# Makefile.in generated by automake 1.14 from Makefile.am.
# @configure_input@

# Copyright (C) 1994-2013 Free Software Foundation, Inc.

# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.

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# Copied from ../util so "gmap_setup -B src" works during "make check"
CLEANFILES = fa_coords gmap_process
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 access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 genome-write.c genome-write.h \
 bitpack64-read.c bitpack64-read.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 chrsubset.c chrsubset.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 \
 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 \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 chimera.c chimera.h datadir.c datadir.h \
 getopt.c getopt1.c getopt.h gmap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmap_CC = $(PTHREAD_CC)
gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
gmap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmap_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 \
 stopwatch.c stopwatch.h access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 genome-write.c genome-write.h \
 bitpack64-read.c bitpack64-read.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 chrsubset.c chrsubset.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 \
 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 \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 chimera.c chimera.h datadir.c datadir.h \
 getopt.c getopt1.c getopt.h gmap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gmapl_CC = $(PTHREAD_CC)
gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
gmapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapl_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 access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.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 samflags.h samprint.c samprint.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h stage3hr.c stage3hr.h \
 goby.c goby.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 gbuffer.c gbuffer.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 sarray-read.c sarray-read.h \
 stage1hr.c stage1hr.h \
 request.c request.h resulthr.c resulthr.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 datadir.c datadir.h mode.h \
 getopt.c getopt1.c getopt.h gsnap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnap_CC = $(PTHREAD_CC)
gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
gsnap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
dist_gsnap_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 access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.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 samflags.h samprint.c samprint.h \
 mapq.c mapq.h shortread.c shortread.h substring.c substring.h stage3hr.c stage3hr.h \
 goby.c goby.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 gbuffer.c gbuffer.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 sarray-read.c sarray-read.h \
 stage1hr.c stage1hr.h \
 request.c request.h resulthr.c resulthr.h \
 inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
 datadir.c datadir.h mode.h \
 getopt.c getopt1.c getopt.h gsnap.c


# Note: dist_ commands get read by bootstrap, and don't follow the flags
gsnapl_CC = $(PTHREAD_CC)
gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) $(GOBY_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
gsnapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(GOBY_LDFLAGS)
gsnapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS) $(GOBY_LIBS)
dist_gsnapl_SOURCES = $(GSNAPL_FILES)
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 access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.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 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 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 sarray-read.c sarray-read.h \
 stage1hr.c stage1hr.h resulthr.c resulthr.h \
 datadir.c datadir.h mode.h \
 getopt.c getopt1.c getopt.h uniqscan.c

uniqscan_CC = $(PTHREAD_CC)
uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
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 access.c access.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 genome_hr.c genome_hr.h genome_sites.c genome_sites.h \
 bitpack64-read.c bitpack64-read.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 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 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 sarray-read.c sarray-read.h \
 stage1hr.c stage1hr.h resulthr.c resulthr.h \
 datadir.c datadir.h mode.h \
 getopt.c getopt1.c getopt.h uniqscan.c

uniqscanl_CC = $(PTHREAD_CC)
uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
uniqscanl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscanl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscanl_SOURCES = $(UNIQSCANL_FILES)
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 access.c access.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 genome_hr.c genome_hr.h \
 bitpack64-read.c bitpack64-read.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 \
 chrom.c chrom.h segmentpos.c segmentpos.h \
 saca-k.c saca-k.h sarray-write.c sarray-write.h \
 gmapindex.c

gmapindex_CC = $(PTHREAD_CC)
gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_FLAGS) $(POPCNT_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 access.c access.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 \
 genome_hr.c genome_hr.h \
 bitpack64-read.c bitpack64-read.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 \
 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 access.c access.h \
 univinterval.c univinterval.h interval.h interval.c \
 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 \
 genome_hr.c genome_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
 cmet.c cmet.h \
 list.c list.h listdef.h datadir.c datadir.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)
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 access.c access.h \
 univinterval.c univinterval.h interval.h interval.c \
 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 \
 genome_hr.c genome_hr.h \
 bitpack64-read.c bitpack64-read.h bitpack64-write.c bitpack64-write.h \
 indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
 atoi.c atoi.h \
 list.c list.h listdef.h datadir.c datadir.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)
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 access.c access.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 chrsubset.c chrsubset.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 access.c access.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 access.c access.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 access.c access.h \
 iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.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)
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*) \
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	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
	$(am__cd) $(top_srcdir) && \
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	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
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$(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 $(top_builddir)/config.status
	@rm -f stamp-h1
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$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 
	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
	rm -f stamp-h1
	touch $@

distclean-hdr:
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install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
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	  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 | \
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	    -e 's|.*|.|' \
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	sed 'N;N;N;s,\n, ,g' | \
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	while read type dir files; do \
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	    $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
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uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
	files=`for p in $$list; do echo "$$p"; done | \
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clean-binPROGRAMS:
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	test -n "$(EXEEXT)" || exit 0; \
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atoiindex$(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)

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)

gmapindex$(EXEEXT): $(gmapindex_OBJECTS) $(gmapindex_DEPENDENCIES) $(EXTRA_gmapindex_DEPENDENCIES) 
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gmapl$(EXEEXT): $(gmapl_OBJECTS) $(gmapl_DEPENDENCIES) $(EXTRA_gmapl_DEPENDENCIES) 
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gsnap$(EXEEXT): $(gsnap_OBJECTS) $(gsnap_DEPENDENCIES) $(EXTRA_gsnap_DEPENDENCIES) 
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gsnapl$(EXEEXT): $(gsnapl_OBJECTS) $(gsnapl_DEPENDENCIES) $(EXTRA_gsnapl_DEPENDENCIES) 
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iit_dump$(EXEEXT): $(iit_dump_OBJECTS) $(iit_dump_DEPENDENCIES) $(EXTRA_iit_dump_DEPENDENCIES) 
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iit_get$(EXEEXT): $(iit_get_OBJECTS) $(iit_get_DEPENDENCIES) $(EXTRA_iit_get_DEPENDENCIES) 
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iit_store$(EXEEXT): $(iit_store_OBJECTS) $(iit_store_DEPENDENCIES) $(EXTRA_iit_store_DEPENDENCIES) 
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snpindex$(EXEEXT): $(snpindex_OBJECTS) $(snpindex_DEPENDENCIES) $(EXTRA_snpindex_DEPENDENCIES) 
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uniqscan$(EXEEXT): $(uniqscan_OBJECTS) $(uniqscan_DEPENDENCIES) $(EXTRA_uniqscan_DEPENDENCIES) 
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uniqscanl$(EXEEXT): $(uniqscanl_OBJECTS) $(uniqscanl_DEPENDENCIES) $(EXTRA_uniqscanl_DEPENDENCIES) 
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mostlyclean-compile:
	-rm -f *.$(OBJEXT)

distclean-compile:
	-rm -f *.tab.c

@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/atoiindex-access.Po@am__quote@
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get_genome-sequence.o: sequence.c
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get_genome-chrom.o: chrom.c
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gmap-reader.o: reader.c
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gmap-genomicpos.o: genomicpos.c
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gmap-compress.o: compress.c
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gmap-gbuffer.o: gbuffer.c
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gmap-genome.o: genome.c
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gmap-genome.obj: genome.c
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gmap-genome_hr.o: genome_hr.c
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gmap-genome-write.o: genome-write.c
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gmap-translation.o: translation.c
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gmap-stage3.o: stage3.c
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gmap-request.o: request.c
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gmap-chimera.o: chimera.c
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gmap-datadir.o: datadir.c
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gmap-gmap.o: gmap.c
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gsnap-md5.obj: md5.c
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gsnap-bzip2.o: bzip2.c
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gsnap-bzip2.obj: bzip2.c
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gsnap-sequence.o: sequence.c
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gsnap-sequence.obj: sequence.c
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gsnap-reader.o: reader.c
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gsnap-reader.obj: reader.c
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gsnap-genomicpos.o: genomicpos.c
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gsnap-genomicpos.obj: genomicpos.c
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gsnap-compress.o: compress.c
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gsnap-compress.obj: compress.c
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gsnap-genome.o: genome.c
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gsnap-genome.obj: genome.c
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gsnap-genome_hr.o: genome_hr.c
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gsnap-genome_hr.obj: genome_hr.c
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gsnap-genome_sites.o: genome_sites.c
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gsnap-genome_sites.obj: genome_sites.c
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gsnap-bitpack64-read.o: bitpack64-read.c
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gsnap-bitpack64-read.obj: bitpack64-read.c
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gsnap-indexdb.o: indexdb.c
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gsnap-indexdb.obj: indexdb.c
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gsnap-oligo.o: oligo.c
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gsnap-chrom.o: chrom.c
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gsnap-segmentpos.o: segmentpos.c
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gsnap-samprint.o: samprint.c
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gsnap-shortread.o: shortread.c
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gsnap-substring.o: substring.c
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gsnap-substring.obj: substring.c
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gsnap-maxent.o: maxent.c
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gsnap-pair.o: pair.c
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gsnap-pairpool.o: pairpool.c
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gsnap-indel.obj: indel.c
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gsnap-bitpack64-access.o: bitpack64-access.c
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gsnap-sarray-read.o: sarray-read.c
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gsnap-stage1hr.o: stage1hr.c
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gsnap-request.o: request.c
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gsnap-request.obj: request.c
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gsnap-resulthr.o: resulthr.c
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gsnap-resulthr.obj: resulthr.c
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gsnap-inbuffer.o: inbuffer.c
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gsnap-inbuffer.obj: inbuffer.c
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gsnap-samheader.o: samheader.c
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gsnap-samheader.obj: samheader.c
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gsnap-outbuffer.o: outbuffer.c
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gsnap-outbuffer.obj: outbuffer.c
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gsnap-datadir.o: datadir.c
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gsnapl-chrom.o: chrom.c
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gsnapl-segmentpos.o: segmentpos.c
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gsnapl-chrnum.o: chrnum.c
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gsnapl-maxent_hr.o: maxent_hr.c
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gsnapl-samprint.o: samprint.c
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gsnapl-shortread.o: shortread.c
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snpindex-chrom.o: chrom.c
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snpindex-md5.o: md5.c
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