.\" 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::AddTagsToSeq 3pm"
.TH Bio::Tradis::AddTagsToSeq 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::AddTagsToSeq \- Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
.SH "VERSION"
.IX Header "VERSION"
version 1.4.5
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Bio::Tradis::AddTagsToSeq parses \s-1BAM\s0 files, adds given tags to the start of the sequence and creates temporary \s-1SAM\s0 file,
which is then converted to \s-1BAM\s0
.PP
.Vb 1
\&   use Bio::Tradis::AddTagsToSeq;
\&   
\&   my $pipeline = Bio::Tradis::AddTagsToSeq\->new(bamfile => \*(Aqabc\*(Aq);
\&   $pipeline\->add_tags_to_seq();
.Ve
.SH "NAME"
Bio::Tradis::AddTagsToSeq
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.SS "Required"
.IX Subsection "Required"
\&\f(CW\*(C`bamfile\*(C'\fR \- path to/name of file containing reads and tags
.SS "Optional"
.IX Subsection "Optional"
\&\f(CW\*(C`outfile\*(C'\fR \- name to assign to output \s-1BAM.\s0 Defaults to \f(CW\*(C`file.tr.bam\*(C'\fR for an input file named \f(CW\*(C`file.bam\*(C'\fR
.SH "METHODS"
.IX Header "METHODS"
\&\f(CW\*(C`add_tags_to_seq\*(C'\fR \- add TraDIS tags to reads. For unmapped reads, the tag
				  is added to the start of the read sequence and quality
				  strings. For reads where the flag indicates that it is
				  mapped and reverse complemented, the reverse complemented
				  tags are added to the end of the read strings.
				  This is because many conversion tools (e.g. picard) takes
				  the read orientation into account and will re-reverse the
				  mapped/rev comp reads during conversion, leaving all tags
				  in the correct orientation at the start of the sequences
				  in the resulting FastQ file.
.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