6 files changed, 45 insertions, 15 deletions

diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
index 7bc6b647d5ec..1c3f7448614f 100644
--- a/biology/iolib/Makefile
+++ b/biology/iolib/Makefile
@@ -1,30 +1,25 @@
-# New ports collection makefile for:	io_lib
-# Date created:				27 Aug, 2009
-# Whom:					Wen Heping <wenheping@gmail.com>
-#
+# Created by: Wen Heping <wenheping@gmail.com>
 # $FreeBSD$
-#
 
 PORTNAME=	io_lib
-PORTVERSION=	1.12.5
+PORTVERSION=	1.13.0
 CATEGORIES=	biology
 MASTER_SITES=	SF
 MASTER_SITE_SUBDIR=	staden/${PORTNAME}/${PORTVERSION}
 
 MAINTAINER=	culot@FreeBSD.org
-COMMENT=	A general purpose trace file(and Experiment File) reading interface
-
-LIB_DEPENDS=	curl.6:${PORTSDIR}/ftp/curl
+COMMENT=	General purpose trace file (and Experiment File) reading interface
 
 LICENSE=	BSD
-LICENSE_FILE=	${WRKSRC}/COPYRIGHT
+
+LIB_DEPENDS=	curl:${PORTSDIR}/ftp/curl
 
 USE_AUTOTOOLS=	libtool:env
 GNU_CONFIGURE=	yes
 USE_GMAKE=	yes
 USE_LDCONFIG=	yes
 
-MAN1=	srf_index_hash.1 srf_info.1 srf_list.1 \
+MAN1=	scramble.1 srf_index_hash.1 srf_info.1 srf_list.1 \
 	srf2fasta.1 srf2fastq.1
 MAN3=	read_scf_header.3 read_allocate.3 ExperimentFile.3 \
 	write_reading.3 write_scf.3 read_deallocate.3 \
diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo
index bf17b63be865..0e6ad73d6d35 100644
--- a/biology/iolib/distinfo
+++ b/biology/iolib/distinfo
@@ -1,2 +1,2 @@
-SHA256 (io_lib-1.12.5.tar.gz) = 0bcecddaad5e94f1f9d2e9f2ae37e4303b6e8d0c9f6dabecb6bbebd6816fe80f
-SIZE (io_lib-1.12.5.tar.gz) = 782430
+SHA256 (io_lib-1.13.0.tar.gz) = c3e0106802bd1a4a41427304944bcf11b7a4dd249cf470454a35d30cde13db5c
+SIZE (io_lib-1.13.0.tar.gz) = 1522227
diff --git a/biology/iolib/files/patch-progs-scram__merge.c b/biology/iolib/files/patch-progs-scram__merge.c
new file mode 100644
index 000000000000..57689f0b785f
--- /dev/null
+++ b/biology/iolib/files/patch-progs-scram__merge.c
@@ -0,0 +1,7 @@
+--- 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
new file mode 100644
index 000000000000..ce81737b6117
--- /dev/null
+++ b/biology/iolib/files/patch-progs-scramble.c
@@ -0,0 +1,7 @@
+--- 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/pkg-descr b/biology/iolib/pkg-descr
index 209139cb3f3e..ed892b9484e5 100644
--- a/biology/iolib/pkg-descr
+++ b/biology/iolib/pkg-descr
@@ -4,4 +4,4 @@ The programmer simply calls the (eg) read_reading to create a "Read"
 C structure with the data loaded into memory. It has been compiled
 and tested on a variety of unix systems, MacOS X and MS Windows.
 
-WWW:	http://staden.sourceforge.net/
+WWW: http://staden.sourceforge.net/
diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
index 36c8fbe8ae66..640b15cb16af 100644
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -2,9 +2,18 @@ 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/compress.h
 include/io_lib/compression.h
+include/io_lib/cram.h
+include/io_lib/cram_codecs.h
+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_structs.h
 include/io_lib/deflate_interlaced.h
+include/io_lib/dstring.h
 include/io_lib/error.h
 include/io_lib/expFileIO.h
 include/io_lib/fpoint.h
@@ -13,26 +22,34 @@ include/io_lib/io_lib_config.h
 include/io_lib/jenkins_lookup3.h
 include/io_lib/mFILE.h
 include/io_lib/mach-io.h
+include/io_lib/md5.h
 include/io_lib/misc.h
 include/io_lib/open_trace_file.h
 include/io_lib/os.h
 include/io_lib/plain.h
 include/io_lib/pooled_alloc.h
+include/io_lib/sam_header.h
 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/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
@@ -45,9 +62,13 @@ 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
@@ -62,5 +83,5 @@ bin/ztr_dump
 lib/libstaden-read.a
 lib/libstaden-read.la
 lib/libstaden-read.so
-lib/libstaden-read.so.2
+lib/libstaden-read.so.3
 @dirrm include/io_lib