- Update to version 1.13.5

PR:		188863
Submitted by:	ports fury

4 files changed, 52 insertions, 43 deletions

diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
index ab2c4669d2a9..abf954c6e5f5 100644
--- a/biology/iolib/Makefile
+++ b/biology/iolib/Makefile
@@ -2,11 +2,9 @@
 # $FreeBSD$
 
 PORTNAME=	io_lib
-PORTVERSION=	1.13.0
-PORTREVISION=	1
+PORTVERSION=	1.13.5
 CATEGORIES=	biology
-MASTER_SITES=	SF
-MASTER_SITE_SUBDIR=	staden/${PORTNAME}/${PORTVERSION}
+MASTER_SITES=	SF/staden/${PORTNAME}/${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	General purpose trace file (and Experiment File) reading interface
diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo
index 0e6ad73d6d35..3193aba5ed55 100644
--- a/biology/iolib/distinfo
+++ b/biology/iolib/distinfo
@@ -1,2 +1,2 @@
-SHA256 (io_lib-1.13.0.tar.gz) = c3e0106802bd1a4a41427304944bcf11b7a4dd249cf470454a35d30cde13db5c
-SIZE (io_lib-1.13.0.tar.gz) = 1522227
+SHA256 (io_lib-1.13.5.tar.gz) = 3e30f1e972d3d75c4efa54032ceca975cea9733ce1eef3982ee8a2b9f799ba56
+SIZE (io_lib-1.13.5.tar.gz) = 1808537
diff --git a/biology/iolib/files/patch-progs__scram_flgstat.c b/biology/iolib/files/patch-progs__scram_flgstat.c
new file mode 100644
index 000000000000..4b3919d2f3b4
--- /dev/null
+++ b/biology/iolib/files/patch-progs__scram_flgstat.c
@@ -0,0 +1,10 @@
+--- progs/scram_flagstat.c.orig
++++ progs/scram_flagstat.c
+@@ -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/pkg-plist b/biology/iolib/pkg-plist
index 66c175cb6c28..aa9a99fba0bf 100644
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -1,8 +1,43 @@
+bin/append_sff
+bin/convert_trace
+bin/cram_dump
+bin/cram_index
+bin/extract_fastq
+bin/extract_qual
+bin/extract_seq
+bin/get_comment
+bin/hash_exp
+bin/hash_extract
+bin/hash_list
+bin/hash_sff
+bin/hash_tar
+bin/index_tar
+bin/io_lib-config
+bin/makeSCF
+bin/scf_dump
+bin/scf_info
+bin/scf_update
+bin/scram_flagstat
+bin/scram_merge
+bin/scram_pileup
+bin/scramble
+bin/srf2fasta
+bin/srf2fastq
+bin/srf_dump_all
+bin/srf_extract_hash
+bin/srf_extract_linear
+bin/srf_filter
+bin/srf_index_hash
+bin/srf_info
+bin/srf_list
+bin/trace_dump
+bin/ztr_dump
 include/io_lib/Read.h
 include/io_lib/abi.h
 include/io_lib/alf.h
 include/io_lib/array.h
 include/io_lib/bam.h
+include/io_lib/binning.h
 include/io_lib/compress.h
 include/io_lib/compression.h
 include/io_lib/cram.h
@@ -11,6 +46,7 @@ include/io_lib/cram_decode.h
 include/io_lib/cram_encode.h
 include/io_lib/cram_index.h
 include/io_lib/cram_io.h
+include/io_lib/cram_stats.h
 include/io_lib/cram_structs.h
 include/io_lib/deflate_interlaced.h
 include/io_lib/dstring.h
@@ -33,57 +69,22 @@ include/io_lib/scf.h
 include/io_lib/scf_extras.h
 include/io_lib/scram.h
 include/io_lib/seqIOABI.h
-include/io_lib/seqIOCTF.h
 include/io_lib/sff.h
 include/io_lib/srf.h
 include/io_lib/stdio_hack.h
 include/io_lib/string_alloc.h
 include/io_lib/tar_format.h
+include/io_lib/thread_pool.h
 include/io_lib/traceType.h
 include/io_lib/translate.h
 include/io_lib/vlen.h
 include/io_lib/xalloc.h
 include/io_lib/zfio.h
 include/io_lib/ztr.h
-bin/append_sff
-bin/convert_trace
-bin/cram_dump
-bin/cram_index
-bin/cram_to_sam
-bin/extract_fastq
-bin/extract_qual
-bin/extract_seq
-bin/get_comment
-bin/hash_exp
-bin/hash_extract
-bin/hash_list
-bin/hash_sff
-bin/hash_tar
-bin/index_tar
-bin/io_lib-config
-bin/makeSCF
-bin/sam_convert
-bin/sam_to_cram
-bin/scf_dump
-bin/scf_info
-bin/scf_update
-bin/scram_merge
-bin/scramble
-bin/srf2fasta
-bin/srf2fastq
-bin/srf_dump_all
-bin/srf_extract_hash
-bin/srf_extract_linear
-bin/srf_filter
-bin/srf_index_hash
-bin/srf_info
-bin/srf_list
-bin/trace_dump
-bin/ztr_dump
 lib/libstaden-read.a
 lib/libstaden-read.la
 lib/libstaden-read.so
-lib/libstaden-read.so.3
+lib/libstaden-read.so.5
 man/man1/scramble.1.gz
 man/man1/srf2fasta.1.gz
 man/man1/srf2fastq.1.gz