Re: [Samtools-help] Indexing sam/bam files by read-names

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

No, at least samtools cannot do this. I heard Fred Long (I do not know if he is in the samtools-help list) has done similar things.

If your data are not huge, you may consider to import the entire SAM to SQLite.

Heng

On Feb 28, 2012, at 7:57 PM, Abhishek Pratap wrote:

> Hi Guys
> 
> 
> Just wondering if there is a way available to index bam files based on
> read names allowing for O(1) or O(log N) lookups later by read name.
> Something like this might already exist as part of the mate pairing
> step in BWA but I am not sure. Also  In my case the index should allow
> to keep multiple values of the keys as reads can map to multiple
> location.
> 
> I have asked similar questions on bioperl/biostar but may be I shud
> have first tried here.
> 
> Thanks!
> -Abhi
> 
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