biology/filter-fastq - The NetBSD Packages Collection

Filter reads from a FASTQ file

Filter reads from a FASTQ file using a list of identifiers.

Each entry in the input FASTQ file (or files) is checked against all
entries in the identifier list. Matches are included by default, or
excluded if the --invert flag is supplied. Paired-end files are kept
consistent (in order).

This is almost certainly not the most efficient way to implement this
filtering procedure. I tested a few different strategies and this one
seemed the fastest. Current timing with 16 processes is about 10
minutes per 1M paired reads with gzip'd input and output, depending on
the length of the identifier list to filter by.

usage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS]
                       [-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]

Build dependencies

pkgtools/cwrappers

Runtime dependencies

lang/python27 lang/python27

Binary packages

OSArchitectureVersion
NetBSD 8.0earmv7hffilter-fastq-0.0.0.20210527.tgz
NetBSD 8.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 8.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 8.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 8.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 8.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 8.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 8.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 8.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 8.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0aarch64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0aarch64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0aarch64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0alphafilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0alphafilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0alphafilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv6hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv6hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv6hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv7hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv7hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv7hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0earmv7hffilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0i386filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0mips64ebfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0mips64ebfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0mips64ebfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0powerpcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0sparc64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0sparc64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0sparc64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0sparcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0sparcfilter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz
NetBSD 9.0x86_64filter-fastq-0.0.0.20210527.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options

(none)

Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.


Problem reports, updates or suggestions for this package should be reported with send-pr.