biology/kallisto: Remove USE_GCC, fix build with clang19

Fix apparent typo in seldom-used code (hayzam@alchemilla.io)

Reported by:    gerald
Tested by:      jwb

Author: Jason W. Bacon

biology/kallisto/Makefile

@@ -1,6 +1,7 @@
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
 DISTVERSION=		0.51.1
+PORTREVISION=		1
 PORTEPOCH=		1
 CATEGORIES=		biology
 
@@ -42,17 +43,8 @@ LDFLAGS+=		-lhts -lz
 
 OPTIONS_DEFINE=	EXAMPLES
 
-.include <bsd.port.pre.mk>
-
-# Build fails with clang19, but succeeds with gcc13
-# Have not figured out where this sz_link member is even supposed to come from
-# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
-.if ${OSVERSION} > 1500000
-USE_GCC=	yes
-.endif
-
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>

biology/kallisto/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1726658334
+TIMESTAMP = 1748283025
 SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516
 SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250

biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc

@@ -0,0 +1,14 @@
+--- ext/bifrost/src/DataStorage.tcc.orig	2024-09-17 05:40:08 UTC
++++ ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co
+ 
+         unitig_cs_link = new atomic<uint64_t>[sz_link];
+ 
+-        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++        // Hayzam Sherif: o.sz_link -> o.unitig_cs_link
++        // Independently proposed by Lucas van Dijk:
++        // https://github.com/pmelsted/bifrost/pull/18/files
++        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+     }
+ 
+     if ((o.data != nullptr) && (o.sz_cs != 0)){