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biology/jellyfish: Update to 2.3.0

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Changelog:      https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
This commit is contained in:
Jason W. Bacon 2021-08-22 12:44:17 -05:00
parent 84c9db61e2
commit 4952cf637a
6 changed files with 4 additions and 58 deletions
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3
biology/jellyfish/Makefile
View File

@ -1,7 +1,6 @@
PORTNAME= Jellyfish
DISTVERSIONPREFIX= v
DISTVERSION= 2.2.10
PORTREVISION= 9
DISTVERSION= 2.3.0
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org

6
biology/jellyfish/distinfo
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@ -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

11
biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp
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@ -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;
}
}

11
biology/jellyfish/files/patch-sub__commands_count__main.cc
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@ -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) {

11
biology/jellyfish/files/patch-sub__commands_merge__main.cc
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@ -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());
}

20
biology/jellyfish/files/patch-sub__commands_query__main.cc
View File

@ -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;
}
}