bwa: Remove following commit to pkgsrc

[Jason W. Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sun Dec 17 21:02:52 2017 -0600
Changeset:	51284dbe97f6d31842037156e8dec4900480a316

Removed Files:
	bwa/DESCR
	bwa/Makefile
	bwa/PLIST
	bwa/distinfo
	bwa/patches/patch-Makefile

Log Message:
bwa: Remove following commit to pkgsrc

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=51284dbe97f6d31842037156e8dec4900480a316

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bwa/DESCR                  |  2 --
 bwa/Makefile               | 30 ------------------------------
 bwa/PLIST                  |  5 -----
 bwa/distinfo               |  7 -------
 bwa/patches/patch-Makefile | 44 --------------------------------------------
 5 files changed, 88 deletions(-)

diffs:
diff --git a/bwa/DESCR b/bwa/DESCR
deleted file mode 100644
index 1a8e65be4a..0000000000
--- a/bwa/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-BWA is a software package for mapping low-divergent sequences against a large
-reference genome, such as the human genome.
diff --git a/bwa/Makefile b/bwa/Makefile
deleted file mode 100644
index fa3a669457..0000000000
--- a/bwa/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# $NetBSD: Makefile,v 1.4 2016/07/09 06:37:51 wiz Exp $
-
-DISTNAME=	bwa-0.7.17
-CATEGORIES=	biology
-GITHUB_TAG=     v${PKGVERSION_NOREV}
-MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://bio-bwa.sourceforge.net/
-COMMENT=	Map low-divergent sequences against a large reference genome
-LICENSE=	gnu-gpl-v3
-
-USE_TOOLS+=	perl:run gmake
-REPLACE_PERL=	*.pl
-
-INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
-
-# unconditionally uses <emmintrin.h>
-ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64
-
-CFLAGS.SunOS+=	-Du_int32_t=uint32_t
-LDFLAGS.SunOS+=	-lsocket -lnsl
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${DESTDIR}${PREFIX}/bin
-	${INSTALL_MAN} ${WRKSRC}/*.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
-
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/bwa/PLIST b/bwa/PLIST
deleted file mode 100644
index 7ca657864f..0000000000
--- a/bwa/PLIST
+++ /dev/null
@@ -1,5 +0,0 @@
-@comment $NetBSD$
-bin/bwa
-bin/qualfa2fq.pl
-bin/xa2multi.pl
-man/man1/bwa.1
diff --git a/bwa/distinfo b/bwa/distinfo
deleted file mode 100644
index 1f95203bfa..0000000000
--- a/bwa/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD$
-
-SHA1 (bwa-0.7.17.tar.gz) = 77f9aac723110227ea51cb42011336d291d03723
-RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
-SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
-Size (bwa-0.7.17.tar.gz) = 232593 bytes
-SHA1 (patch-Makefile) = ae66ec8b80c03c2f5a54924d21e1fe3b9bb3e004
diff --git a/bwa/patches/patch-Makefile b/bwa/patches/patch-Makefile
deleted file mode 100644
index b86e7e9f6e..0000000000
--- a/bwa/patches/patch-Makefile
+++ /dev/null
@@ -1,44 +0,0 @@
-$NetBSD$
-
-# Respect env, add librt for NetBSD
---- Makefile.orig	2017-10-23 17:10:17.000000000 +0000
-+++ Makefile
-@@ -1,6 +1,6 @@
--CC=			gcc
-+CC?=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS?=		-g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
- AR=			ar
- DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
-@@ -12,11 +12,14 @@ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtg
- 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
- PROG=		bwa
- INCLUDES=	
--LIBS=		-lm -lz -lpthread
-+LDFLAGS+=	-lm -lz -lpthread
- SUBDIRS=	.
- 
- ifeq ($(shell uname -s),Linux)
--	LIBS += -lrt
-+	LDFLAGS += -lrt
-+endif
-+ifeq ($(shell uname -s),NetBSD)
-+	LDFLAGS += -lrt
- endif
- 
- .SUFFIXES:.c .o .cc
-@@ -27,10 +30,10 @@ endif
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LDFLAGS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LDFLAGS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)