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