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diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
--- a/biology/iolib/Makefile
+++ b/biology/iolib/Makefile
@@ -1,27 +1,24 @@
PORTNAME= io_lib
-DISTVERSIONPREFIX= ${PORTNAME}-
-DISTVERSION= 1-14-10
-PORTREVISION= 1
+DISTVERSION= 1-15-1
CATEGORIES= biology
+MASTER_SITES= https://github.com/jkbonfield/${PORTNAME}/releases/download/${DISTNAME:S/./-/g}/
+DISTNAME= ${PORTNAME}-${PORTVERSION}
-MAINTAINER= ports@FreeBSD.org
+MAINTAINER= alven@FreeBSD.org
COMMENT= General purpose trace file (and Experiment File) reading interface
-WWW= https://staden.sourceforge.net/
+WWW= https://staden.sourceforge.net/ \
+ https://github.com/jkbonfield/io_lib/
LICENSE= BSD3CLAUSE
LIB_DEPENDS= libcurl.so:ftp/curl
USES= autoreconf gmake libtool
-
-USE_GITHUB= yes
-GH_ACCOUNT= jkbonfield
+USE_LDCONFIG= yes
GNU_CONFIGURE= yes
-GNU_CONFIGURE_MANPREFIX=${PREFIX}/share
-USE_LDCONFIG= yes
+
INSTALL_TARGET= install-strip
-LDFLAGS+= -lpthread
CONFLICTS_INSTALL= filters scramble # bin/scramble
diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo
--- a/biology/iolib/distinfo
+++ b/biology/iolib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1538157628
-SHA256 (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 4bd576e52bb7e6be6c2efe42db2764b713c8b61b44a025ad0567dba052b6db1c
-SIZE (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 3391479
+TIMESTAMP = 1767736222
+SHA256 (io_lib-1.15.1.tar.gz) = 4e6f08265bee63211bb20feb4dc03993e57b447b90dc84a4c272cf1aed954e4f
+SIZE (io_lib-1.15.1.tar.gz) = 7357740
diff --git a/biology/iolib/files/patch-io__lib_c__range__coder.h b/biology/iolib/files/patch-io__lib_c__range__coder.h
deleted file mode 100644
--- a/biology/iolib/files/patch-io__lib_c__range__coder.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- io_lib/c_range_coder.h.orig 2018-10-18 16:44:55 UTC
-+++ io_lib/c_range_coder.h
-@@ -14,8 +14,6 @@
- #define DO(n) int _;for (_=0; _<n; _++)
- #define TOP (1<<24)
-
--typedef unsigned char uc;
--
- typedef struct {
- uint64_t low;
- uint32_t range, code;
diff --git a/biology/iolib/files/patch-io__lib_tokenise__name3.c b/biology/iolib/files/patch-io__lib_tokenise__name3.c
deleted file mode 100644
--- a/biology/iolib/files/patch-io__lib_tokenise__name3.c
+++ /dev/null
@@ -1,18 +0,0 @@
---- io_lib/tokenise_name3.c.orig 2018-10-18 16:21:37 UTC
-+++ io_lib/tokenise_name3.c
-@@ -457,13 +457,13 @@ static int encode_token_diff(name_context *ctx, uint32
-
- //-----------------------------------------------------------------------------
- // Trie implementation for tracking common name prefixes.
--typedef struct trie {
-+struct trie {
- char c;
- int count;
- //struct trie *next[128];
- struct trie *next, *sibling;
- int n; // Nth line
--} trie_t;
-+};
-
- //static trie_t *t_head = NULL;
-
diff --git a/biology/iolib/files/patch-progs-scram__merge.c b/biology/iolib/files/patch-progs-scram__merge.c
deleted file mode 100644
--- a/biology/iolib/files/patch-progs-scram__merge.c
+++ /dev/null
@@ -1,7 +0,0 @@
---- progs/scram_merge.c.orig 2013-04-30 08:30:10.000000000 -0400
-+++ progs/scram_merge.c 2013-04-30 08:30:23.000000000 -0400
-@@ -1,3 +1,4 @@
-+#include <unistd.h>
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
diff --git a/biology/iolib/files/patch-progs-scramble.c b/biology/iolib/files/patch-progs-scramble.c
deleted file mode 100644
--- a/biology/iolib/files/patch-progs-scramble.c
+++ /dev/null
@@ -1,7 +0,0 @@
---- progs/scramble.c.orig 2013-04-30 08:28:30.000000000 -0400
-+++ progs/scramble.c 2013-04-30 08:28:43.000000000 -0400
-@@ -1,3 +1,4 @@
-+#include <unistd.h>
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
diff --git a/biology/iolib/files/patch-progs__scram_test.c b/biology/iolib/files/patch-progs__scram_test.c
deleted file mode 100644
--- a/biology/iolib/files/patch-progs__scram_test.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- ./progs/scram_test.c.orig 2014-05-31 14:25:16.000000000 -0300
