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.

VERSION

       version 1.4.5

SYNOPSIS

       Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence
       and creates temporary SAM file, which is then converted to BAM

          use Bio::Tradis::AddTagsToSeq;

          my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc');
          $pipeline->add_tags_to_seq();

NAME

       Bio::Tradis::AddTagsToSeq

PARAMETERS

   Required
       "bamfile" - path to/name of file containing reads and tags

   Optional
       "outfile" - name to assign to output BAM. Defaults to "file.tr.bam" for an input file
       named "file.bam"

METHODS

       "add_tags_to_seq" - 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.

AUTHOR

       Carla Cummins <path-help@sanger.ac.uk>

COPYRIGHT AND LICENSE

       This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

       This is free software, licensed under:

         The GNU General Public License, Version 3, June 2007