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Re: De referencing

by poj (Curate)
on Jun 22, 2013 at 07:01 UTC ( #1040253=note: print w/ replies, xml ) Need Help??


in reply to De referencing

From the docs;

$alignment = $bam->read1() Read one alignment from the BAM file and return it as a Bio::DB::Bam:: +Alignment object.

You need to use the methods in Bio::DB::Bam::Alignment to access the information. For example

while (my $align = $bam->read1) { my $seqid = $align->seq_id; my $start = $align->start; my $end = $align->end; my $strand = $align->strand; my $ref_dna= $align->dna; }

poj


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