[pkgsrc/trunk]: pkgsrc/biology/bwa biology/bwa: Update to 0.7.17

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/26f508b198e0
branches:  trunk
changeset: 372790:26f508b198e0
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sun Dec 17 14:30:36 2017 +0000

description:
biology/bwa: Update to 0.7.17

Numerous bug fixes, enhancements, and new command-line options

ok wiz@

diffstat:

 biology/bwa/Makefile               |  12 +++++-------
 biology/bwa/distinfo               |  13 ++++++-------
 biology/bwa/patches/patch-Makefile |  36 ++++++++++++++++++++++++++++--------
 biology/bwa/patches/patch-kopen.c  |  12 ------------
 4 files changed, 39 insertions(+), 34 deletions(-)

diffs (112 lines):

diff -r 9932f577d938 -r 26f508b198e0 biology/bwa/Makefile
--- a/biology/bwa/Makefile      Sun Dec 17 14:20:50 2017 +0000
+++ b/biology/bwa/Makefile      Sun Dec 17 14:30:36 2017 +0000
@@ -1,13 +1,11 @@
-# $NetBSD: Makefile,v 1.4 2016/07/09 06:37:51 wiz Exp $
-#
+# $NetBSD: Makefile,v 1.5 2017/12/17 14:30:36 bacon Exp $
 
-DISTNAME=      bwa-0.7.9a
+DISTNAME=      bwa-0.7.17
 CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_SOURCEFORGE:=bio-bwa/}
-EXTRACT_SUFX=  .tar.bz2
-PKGREVISION=   2
+GITHUB_TAG=     v${PKGVERSION_NOREV}
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
 
-MAINTAINER=    jwbacon%tds.net@localhost
+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
diff -r 9932f577d938 -r 26f508b198e0 biology/bwa/distinfo
--- a/biology/bwa/distinfo      Sun Dec 17 14:20:50 2017 +0000
+++ b/biology/bwa/distinfo      Sun Dec 17 14:30:36 2017 +0000
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.4 2017/02/14 21:34:34 joerg Exp $
+$NetBSD: distinfo,v 1.5 2017/12/17 14:30:36 bacon Exp $
 
-SHA1 (bwa-0.7.9a.tar.bz2) = a77ce327e8acba554b1d27bfdd1c148f79726484
-RMD160 (bwa-0.7.9a.tar.bz2) = a51b7c686a206144eab2aee0a372d5ae46fcfce1
-SHA512 (bwa-0.7.9a.tar.bz2) = 93804b2c0ac0f675e76f762441e1eec039d7f1cf77b033fd88f2e6c39d9cd4b5c21bba9fb44e34a3dab28c630c3855792a707e5b33109d4be0097cec97eaa686
-Size (bwa-0.7.9a.tar.bz2) = 166193 bytes
-SHA1 (patch-Makefile) = 2bb665cb579d20a07ae7c2be8ba0ed874d60d5b0
-SHA1 (patch-kopen.c) = 9c92b812a7e55bf9d7d136d91be02982610d9f51
+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) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
diff -r 9932f577d938 -r 26f508b198e0 biology/bwa/patches/patch-Makefile
--- a/biology/bwa/patches/patch-Makefile        Sun Dec 17 14:20:50 2017 +0000
+++ b/biology/bwa/patches/patch-Makefile        Sun Dec 17 14:30:36 2017 +0000
@@ -1,24 +1,44 @@
-$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
+$NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $
 
-Don't overwrite pkgsrc CC and CFLAGS
-
---- Makefile.orig      2014-05-19 13:11:41.000000000 +0000
+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?=                  gcc
  #CC=                  clang --analyze
 -CFLAGS=               -g -Wall -Wno-unused-function -O2
-+#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)
-@@ -11,7 +11,7 @@ AOBJS=               QSufSort.o bwt_gen.o bwase.o bwa
+@@ -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
-+LIBS=         -lm -lz -lpthread $(LDFLAGS)
++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 $@ $(LOBJS)
diff -r 9932f577d938 -r 26f508b198e0 biology/bwa/patches/patch-kopen.c
--- a/biology/bwa/patches/patch-kopen.c Sun Dec 17 14:20:50 2017 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-$NetBSD: patch-kopen.c,v 1.1 2017/02/14 21:34:34 joerg Exp $
-
---- kopen.c.orig       2017-02-09 15:42:47.246248867 +0000
-+++ kopen.c
-@@ -8,6 +8,7 @@
- #include <signal.h>
- #include <sys/wait.h>
- #include <sys/types.h>
-+#include <sys/time.h>
- #ifndef _WIN32
- #include <netdb.h>
- #include <arpa/inet.h>