From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 4 Apr 2012 09:07:27 +0000 (+0100)
Subject: Merge remote branch 'main/master'
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5941304148f69879e1df9fbbdc749117a5bf2fac;hp=-c;p=samtools.git

Merge remote branch 'main/master'

Conflicts:
	misc/Makefile
	misc/bamcheck.c
---

5941304148f69879e1df9fbbdc749117a5bf2fac
diff --combined misc/Makefile
index 64aa9df,8a50ea3..e1a5add
--- a/misc/Makefile
+++ b/misc/Makefile
@@@ -4,7 -4,7 +4,7 @@@ CFLAGS=		-g -Wall -O2 #-m64 #-arch pp
  CXXFLAGS=	$(CFLAGS)
  DFLAGS=		-D_FILE_OFFSET_BITS=64
  OBJS=		
- PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim seqtk bamcheck
+ PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
  INCLUDES=	-I..
  SUBDIRS=	.
  
@@@ -28,7 -28,7 +28,7 @@@ lib-recur all-recur clean-recur cleanlo
  lib:
  
  bamcheck:bamcheck.o
--		$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
++		$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam -lpthread
  
  bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
  		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
@@@ -36,9 -36,6 +36,6 @@@
  ace2sam:ace2sam.o
  		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
  
- seqtk:seqtk.o
- 		$(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
- 
  wgsim:wgsim.o
  		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
  
@@@ -60,9 -57,6 +57,6 @@@ maq2sam-long:maq2sam.
  md5fa.o:md5.h md5fa.c
  		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
  
- seqtk.o:seqtk.c ../khash.h ../kseq.h
- 		$(CC) $(CFLAGS) -c -I.. -o $@ seqtk.c
- 
  wgsim.o:wgsim.c ../kseq.h
  		$(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c