biology/jellyfish: Update to 2.3.0

Changelog:      https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0

6 files changed, 4 insertions, 58 deletions

diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
index d84f96e88420..9937ac96c1b2 100644
--- a/biology/jellyfish/Makefile
+++ b/biology/jellyfish/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		Jellyfish
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.2.10
-PORTREVISION=		9
+DISTVERSION=		2.3.0
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/jellyfish/distinfo b/biology/jellyfish/distinfo
index 9bea24513108..8e77167cbbfa 100644
--- a/biology/jellyfish/distinfo
+++ b/biology/jellyfish/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557758001
-SHA256 (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 49137356b1cdd014cb70e866f0739fc3fafea6421fa22cc64bcfeba55fc1dc27
-SIZE (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 677009
+TIMESTAMP = 1629646709
+SHA256 (gmarcais-Jellyfish-v2.3.0_GH0.tar.gz) = 23819da9edb579a0cfb8baac9eff473a9477f4f749930cdb754dce1d117495cd
+SIZE (gmarcais-Jellyfish-v2.3.0_GH0.tar.gz) = 679144
diff --git a/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp b/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp
deleted file mode 100644
index 7410c3edcb71..000000000000
--- a/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- include/jellyfish/hash_counter.hpp.orig	2018-04-16 12:46:09 UTC
-+++ include/jellyfish/hash_counter.hpp
-@@ -213,7 +213,7 @@ class hash_counter { (protected)
-           new_ary_ = new  array(ary_->size(), ary_->key_len(), ary_->val_len() + 1,
-                                 ary_->max_reprobe(), ary_->reprobes());
-         }
--      } catch(typename array::ErrorAllocation e) {
-+      } catch(typename array::ErrorAllocation &e) {
-         new_ary_ = 0;
-       }
-     }
diff --git a/biology/jellyfish/files/patch-sub__commands_count__main.cc b/biology/jellyfish/files/patch-sub__commands_count__main.cc
deleted file mode 100644
index b4f2404b6cb2..000000000000
--- a/biology/jellyfish/files/patch-sub__commands_count__main.cc
+++ /dev/null
@@ -1,11 +0,0 @@
---- sub_commands/count_main.cc.orig	2018-04-16 12:46:09 UTC
-+++ sub_commands/count_main.cc
-@@ -360,7 +360,7 @@ int count_main(int argc, char *argv[])
-         uint64_t max = args.upper_count_given ? args.upper_count_arg : std::numeric_limits<uint64_t>::max();
-         try {
-           merge_files(files, args.output_arg, header, min, max);
--        } catch(MergeError e) {
-+        } catch(MergeError &e) {
-           err::die(err::msg() << e.what());
-         }
-         if(!args.no_unlink_flag) {
diff --git a/biology/jellyfish/files/patch-sub__commands_merge__main.cc b/biology/jellyfish/files/patch-sub__commands_merge__main.cc
deleted file mode 100644
index 0b331da069ff..000000000000
--- a/biology/jellyfish/files/patch-sub__commands_merge__main.cc
+++ /dev/null
@@ -1,11 +0,0 @@
---- sub_commands/merge_main.cc.orig	2019-05-13 07:46:43 UTC
-+++ sub_commands/merge_main.cc
-@@ -33,7 +33,7 @@ int merge_main(int argc, char *argv[])
- 
-   try {
-     merge_files(args.input_arg, args.output_arg, out_header, min, max);
--  } catch(MergeError e) {
-+  } catch(MergeError &e) {
-     err::die(err::msg() << e.what());
-   }
- 
diff --git a/biology/jellyfish/files/patch-sub__commands_query__main.cc b/biology/jellyfish/files/patch-sub__commands_query__main.cc
deleted file mode 100644
index 243b0df29485..000000000000
--- a/biology/jellyfish/files/patch-sub__commands_query__main.cc
+++ /dev/null
@@ -1,20 +0,0 @@
---- sub_commands/query_main.cc.orig	2019-05-13 07:47:53 UTC
-+++ sub_commands/query_main.cc
-@@ -60,7 +60,7 @@ void query_from_cmdline(std::vector<const char*> mers,
-       if(canonical)
-         m.canonicalize();
-       out << m << " " << db.check(m) << "\n";
--    } catch(std::length_error e) {
-+    } catch(std::length_error &e) {
-       std::cerr << "Invalid mer '" << *it << "'\n";
-     }
-   }
-@@ -77,7 +77,7 @@ void query_from_stdin(const Database& db, std::ostream
-       if(canonical)
-         m.canonicalize();
-       out << db.check(m) << std::endl;  // a flush is need for interactive use
--    } catch(std::length_error e) {
-+    } catch(std::length_error &e) {
-       std::cerr << "Invalid mer '" << buffer << "'" << std::endl;
-     }
-   }