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.\" ========================================================================
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.IX Title "Bio::Tradis::Parser::Bam 3pm"
.TH Bio::Tradis::Parser::Bam 3pm "2020-01-11" "perl v5.30.0" "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 \s-1BAM\s0 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 \s-1BAM\s0 header and returns a hash (keys are sequence ids, values are hash
refs with keys as tags (like \s-1LN\s0 and M5))
.PP
=next_read 
Moves _currentread to the next entry in the \s-1BAM.\s0 Returns 0 if \s-1EOF.\s0
.PP
=read_info 
Returns info from _currentread = hash reference with field name as key. 
Standard fields are named as per the \s-1SAM\s0 format specification:
1 : \s-1QNAME
2 : FLAG
3 : RNAME
4 : POS
5 : MAPQ
6 : CIGAR
7 : RNEXT
8 : PNEXT
9 : TLEN
10 : SEQ
11 : QUAL\s0
Additional fields will use their tag names.
Complete line is returned with key \s-1READ\s0
.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
.Ve