-+++ ./progs/scram_test.c 2014-05-31 14:25:27.000000000 -0300
-@@ -44,6 +44,7 @@
- #include <assert.h>
- #include <ctype.h>
- #include <errno.h>
-+#include <unistd.h>
-
- #if defined(__MINGW32__)
- # include <getopt.h>
diff --git a/biology/iolib/files/patch-progs__scram_flgstat.c b/biology/iolib/files/patch-progs_scram__flagstat.c
rename from biology/iolib/files/patch-progs__scram_flgstat.c
rename to biology/iolib/files/patch-progs_scram__flagstat.c
--- a/biology/iolib/files/patch-progs__scram_flgstat.c
+++ b/biology/iolib/files/patch-progs_scram__flagstat.c
@@ -1,4 +1,4 @@
---- progs/scram_flagstat.c.orig
+--- progs/scram_flagstat.c.orig 2025-07-14 08:18:28 UTC
+++ progs/scram_flagstat.c
@@ -44,6 +44,7 @@
#include <assert.h>
@@ -6,5 +6,5 @@
#include <errno.h>
+#include <unistd.h>
- #if defined(__MINGW32__)
+ #if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__)
# include <getopt.h>
diff --git a/biology/iolib/files/patch-progs_scram__merge.c b/biology/iolib/files/patch-progs_scram__merge.c
new file mode 100644
--- /dev/null
+++ b/biology/iolib/files/patch-progs_scram__merge.c
@@ -0,0 +1,10 @@
+--- progs/scram_merge.c.orig 2025-07-14 08:18:28 UTC
++++ progs/scram_merge.c
+@@ -39,6 +39,7 @@
+ #include "io_lib_config.h"
+ #endif
+
++#include <unistd.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
diff --git a/biology/iolib/files/patch-progs_scram__test.c b/biology/iolib/files/patch-progs_scram__test.c
new file mode 100644
--- /dev/null
+++ b/biology/iolib/files/patch-progs_scram__test.c
@@ -0,0 +1,10 @@
+--- progs/scram_test.c.orig 2025-07-14 08:18:28 UTC
++++ progs/scram_test.c
+@@ -48,6 +48,7 @@
+ #include <assert.h>
+ #include <ctype.h>
+ #include <errno.h>
++#include <unistd.h>
+
+ #if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__)
+ # include <getopt.h>
diff --git a/biology/iolib/files/patch-progs_scramble.c b/biology/iolib/files/patch-progs_scramble.c
new file mode 100644
--- /dev/null
+++ b/biology/iolib/files/patch-progs_scramble.c
@@ -0,0 +1,10 @@
+--- progs/scramble.c.orig 2025-07-14 08:18:28 UTC
++++ progs/scramble.c
+@@ -39,6 +39,7 @@
+ #include "io_lib_config.h"
+ #endif
+
++#include <unistd.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -35,6 +35,15 @@
bin/srf_list
bin/trace_dump
bin/ztr_dump
+include/htscodecs/arith_dynamic.h
+include/htscodecs/fqzcomp_qual.h
+include/htscodecs/htscodecs.h
+include/htscodecs/pack.h
+include/htscodecs/rANS_static.h
+include/htscodecs/rANS_static4x16.h
+include/htscodecs/rle.h
+include/htscodecs/tokenise_name3.h
+include/htscodecs/varint.h
include/io_lib/Read.h
include/io_lib/abi.h
include/io_lib/alf.h
@@ -45,6 +54,7 @@
include/io_lib/compress.h
include/io_lib/compression.h
include/io_lib/cram.h
+include/io_lib/cram_bambam.h
include/io_lib/cram_codecs.h
include/io_lib/cram_decode.h
include/io_lib/cram_encode.h
@@ -58,7 +68,6 @@
include/io_lib/expFileIO.h
include/io_lib/fpoint.h
include/io_lib/hash_table.h
-include/io_lib/io_lib_config.h
include/io_lib/jenkins_lookup3.h
include/io_lib/mFILE.h
include/io_lib/mach-io.h
@@ -81,14 +90,16 @@
include/io_lib/thread_pool.h
include/io_lib/traceType.h
include/io_lib/translate.h
+include/io_lib/version.h
include/io_lib/vlen.h
include/io_lib/xalloc.h
include/io_lib/zfio.h
include/io_lib/ztr.h
+lib/libhtscodecs.a
lib/libstaden-read.a
lib/libstaden-read.so
-lib/libstaden-read.so.13
-lib/libstaden-read.so.13.0.0
+lib/libstaden-read.so.14
+lib/libstaden-read.so.14.1.4
share/man/man1/scramble.1.gz
share/man/man1/srf2fasta.1.gz
share/man/man1/srf2fastq.1.gz
diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile
--- a/biology/p5-Bio-SCF/Makefile
+++ b/biology/p5-Bio-SCF/Makefile
@@ -1,6 +1,6 @@
PORTNAME= Bio-SCF
PORTVERSION= 1.03
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= biology perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-

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