.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH FASTAQ-FILTER "1" "December 2023" "fastaq_filter 3.17.0" "User Commands"
.SH NAME
fastaq_filter \- Filter sequences to get a subset of them
.SH DESCRIPTION
usage: fastaq_filter [options] <infile> <outfile>
.PP
Filters a sequence file by sequence length and/or by name matching a regular
expression
.SS "positional arguments:"
.TP
infile
Name of input file to be filtered
.TP
outfile
Name of output file
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-min_length\fR INT
Minimum length of sequence to keep [0]
.TP
\fB\-\-max_length\fR INT
Maximum length of sequence to keep [inf]
.TP
\fB\-\-regex\fR REGEX
If given, only reads with a name matching the regular
expression will be kept
.TP
\fB\-\-ids_file\fR FILENAME
If given, only reads whose ID is in th given file will
be used. One ID per line of file.
.TP
\fB\-v\fR, \fB\-\-invert\fR
Only keep sequences that do not match the filters
.SS "Mate file for read pairs options:"
.TP
\fB\-\-mate_in\fR FILENAME
Name of mates input file. If used, must also provide
\fB\-\-mate_out\fR
.TP
\fB\-\-mate_out\fR FILENAME
Name of mates output file
.TP
\fB\-\-both_mates_pass\fR
By default, if either mate passes filter, then both
reads output. Use this flag to require that both reads
of a pair pass the filter