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