Isn't this what 'samtools idxstats <file>' does ? Can't remember, exactly.
- tom blackwell -
On Wed, 27 Jan 2016, Claudio Alberti wrote:
> Hello,
> I'm looking for a way to programmatically get the number of reads
> contained in a BAM file which are mapped on one of the used references.
> I'm currently using htslib and I'm wondering if any API is available to
> do that.
> Something like the output of
>
> samtools view chr1 | wc
>
> where I would pick the number of lines.
>
> Thank you!
> regards,
> Claudio
>
> --
> Claudio Alberti
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