From 115b2e9f98151f208207aae6286acd12adf019de Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 26 Feb 2009 14:02:57 +0000
Subject: [PATCH]  * wgsim: added a note

---
 misc/Makefile | 16 ++++++++++++----
 misc/wgsim.c  |  3 ++-
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/misc/Makefile b/misc/Makefile
index de37cd4..792cbbb 100644
--- 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 b7e7b2f..1ae7572 100644
--- 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;
 }
 
-- 
2.39.5