Attachment 161120 Details for Bug 203158 – Shar archive

Shar archive

bwa-shar.txt (text/plain), 4.10 KB, created by Jason W. Bacon on 2015-09-16 18:17:41 UTC

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Creator: Jason W. Bacon

Created: 2015-09-16 18:17:41 UTC

Size: 4.10 KB

patch

obsolete

># 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
>

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Attachments on bug 203158: 161120