Bio::Tradis::Parser::Bam3pm

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.