction.c
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gsnapl_sse42-stage3hr.o: stage3hr.c
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gsnapl_sse42-spanningelt.o: spanningelt.c
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gsnapl_sse42-cmet.o: cmet.c
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gsnapl_sse42-chimera.o: chimera.c
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gsnapl_sse42-splicetrie_build.o: splicetrie_build.c
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iit_store-littleendian.o: littleendian.c
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iit_store-univinterval.o: univinterval.c
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iit_store-uintlist.o: uintlist.c
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iit_store-stopwatch.o: stopwatch.c
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iit_store-semaphore.o: semaphore.c
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uniqscan-md5.o: md5.c
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uniqscan-md5.obj: md5.c
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uniqscan-bzip2.o: bzip2.c
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uniqscan-bzip2.obj: bzip2.c
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uniqscan-sequence.o: sequence.c
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uniqscan-sequence.obj: sequence.c
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uniqscan-reader.o: reader.c
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uniqscan-reader.obj: reader.c
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uniqscan-genomicpos.o: genomicpos.c
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uniqscan-genomicpos.obj: genomicpos.c
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uniqscan-compress.o: compress.c
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uniqscan-compress.obj: compress.c
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uniqscan-genome.o: genome.c
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uniqscan-genome.obj: genome.c
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uniqscan-popcount.o: popcount.c
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uniqscan-popcount.obj: popcount.c
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uniqscan-genome128_hr.o: genome128_hr.c
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uniqscan-genome128_hr.obj: genome128_hr.c
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uniqscan-indexdb_hr.o: indexdb_hr.c
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uniqscan-boyer-moore.o: boyer-moore.c
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uniqscan-changepoint.o: changepoint.c
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uniqscan-pbinom.o: pbinom.c
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uniqscan-dynprog.o: dynprog.c
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uniqscan-dynprog.obj: dynprog.c
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uniqscan-dynprog_simd.o: dynprog_simd.c
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uniqscan-dynprog_genome.o: dynprog_genome.c
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uniqscan-dynprog_end.o: dynprog_end.c
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uniqscan-dynprog_end.obj: dynprog_end.c
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uniqscan-translation.o: translation.c
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uniqscan-translation.obj: translation.c
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uniqscan-doublelist.o: doublelist.c
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uniqscan-doublelist.obj: doublelist.c
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uniqscan-smooth.o: smooth.c
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uniqscan-smooth.obj: smooth.c
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uniqscan-chimera.o: chimera.c
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uniqscan-chimera.obj: chimera.c
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uniqscan-stage3.o: stage3.c
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uniqscan-stage3.obj: stage3.c
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uniqscan-splicestringpool.o: splicestringpool.c
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uniqscan-splicetrie_build.o: splicetrie_build.c
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uniqscan-splice.o: splice.c
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uniqscanl-popcount.o: popcount.c
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uniqscanl-popcount.obj: popcount.c
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uniqscanl-genome128_hr.o: genome128_hr.c
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uniqscanl-genome128_hr.obj: genome128_hr.c
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uniqscanl-genome_sites.o: genome_sites.c
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uniqscanl-genome_sites.obj: genome_sites.c
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uniqscanl-bitpack64-read.o: bitpack64-read.c
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uniqscanl-bitpack64-read.obj: bitpack64-read.c
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uniqscanl-bitpack64-readtwo.o: bitpack64-readtwo.c
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uniqscanl-merge.o: merge.c
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uniqscanl-merge.obj: merge.c
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uniqscanl-indexdb.o: indexdb.c
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uniqscanl-indexdb_hr.o: indexdb_hr.c
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uniqscanl-chrnum.o: chrnum.c
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uniqscanl-maxent_hr.o: maxent_hr.c
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uniqscanl-mapq.o: mapq.c
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uniqscanl-dynprog_genome.o: dynprog_genome.c
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uniqscanl-dynprog_cdna.o: dynprog_cdna.c
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uniqscanl-chimera.o: chimera.c
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maintainer-clean: maintainer-clean-am
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-am

mostlyclean-am: mostlyclean-compile mostlyclean-generic \
	mostlyclean-libtool

pdf: pdf-am

pdf-am:

ps: ps-am

ps-am:

uninstall-am: uninstall-binPROGRAMS uninstall-includeHEADERS \
	uninstall-libLTLIBRARIES

.MAKE: all install-am install-strip

.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
	clean-binPROGRAMS clean-generic clean-libLTLIBRARIES \
	clean-libtool cscopelist-am ctags ctags-am distclean \
	distclean-compile distclean-generic distclean-hdr \
	distclean-libtool distclean-tags distdir dvi dvi-am html \
	html-am info info-am install install-am install-binPROGRAMS \
	install-data install-data-am install-dvi install-dvi-am \
	install-exec install-exec-am install-html install-html-am \
	install-includeHEADERS install-info install-info-am \
	install-libLTLIBRARIES install-man install-pdf install-pdf-am \
	install-ps install-ps-am install-strip installcheck \
	installcheck-am installdirs maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-compile \
	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
	tags tags-am uninstall uninstall-am uninstall-binPROGRAMS \
	uninstall-includeHEADERS uninstall-libLTLIBRARIES

.PRECIOUS: Makefile


#SPLICING_SCORE_FILES = fopen.h bool.h types.h \
# except.c except.h assert.c assert.h mem.c mem.h \
# intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
# univinterval.c univinterval.h interval.c interval.h \
# uintlist.c uintlist.h \
# chrom.c chrom.h stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
# iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
# filestring.c filestring.h \
# md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
# genome.c genome.h \
# genomicpos.c genomicpos.h \
# chrnum.c chrnum.h \
# maxent.c maxent.h maxent_hr.c maxent_hr.h \
# branchpoint.c branchpoint.h \
# parserange.c parserange.h datadir.c datadir.h getopt.c getopt1.c getopt.h splicing-score.c
#
#splicing_score_CFLAGS = $(AM_CFLAGS)  $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\"
#splicing_score_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)
#splicing_score_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
#dist_splicing_score_SOURCES =
#nodist_splicing_score_SOURCES = $(SPLICING_SCORE_FILES)

# 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:
