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193 lines
6.2 KiB
193 lines
6.2 KiB
diff --git a/core/Makefile b/core/Makefile
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index 8bb8baf..cf28559 100644
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--- a/core/Makefile
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+++ b/core/Makefile
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@@ -1,5 +1,5 @@
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PREFIX = /usr/local
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-LIBDIR = $(PREFIX)/lib/mafft
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+LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
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BINDIR = $(PREFIX)/bin
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MANDIR = $(PREFIX)/man/man1
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@@ -127,136 +127,136 @@ mltaln.h : functions.h
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touch mltaln.h
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ord : $(OBJORD)
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- $(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
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tbfast : $(OBJTBFAST)
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- $(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
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tbfast2 : $(OBJTBFAST2)
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- $(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
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disttbfast : $(OBJDISTTBFAST)
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- $(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
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splittbfast : $(OBJSPLITTBFAST)
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- $(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
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splitfromaln : $(OBJSPLITFROMALN)
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- $(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
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splittbfast2 : $(OBJSPLITTBFAST2)
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- $(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
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dummy : $(OBJDUMMY)
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- $(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
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setcore : $(OBJSETCORE)
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- $(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
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countlen : $(OBJCOUNTLEN)
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- $(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
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seq2regtable : $(OBJSEQ2REGTABLE)
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- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
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regtable2seq : $(OBJREGTABLE2SEQ)
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- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
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f2cl : $(OBJF2CL)
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- $(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
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mccaskillwrap : $(OBJMCCASKILLWRAP)
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- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
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contrafoldwrap : $(OBJCONTRAFOLDWRAP)
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- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
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pairlocalalign : $(OBJPAIRLOCALALIGN)
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- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
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pairash : $(OBJPAIRASH)
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- $(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
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rnatest : $(OBJRNATEST)
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- $(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
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pair2hat3s : $(OBJPAIR2HAT3S)
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- $(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
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multi2hat3s : $(OBJMULTI2HAT3S)
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- $(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
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getlag : $(OBJGETLAG)
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- $(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
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tditr : $(OBJTDITR)
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- $(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
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dvtditr : $(OBJDVTDITR)
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- $(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
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mafft-profile : $(OBJGALN)
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- $(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
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gapfill : $(OBJGAPFILL)
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- $(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
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dndfast4 : $(OBJDNDFAST4)
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- $(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
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dndfast5 : $(OBJDNDFAST5)
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- $(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
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dndfast6 : $(OBJDNDFAST6)
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- $(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
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dndfast7 : $(OBJDNDFAST7)
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- $(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
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dndblast : $(OBJDNDBLAST)
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- $(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
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dndfast3 : $(OBJDNDFAST3)
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- $(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
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triplet : $(OBJTRIPLET)
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- $(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
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triplet3 : $(OBJTRIPLET3)
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- $(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
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sextet3 : $(OBJSEXTET3)
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- $(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
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sextet4 : $(OBJSEXTET4)
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- $(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
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sextet5 : $(OBJSEXTET5)
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- $(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
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mafft-distance : $(OBJDISTANCE)
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- $(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
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triplet5 : $(OBJTRIPLET5)
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- $(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
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triplet6 : $(OBJTRIPLET6)
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- $(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
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octet4 : $(OBJOCTET4)
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- $(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
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dndpre : $(OBJDNDPRE)
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- $(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
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dndpre2 : $(OBJDNDPRESCORE)
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- $(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
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score : $(OBJSCORE)
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- $(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
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genMtx : $(OBJGENMTX)
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- $(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
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gapfill.o : gapfill.c $(HEADER)
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$(CC) $(CFLAGS) -c gapfill.c
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