# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	bwa
#	bwa/files
#	bwa/files/patch-Makefile
#	bwa/files/patch-bwt_lite.c
#	bwa/files/patch-bwtgap.c
#	bwa/files/patch-bwtgap.h
#	bwa/Makefile
#	bwa/distinfo
#	bwa/pkg-descr
#
echo c - bwa
mkdir -p bwa > /dev/null 2>&1
echo c - bwa/files
mkdir -p bwa/files > /dev/null 2>&1
echo x - bwa/files/patch-Makefile
sed 's/^X//' >bwa/files/patch-Makefile << 'b0875dea839f27698cf5164e2e6f9d0c'
X--- Makefile.orig	2014-05-19 13:11:41 UTC
X+++ Makefile
X@@ -1,6 +1,6 @@
X-CC=			gcc
X+CC?=			gcc
X #CC=			clang --analyze
X-CFLAGS=		-g -Wall -Wno-unused-function -O2
X+CFLAGS?=		-g -Wall -Wno-unused-function -O2
X WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
X AR=			ar
X DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
b0875dea839f27698cf5164e2e6f9d0c
echo x - bwa/files/patch-bwt_lite.c
sed 's/^X//' >bwa/files/patch-bwt_lite.c << '93737eed723ace16645081018aec10ec'
X--- bwt_lite.c.orig	2014-05-19 13:11:41 UTC
X+++ bwt_lite.c
X@@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uin
X 	}
X 	{ // generate cnt_table
X 		for (i = 0; i != 256; ++i) {
X-			u_int32_t j, x = 0;
X+			uint32_t j, x = 0;
X 			for (j = 0; j != 4; ++j)
X 				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
X 			b->cnt_table[i] = x;
93737eed723ace16645081018aec10ec
echo x - bwa/files/patch-bwtgap.c
sed 's/^X//' >bwa/files/patch-bwtgap.c << '7ab5345419a9dd50946d53dc44bad0ca'
X--- bwtgap.c.orig	2014-02-25 21:20:01 UTC
X+++ bwtgap.c
X@@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t 
X 		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
X 	}
X 	p = q->stack + q->n_entries;
X-	p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
X+	p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l;
X 	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape;
X 	p->n_ins = n_ins; p->n_del = n_del;
X 	p->state = state; 
7ab5345419a9dd50946d53dc44bad0ca
echo x - bwa/files/patch-bwtgap.h
sed 's/^X//' >bwa/files/patch-bwtgap.h << '8c9327d7eeb2172524b66da12c0ec6fd'
X--- bwtgap.h.orig	2014-02-25 21:20:01 UTC
X+++ bwtgap.h
X@@ -5,9 +5,9 @@
X #include "bwtaln.h"
X 
X typedef struct { // recursion stack
X-	u_int32_t info; // score<<21 | i
X-	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
X-	u_int32_t n_ins:16, n_del:16;
X+	uint32_t info; // score<<21 | i
X+	uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
X+	uint32_t n_ins:16, n_del:16;
X 	int last_diff_pos;
X 	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
X } gap_entry_t;
8c9327d7eeb2172524b66da12c0ec6fd
echo x - bwa/Makefile
sed 's/^X//' >bwa/Makefile << '1c0e869359ad5f076344d41f8ee9fee9'
X# Created by: Jason Bacon <jwbacon@tds.net>
X# $FreeBSD$
X
XPORTNAME=	bwa
XPORTVERSION=	0.7.9a
XCATEGORIES=	biology
XMASTER_SITES=	SF/bio-bwa/
X
XMAINTAINER=	jwbacon@tds.net
XCOMMENT=	Burrows-Wheeler sequence aligner
X
XLICENSE=	GPLv3
X
XUSES=		perl5 shebangfix tar:bzip2
XSHEBANG_FILES=	qualfa2fq.pl xa2multi.pl
XUSE_PERL5=	run
X
XPLIST_FILES=	bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz
X
X# Avoid #error in emmintrin.h
XCFLAGS+=	-msse2
X
Xdo-install:
X	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin
X	${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${STAGEDIR}${PREFIX}/bin
X	${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
X
X.include <bsd.port.mk>
1c0e869359ad5f076344d41f8ee9fee9
echo x - bwa/distinfo
sed 's/^X//' >bwa/distinfo << 'dc2323e4455816a17c4ee8246b99e221'
XSHA256 (bwa-0.7.9a.tar.bz2) = f5ad30e4e5ea86a8dcd6febcb6f620a75c82b03024f64a572017c295a962eadc
XSIZE (bwa-0.7.9a.tar.bz2) = 166193
dc2323e4455816a17c4ee8246b99e221
echo x - bwa/pkg-descr
sed 's/^X//' >bwa/pkg-descr << '1c0751f9b2099b0f8f1d3d3617eeaabb'
XBWA is a program for aligning sequencing reads against a large reference
Xgenome (e.g. human genome). It has two major components, one for read shorter
Xthan 150bp and the other for longer reads.
X
XWWW: http://sourceforge.net/projects/bio-bwa/
1c0751f9b2099b0f8f1d3d3617eeaabb
exit