.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Tradis::FilterTags 3pm"
.TH Bio::Tradis::FilterTags 3pm "2020-01-11" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tradis::FilterTags \- Filter tags in a fastq file
.SH "VERSION"
.IX Header "VERSION"
version 1.4.5
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Reads in a fastq file with tradis tags already attached to the start of the sequence
Filters reads that contain the provided tag
Outputs a file *.tag.fastq unless an alternative outfile name is specified
.PP
.Vb 1
\&   use Bio::Tradis::FilterTags;
\&   
\&   my $pipeline = Bio::Tradis::FilterTags\->new(fastqfile => \*(Aqabc\*(Aq, tag => \*(Aqabc\*(Aq);
\&   $pipeline\->filter_tags();
.Ve
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.SS "Required"
.IX Subsection "Required"
.IP "\(bu" 4
\&\f(CW\*(C`fastqfile\*(C'\fR \- path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.
.IP "\(bu" 4
\&\f(CW\*(C`tag\*(C'\fR \- TraDIS tag to match
.SS "Optional"
.IX Subsection "Optional"
.IP "\(bu" 4
\&\f(CW\*(C`mismatch\*(C'\fR \- number of mismatches to allow when matching the tag. Default = 0
.IP "\(bu" 4
\&\f(CW\*(C`outfile\*(C'\fR \- output file name. Defaults to \f(CW\*(C`file.tag.fastq\*(C'\fR for an input file named \f(CW\*(C`file.fastq\*(C'\fR
.SH "METHODS"
.IX Header "METHODS"
\&\f(CW\*(C`filter_tags\*(C'\fR \- outputs all reads containing the provided tag to \f(CW\*(C`outfile\*(C'\fR
.SH "AUTHOR"
.IX Header "AUTHOR"
Carla Cummins <path\-help@sanger.ac.uk>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
.PP
This is free software, licensed under:
.PP
.Vb 1
\&  The GNU General Public License, Version 3, June 2007
.Ve