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.IX Title "Bio::Tradis::Parser::Bam 3pm"
.TH Bio::Tradis::Parser::Bam 3pm 2024-01-25 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
Bio::Tradis::Parser::Bam \- Very basic BAM parser. Limited functionality.
.SH VERSION
.IX Header "VERSION"
version 1.4.5
.SH SYNOPSIS
.IX Header "SYNOPSIS"
Parses BAM files and gives access to basic info in them.
.PP
.Vb 1
\&   use Bio::Tradis::Parser::Bam;
\&   
\&   my $pipeline = Bio::Tradis::Parser::Bam\->new(file => \*(Aqabc\*(Aq);
\&   $pipeline\->read_info;
\&   $pipeline\->next_read;
\&   $pipeline\->seq_info;
\&   $pipeline\->is_mapped;
\&   $pipeline\->is_reverse;
.Ve
.PP
=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))
.PP
=next_read 
Moves _currentread to the next entry in the BAM. Returns 0 if EOF.
.PP
=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
.PP
=is_mapped 
Parses the flag for the current read and determines if mapped.
Returns 0 or 1.
.PP
=is_reverse 
Parses the flag for the current read and determines if reverse 
complemented. Returns 0 or 1.
.SH AUTHOR
.IX Header "AUTHOR"
Carla Cummins <path\-help@sanger.ac.uk>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
.PP
This is free software, licensed under:
.PP
.Vb 1
\&  The GNU General Public License, Version 3, June 2007
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