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

Browse Source 
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>
This commit is contained in:
Martin Wilke 2009-08-28 23:34:20 +00:00
parent 5aa6f9382f
commit 4afd96b25b
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=240487
5 changed files with 107 additions and 0 deletions
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1
biology/Makefile
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@ -37,6 +37,7 @@
SUBDIR += gperiodic
SUBDIR += grappa
SUBDIR += hmmer
SUBDIR += iolib
SUBDIR += jalview
SUBDIR += kinemage
SUBDIR += lagan

32
biology/iolib/Makefile Normal file
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@ -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>

3
biology/iolib/distinfo Normal file
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@ -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

7
biology/iolib/pkg-descr Normal file
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@ -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/

64
biology/iolib/pkg-plist Normal file
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@ -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