CXXFLAGS= $(CFLAGS)
DFLAGS= #-D_FILE_OFFSET_BITS=64
OBJS=
-PROG= faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
-INCLUDES=
+PROG= faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim fa2csfa
+INCLUDES= -I..
LIBS= -lm -lz
SUBDIRS= .
faidx:../faidx.c ../faidx.h
$(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+fa2csfa:fa2csfa.o
+ $(CC) $(CFLAGS) -o $@ fa2csfa.o -lz
+
md5fa:md5.o md5fa.o md5.h ../kseq.h
$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-md5sum-lite:md5.c md5.h
- $(CC) $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+md5sum-lite:md5sum-lite.o
+ $(CC) $(CFLAGS) -o $@ md5sum-lite.o
+
+md5sum-lite.o:md5.c md5.h
+ $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+
+fa2csfa:fa2csfa.c ../kseq.h
maq2sam-short:maq2sam.c
$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
fprintf(stderr, " -R FLOAT fraction of indels [%.2f]\n", INDEL_FRAC);
fprintf(stderr, " -X FLOAT probability an indel is extended [%.2f]\n", INDEL_EXTEND);
fprintf(stderr, " -c generate reads in color space (SOLiD reads)\n");
- fprintf(stderr, " -h haploid mode\n");
+ fprintf(stderr, " -h haplotype mode\n");
fprintf(stderr, "\n");
+ fprintf(stderr, "Note: For SOLiD reads, the first read is F3 and the second is R3.\n\n");
return 1;
}