NAME

       Bio::Tradis::Parser::Bam - Very basic BAM parser. Limited functionality.

VERSION

       version 1.4.5

SYNOPSIS

       Parses BAM files and gives access to basic info in them.

          use Bio::Tradis::Parser::Bam;

          my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc');
          $pipeline->read_info;
          $pipeline->next_read;
          $pipeline->seq_info;
          $pipeline->is_mapped;
          $pipeline->is_reverse;

       =seq_info Reads BAM header and returns a hash (keys are sequence ids, values are hash refs
       with keys as tags (like LN and M5))

       =next_read Moves _currentread to the next entry in the BAM. Returns 0 if EOF.

       =read_info Returns info from _currentread = hash reference with field name as key.
       Standard fields are named as per the SAM format specification: 1 : QNAME 2 : FLAG 3 :
       RNAME 4 : POS 5 : MAPQ 6 : CIGAR 7 : RNEXT 8 : PNEXT 9 : TLEN 10 : SEQ 11 : QUAL
       Additional fields will use their tag names.  Complete line is returned with key READ

       =is_mapped Parses the flag for the current read and determines if mapped.  Returns 0 or 1.

       =is_reverse Parses the flag for the current read and determines if reverse complemented.
       Returns 0 or 1.

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