bwa: Test fixes to biology/bwa genome aligner
This commit is contained in:
Jason Bacon
parent
cd964df81a
commit
91e32433e1
1
Makefile
1
Makefile
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@ -295,6 +295,7 @@ SUBDIR+= bugzilla
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SUBDIR+= bullet
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SUBDIR+= bup-git
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SUBDIR+= busybox
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SUBDIR+= bwa
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SUBDIR+= bwm-ng
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SUBDIR+= byzanz
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SUBDIR+= c-news
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@ -0,0 +1,2 @@
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BWA is a software package for mapping low-divergent sequences against a large
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reference genome, such as the human genome.
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@ -0,0 +1,31 @@
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# $NetBSD: Makefile,v 1.6 2017/12/27 23:44:01 he Exp $
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DISTNAME= bwa-0.7.17
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CATEGORIES= biology
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PKGREVISION= 1
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GITHUB_TAG= v${PKGVERSION_NOREV}
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MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://bio-bwa.sourceforge.net/
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COMMENT= Map low-divergent sequences against a large reference genome
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LICENSE= gnu-gpl-v3
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USE_TOOLS+= perl:run gmake
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REPLACE_PERL= *.pl
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INSTALLATION_DIRS= bin ${PKGMANDIR}/man1
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# unconditionally uses <emmintrin.h>
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ONLY_FOR_PLATFORM= *-*-x86_64 *-*-i386 *-*-ia64
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CFLAGS.SunOS+= -Du_int32_t=uint32_t
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LDFLAGS.SunOS+= -lsocket -lnsl
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/bwa ${DESTDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${DESTDIR}${PREFIX}/bin
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${INSTALL_MAN} ${WRKSRC}/*.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,5 @@
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@comment $NetBSD: PLIST,v 1.1 2015/10/14 17:12:52 leot Exp $
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bin/bwa
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bin/qualfa2fq.pl
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bin/xa2multi.pl
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man/man1/bwa.1
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@ -0,0 +1,9 @@
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$NetBSD: distinfo,v 1.6 2017/12/27 23:44:01 he Exp $
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SHA1 (bwa-0.7.17.tar.gz) = 77f9aac723110227ea51cb42011336d291d03723
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RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
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SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
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Size (bwa-0.7.17.tar.gz) = 232593 bytes
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SHA1 (patch-Makefile) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
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SHA1 (patch-fastmap.c) = e96f972a65ecc68c92eb82816e9e24b057435d1d
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SHA1 (patch-kopen.c) = ecc92efa3ebe4da484aa6760e23de9437b000644
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@ -0,0 +1,44 @@
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$NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $
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Respect env, add librt for NetBSD
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--- Makefile.orig 2017-10-23 17:10:17.000000000 +0000
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+++ Makefile
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@@ -1,6 +1,6 @@
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-CC= gcc
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+CC?= gcc
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#CC= clang --analyze
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-CFLAGS= -g -Wall -Wno-unused-function -O2
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+CFLAGS?= -g -Wall -Wno-unused-function -O2
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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AR= ar
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
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@@ -12,11 +12,14 @@ AOBJS= bwashm.o bwase.o bwaseqio.o bwtg
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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PROG= bwa
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INCLUDES=
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-LIBS= -lm -lz -lpthread
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+LDFLAGS+= -lm -lz -lpthread
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SUBDIRS= .
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ifeq ($(shell uname -s),Linux)
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- LIBS += -lrt
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+ LDFLAGS += -lrt
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+endif
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+ifeq ($(shell uname -s),NetBSD)
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+ LDFLAGS += -lrt
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endif
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.SUFFIXES:.c .o .cc
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@@ -27,10 +30,10 @@ endif
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all:$(PROG)
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bwa:libbwa.a $(AOBJS) main.o
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- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
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+ $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LDFLAGS)
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bwamem-lite:libbwa.a example.o
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- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
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+ $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LDFLAGS)
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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@ -0,0 +1,14 @@
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$NetBSD$
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--- fastmap.c.orig 2018-04-19 22:02:10.516983388 +0000
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+++ fastmap.c
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@@ -130,7 +130,9 @@ int main_mem(int argc, char *argv[])
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aux.opt = opt = mem_opt_init();
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memset(&opt0, 0, sizeof(mem_opt_t));
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+ fprintf(stderr, "argc = %d argv[1] = %s\n", argc, argv[1]);
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while ((c = getopt(argc, argv, "51qpaMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
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+ fprintf(stderr, "c = %d %c\n", c, c);
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if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
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else if (c == '1') no_mt_io = 1;
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else if (c == 'x') mode = optarg;
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@ -0,0 +1,15 @@
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$NetBSD: patch-kopen.c,v 1.3 2017/12/27 23:44:01 he Exp $
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Add includes for getting timevals and select prototype into scope.
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--- kopen.c.orig 2017-10-23 17:10:17.000000000 +0000
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+++ kopen.c
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@@ -12,6 +12,8 @@
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#include <netdb.h>
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#include <arpa/inet.h>
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#include <sys/socket.h>
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+#include <sys/time.h>
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+#include <sys/select.h>
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#endif
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#ifdef USE_MALLOC_WRAPPERS
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