ports/188863: biology/iolib: Update to version 1.13.5

[KATO Tsuguru]

>Number:         188863
>Category:       ports
>Synopsis:       biology/iolib: Update to version 1.13.5
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Apr 21 18:10:02 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p8 i386
>Organization:
>Environment:
>Description:
- Update to version 1.13.5 

New file:
files/patch-progs__scram_flgstat.c

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/iolib/Makefile biology/iolib/Makefile
--- /usr/ports/biology/iolib/Makefile	2014-04-12 16:45:33.000000000 +0900
+++ biology/iolib/Makefile	2014-04-22 00:00:00.000000000 +0900
@@ -2,11 +2,9 @@
 # $FreeBSD: head/biology/iolib/Makefile 351071 2014-04-12 07:42:33Z culot $
 
 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 at FreeBSD.org
 COMMENT=	General purpose trace file (and Experiment File) reading interface
diff -urN /usr/ports/biology/iolib/distinfo biology/iolib/distinfo
--- /usr/ports/biology/iolib/distinfo	2013-11-06 22:05:39.000000000 +0900
+++ biology/iolib/distinfo	2014-04-22 00:00:00.000000000 +0900
@@ -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 -urN /usr/ports/biology/iolib/files/patch-progs__scram_flgstat.c biology/iolib/files/patch-progs__scram_flgstat.c
--- /usr/ports/biology/iolib/files/patch-progs__scram_flgstat.c	1970-01-01 09:00:00.000000000 +0900
+++ biology/iolib/files/patch-progs__scram_flgstat.c	2014-04-22 00:00:00.000000000 +0900
@@ -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 -urN /usr/ports/biology/iolib/pkg-plist biology/iolib/pkg-plist
--- /usr/ports/biology/iolib/pkg-plist	2014-01-21 17:34:34.000000000 +0900
+++ biology/iolib/pkg-plist	2014-04-22 00:00:00.000000000 +0900
@@ -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_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_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
>Release-Note:
>Audit-Trail:
>Unformatted: