Re: [Samtools-help] Rightmost position of alignment

[Heng Li <lh...@sa...>]

I am afraid that parsing the CIGAR is the only solution. In Perl, you
can do something like this:

@t = split("\t");
$_ = $t[5];
$end = $t[3]-1;
s/(\d+)[SMI]/$end+=$1/eg;
print $end, "\n";

Heng

On Mon, Jul 27, 2009 at 03:19:47PM +0100, Adam Reid wrote:
> Hi there,
> 
> Does anyone know of a simpler way to identify the rightmost position  
> of the alignment between
> the query and the reference than parsing the cigar string in a SAM/BAM  
> file?
> 
> Adam Reid
> 
> 
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-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.