* wgsim: added a note

diff --git a/misc/Makefile b/misc/Makefile
index de37cd489281b5e6e43b645c825fcd7a471a4fbb..792cbbbeb67e335ba65f4f93b920a31b4133f632 100644 (file)
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -4,8 +4,8 @@ CFLAGS=         -g -Wall -O2 -m64 #-arch ppc
 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=       .
 
@@ -34,11 +34,19 @@ wgsim:wgsim.o
 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

diff --git a/misc/wgsim.c b/misc/wgsim.c
index b7e7b2fe3751170944d3f75fccd5a6e213837333..1ae7572a6a6aff77b04acfea9f6fd194f3ee6f3e 100644 (file)
--- a/misc/wgsim.c
+++ b/misc/wgsim.c
@@ -453,8 +453,9 @@ static int simu_usage()
        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;
 }