Bio::Tradis::Parser::Bam(3pm) | User Contributed Perl Documentation | Bio::Tradis::Parser::Bam(3pm) |
Bio::Tradis::Parser::Bam - Very basic BAM parser. Limited functionality.
version 1.4.5
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.
Carla Cummins <path-help@sanger.ac.uk>
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
2020-01-11 | perl v5.30.0 |