Re: [Samtools-devel] samtools sort bug

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

Do you have some small example files that trigger the bug?

Many thanks,

Heng

On Tue, Dec 15, 2009 at 08:58:28PM +0000, Gerton Lunter wrote:
> Hi all,
> 
> There seems to be a bug in samtools sort.  In most examples I looked
> at the bulk of the data seems fine, but the last dozen or so lines
> are out of order.
> 
> In another example I found one out-of-order read within an otherwise
> sorted lot, again followed by a few dozen lines out of order.
> 
> See below for the output of:  samtools view SRR004781_PE.bam | awk
> '{print $3}' | uniq -c.  Note the two reads mapped to chromosome 1
> within the chromosome 7 reads.
> The bam file was sorted using "samtools sort -m 750000000".
> 
> Any ideas?
> Cheers
> 
> Gerton.
> 
> 
> 


> 

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