Io_lib is a library of file reading and writing code to provide a

general purpose trace file (and Experiment File) reading interface.
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/

PR:		ports/138254
Submitted by:	Wen Heping <wenheping at gmail.com>

5 files changed, 107 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index bd5929869cc9..54316dd95a6d 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -37,6 +37,7 @@
     SUBDIR += gperiodic
     SUBDIR += grappa
     SUBDIR += hmmer
+    SUBDIR += iolib
     SUBDIR += jalview
     SUBDIR += kinemage
     SUBDIR += lagan
diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
new file mode 100644
index 000000000000..3d4bd68df207
--- /dev/null
+++ b/biology/iolib/Makefile
@@ -0,0 +1,32 @@
+# New ports collection makefile for:	io_lib
+# Date created:				27 Aug, 2009
+# Whom:					Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	io_lib
+PORTVERSION=	1.12.1
+CATEGORIES=	biology
+MASTER_SITES=	SF
+MASTER_SITE_SUBDIR=	staden/${PORTNAME}/${PORTVERSION}
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	A general purpose trace file(and Experiment File) reading interface
+
+USE_AUTOTOOLS=	libtool:22:env
+GNU_CONFIGURE=	yes
+USE_GMAKE=	yes
+USE_LDCONFIG=	yes
+
+MAN1=	srf_index_hash.1 srf_info.1 srf_list.1 illumina2srf.1 \
+	srf2fasta.1 srf2fastq.1
+MAN3=	read_scf_header.3 read_allocate.3 ExperimentFile.3 \
+	write_reading.3 write_scf.3 read_deallocate.3 \
+	fwrite_reading.3 read2scf.3 scf2read.3 \
+	fwrite_scf.3 write_scf_header.3 read_reading.3 \
+	read_scf.3 exp2read.3 fread_reading.3 \
+	read2exp.3 fread_scf.3
+MAN4=	Read.4
+
+.include <bsd.port.mk>
diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo
new file mode 100644
index 000000000000..9b7199e052b1
--- /dev/null
+++ b/biology/iolib/distinfo
@@ -0,0 +1,3 @@
+MD5 (io_lib-1.12.1.tar.gz) = f511698b766d5bd7d15a8269bdcddf84
+SHA256 (io_lib-1.12.1.tar.gz) = 732fc729662f380861e12fd9006a1a1c072f459589b6d2c49a7c01c88a9cdf01
+SIZE (io_lib-1.12.1.tar.gz) = 772314
diff --git a/biology/iolib/pkg-descr b/biology/iolib/pkg-descr
new file mode 100644
index 000000000000..209139cb3f3e
--- /dev/null
+++ b/biology/iolib/pkg-descr
@@ -0,0 +1,7 @@
+Io_lib is a library of file reading and writing code to provide a
+general purpose trace file (and Experiment File) reading interface.
+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/
diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
new file mode 100644
index 000000000000..e7cebf838a16
--- /dev/null
+++ b/biology/iolib/pkg-plist
@@ -0,0 +1,64 @@
+include/io_lib/Read.h
+include/io_lib/abi.h
+include/io_lib/alf.h
+include/io_lib/array.h
+include/io_lib/compress.h
+include/io_lib/compression.h
+include/io_lib/deflate_interlaced.h
+include/io_lib/error.h
+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
+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/scf.h
+include/io_lib/scf_extras.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/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/ztr.h
+bin/append_sff
+bin/convert_trace
+bin/extract_fastq
+bin/extract_qual
+bin/extract_seq
+bin/get_comment
+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/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.1
+@dirrm include/io_lib