BSD Portsbiology/iolib 1.16.0 FreeBSD
General purpose trace file (and Experiment File) reading interface
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
4724b7df2a- License
- BSD3CLAUSE
- Categories
- biology
- Package size
- 332.0 KiB, 1436.1 KiB installed
Description
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/iolib | 1.16.0 |
| DragonFly | biology/iolib | 1.14.10_1 |
| HardenedBSD | biology/iolib | 1.16.0 |
| GhostBSD | biology/iolib | 1.16.0 |
Install
Binary package:
pkg install io_libFrom the ports tree:
cd /usr/ports/biology/iolib/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= io_lib>0:biology/iolib
LIB_DEPENDS= libstaden-read.so:biology/iolibPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 1.16.0 | 1.16.0 | 1.14.10 | 1.14.10_1 | 1.16.0 |
| FreeBSD:14:quarterly | 1.16.0 | 1.16.0 | n/a | 1.14.10_1 | 1.16.0 |
| FreeBSD:15:latest | 1.16.0 | 1.16.0 | n/a | 1.14.10_1 | 1.14.10_1 |
| FreeBSD:15:quarterly | 1.16.0 | 1.16.0 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.16.0 | 1.16.0 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 2
libcurl.so: ftp/curllibhts.so: biology/htslib
The full lists below include those, and their dependencies in turn.
Build dependencies 20
Run dependencies 12
Required by 2
Configuration
No options to configure.
- USES
- autoreconf gmake libtool localbase
- Service scripts
- none
- Conflicts with
- filters scramble
Files
Manual pages 24
- ExperimentFile(3)
- Read(4)
- exp2read(3)
- fread_reading(3)
- fread_scf(3)
- fwrite_reading(3)
- fwrite_scf(3)
- read2exp(3)
- read2scf(3)
- read_allocate(3)
- read_deallocate(3)
- read_reading(3)
- read_scf(3)
- read_scf_header(3)
- scf2read(3)
- scramble(1)
- srf2fasta(1)
- srf2fastq(1)
- srf_index_hash(1)
- srf_info(1)
- srf_list(1)
- write_reading(3)
- write_scf(3)
- write_scf_header(3)
pkg-plist 104
- bin/append_sff
- bin/convert_trace
- 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/scram_test
- 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/bgzip.h
- include/io_lib/binning.h
- include/io_lib/compress.h
- include/io_lib/compression.h
- include/io_lib/cram.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
- include/io_lib/hash_table.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/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/version.h
- include/io_lib/vlen.h
- include/io_lib/xalloc.h
- include/io_lib/zfio.h
- include/io_lib/ztr.h
- lib/libstaden-read.a
- lib/libstaden-read.so
- lib/libstaden-read.so.16
- lib/libstaden-read.so.16.0.0
- share/man/man1/scramble.1.gz
- share/man/man1/srf2fasta.1.gz
- share/man/man1/srf2fastq.1.gz
- share/man/man1/srf_index_hash.1.gz
- share/man/man1/srf_info.1.gz
- share/man/man1/srf_list.1.gz
- share/man/man3/ExperimentFile.3.gz
- share/man/man3/exp2read.3.gz
- share/man/man3/fread_reading.3.gz
- share/man/man3/fread_scf.3.gz
- share/man/man3/fwrite_reading.3.gz
- share/man/man3/fwrite_scf.3.gz
- share/man/man3/read2exp.3.gz
- share/man/man3/read2scf.3.gz
- share/man/man3/read_allocate.3.gz
- share/man/man3/read_deallocate.3.gz
- share/man/man3/read_reading.3.gz
- share/man/man3/read_scf.3.gz
- share/man/man3/read_scf_header.3.gz
- share/man/man3/scf2read.3.gz
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| io_lib-1.16.0.tar.gz | 3.644833e+06 | db18f5ad2cc0c9ec0df4f14664df29362315fed13d8053dc24d00ef11e87d02a |
Master sites 1
- https://github.com/jkbonfield/io_lib/releases/download/${DISTNAME:S/./-/g}/