svn commit: r541097 - in head/biology/diamond: . files

[Joseph Mingrone]

Author: jrm
Date: Fri Jul  3 11:22:49 2020
New Revision: 541097
URL: https://svnweb.freebsd.org/changeset/ports/541097

Log:
  biology/diamond: Update to version 0.9.36
  
  Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36

Added:
  head/biology/diamond/files/
  head/biology/diamond/files/patch-src_search_collision.cpp   (contents, props changed)
Modified:
  head/biology/diamond/Makefile   (contents, props changed)
  head/biology/diamond/distinfo   (contents, props changed)

Modified: head/biology/diamond/Makefile
==============================================================================
--- head/biology/diamond/Makefile	Fri Jul  3 10:39:06 2020	(r541096)
+++ head/biology/diamond/Makefile	Fri Jul  3 11:22:49 2020	(r541097)
@@ -2,7 +2,7 @@
 
 PORTNAME=	diamond
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.9.35
+DISTVERSION=	0.9.36
 CATEGORIES=	biology
 
 MAINTAINER=	jrm at FreeBSD.org

Modified: head/biology/diamond/distinfo
==============================================================================
--- head/biology/diamond/distinfo	Fri Jul  3 10:39:06 2020	(r541096)
+++ head/biology/diamond/distinfo	Fri Jul  3 11:22:49 2020	(r541097)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1593274744
-SHA256 (bbuchfink-diamond-v0.9.35_GH0.tar.gz) = 21d25780de6dacf4f965a1c583cf511b19f04def9289387c793e5a175061452d
-SIZE (bbuchfink-diamond-v0.9.35_GH0.tar.gz) = 1102711
+TIMESTAMP = 1593736895
+SHA256 (bbuchfink-diamond-v0.9.36_GH0.tar.gz) = 870af89606330f6c0b57ed478d2d8237334ce8f5630eac770399ff431948bd59
+SIZE (bbuchfink-diamond-v0.9.36_GH0.tar.gz) = 1104423

Added: head/biology/diamond/files/patch-src_search_collision.cpp
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/diamond/files/patch-src_search_collision.cpp	Fri Jul  3 11:22:49 2020	(r541097)
@@ -0,0 +1,10 @@
+--- src/search/collision.cpp.orig	2020-07-03 10:58:27 UTC
++++ src/search/collision.cpp
+@@ -92,7 +92,6 @@ bool is_primary_hit(const Letter *query,
+ 	const unsigned sid,
+ 	const unsigned len)
+ {
+-	assert(len > 0 && len <= config.window * 2);
+ 	const bool chunked(config.lowmem > 1);
+ 	uint64_t mask = reduced_match32(query, subject, len);
+ 	unsigned i = 0;