jellyfish2: Upgrade to 2.2.10 and clean up

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 14:22:33 2018 -0500
Changeset:	1d19dbf336c813ff979869906459f8c81eb5aea0

Modified Files:
	jellyfish2/Makefile
	jellyfish2/PLIST
	jellyfish2/distinfo
Removed Files:
	jellyfish2/patches/patch-include_jellyfish_file__header.hpp

Log Message:
jellyfish2: Upgrade to 2.2.10 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1d19dbf336c813ff979869906459f8c81eb5aea0

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

diffstat:
 jellyfish2/Makefile                                | 20 ++++-------
 jellyfish2/PLIST                                   |  2 ++
 jellyfish2/distinfo                                |  9 +++--
 .../patch-include_jellyfish_file__header.hpp       | 39 ----------------------
 4 files changed, 13 insertions(+), 57 deletions(-)

diffs:
diff --git a/jellyfish2/Makefile b/jellyfish2/Makefile
index 3eac19c3bf..979c275437 100644
--- a/jellyfish2/Makefile
+++ b/jellyfish2/Makefile
@@ -4,32 +4,26 @@
 #               Generated by fbsd2pkg                     #
 ###########################################################
 
-DISTNAME=	jellyfish-${PORTVERSION}
+DISTNAME=	jellyfish-${PV}
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=gmarcais/}
+# https://github.com/gmarcais/Jellyfish/issues/126
+MASTER_SITES=	${MASTER_SITE_GITHUB:=gmarcais/Jellyfish/releases/download/v2.2.10/}
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://www.genome.umd.edu/jellyfish.html
-GITHUB_TAG=	v${PORTVERSION}
 
 COMMENT=	Fast, memory-efficient counting of k-mers in DNA
 LICENSE=	gnu-gpl-v3
 
-USE_TOOLS=	autoreconf autoconf automake
 USE_LANGUAGES=	c c++
 USE_LIBTOOL=	yes
 GNU_CONFIGURE=	yes
 
 DEPENDS+=	yaggo>=0:../../wip/yaggo
 
-CFLAGS=		-fopenmp
+# Is this still necessary?
+CFLAGS+=	-fopenmp
 
-CXXFLAGS+=	-std=c++0x
-
-WRKSRC=		${WRKDIR}/Jellyfish-${PORTVERSION}
-
-PORTVERSION=	2.2.6
-
-pre-configure:
-	cd ${WRKSRC} && autoreconf -if
+PV=		2.2.10
 
+.include "../../devel/gettext-lib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/jellyfish2/PLIST b/jellyfish2/PLIST
index 5b472b0d23..62c73ca81b 100644
--- a/jellyfish2/PLIST
+++ b/jellyfish2/PLIST
@@ -36,7 +36,9 @@ include/${PKGNAME}/jellyfish/mer_overlap_sequence_parser.hpp
 include/${PKGNAME}/jellyfish/mer_qual_iterator.hpp
 include/${PKGNAME}/jellyfish/misc.hpp
 include/${PKGNAME}/jellyfish/offsets_key_value.hpp
+include/${PKGNAME}/jellyfish/parser_common.hpp
 include/${PKGNAME}/jellyfish/rectangular_binary_matrix.hpp
+include/${PKGNAME}/jellyfish/sam_format.hpp
 include/${PKGNAME}/jellyfish/simple_circular_buffer.hpp
 include/${PKGNAME}/jellyfish/sorted_dumper.hpp
 include/${PKGNAME}/jellyfish/stdio_filebuf.hpp
diff --git a/jellyfish2/distinfo b/jellyfish2/distinfo
index db948a99f6..1949d16a6b 100644
--- a/jellyfish2/distinfo
+++ b/jellyfish2/distinfo
@@ -1,7 +1,6 @@
 $NetBSD$
 
-SHA1 (jellyfish-2.2.6.tar.gz) = 8654c50c56b506da24dd4a44fcbdc94c953e88da
-RMD160 (jellyfish-2.2.6.tar.gz) = 238cbcf4340e5777e7a58e33e92979f07e069e0d
-SHA512 (jellyfish-2.2.6.tar.gz) = 7d61d823feaaab05fbb43eaca22823a988bd05da318431e74092b42c7e33ce39f387ac15db30906341f084223b7c2726e199592555aea4b21a5b517e8d0c08f9
-Size (jellyfish-2.2.6.tar.gz) = 660858 bytes
-SHA1 (patch-include_jellyfish_file__header.hpp) = 6876cf0e62b6c87118effe752d559e19b6c89cb5
+SHA1 (jellyfish-2.2.10.tar.gz) = dc1d347944f7c8fd90b8910701572b6510940c23
+RMD160 (jellyfish-2.2.10.tar.gz) = 6de70b1f70d08f2c18e58b964e1e69b442193b9b
+SHA512 (jellyfish-2.2.10.tar.gz) = 241f151981c840f8c68b39465d19db2c2199183908e7de337ccb1bf0fb107a088c2ea116f8a023ca6eab338a6a63c46d6b7915ce508577d8a5bc1d5537f8de19
+Size (jellyfish-2.2.10.tar.gz) = 1123173 bytes
diff --git a/jellyfish2/patches/patch-include_jellyfish_file__header.hpp b/jellyfish2/patches/patch-include_jellyfish_file__header.hpp
deleted file mode 100644
index b424b1f0e0..0000000000
--- a/jellyfish2/patches/patch-include_jellyfish_file__header.hpp
+++ /dev/null
@@ -1,39 +0,0 @@
-$NetBSD$
-
-# Some GCC installations appear to be missing certain to_string() morphs
-
---- include/jellyfish/file_header.hpp.orig	2013-12-13 19:04:16 UTC
-+++ include/jellyfish/file_header.hpp
-@@ -21,6 +21,8 @@
- #include <jellyfish/generic_file_header.hpp>
- #include <jellyfish/rectangular_binary_matrix.hpp>
- 
-+using std::string;
-+
- namespace jellyfish {
- /// A header with jellyfish hash specific entries: size, matrix, etc.
- class file_header : public generic_file_header {
-@@ -42,7 +44,10 @@ public:
- 
-   RectangularBinaryMatrix matrix(int i = 1) const {
-     std::string name("matrix");
--    name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
-+    char   buff[100];
-+    // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
-+    snprintf(buff, 99, "%d", i);
-+    name += buff;
-     const unsigned int r = root_[name]["r"].asUInt();
-     const unsigned int c = root_[name]["c"].asUInt();
-     std::vector<uint64_t> raw(c, (uint64_t)0);
-@@ -53,7 +58,10 @@ public:
- 
-   void matrix(const RectangularBinaryMatrix& m, int i = 1) {
-     std::string name("matrix");
--    name += std::to_string((long long int)i);
-+    char   buff[100];
-+    // name += std::to_string((long long int)i);
-+    snprintf(buff, 99, "%d", i);
-+    name += buff;
-     root_[name].clear();
-     root_[name]["r"] = m.r();
-     root_[name]["c"] = m.c();