Maybe yes, but I don't need a scripted solution, but a C API to integrate my code. regards, Claudio
On 27/01/2016 16:21, Thomas W. Blackwell wrote: > > 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 >> ---------------------------------------------- >> http://gramm.epfl.ch >> EPFL SCI STI MM >> ELG 140 (ELG Building) >> Station 11 >> CH-1015 Lausanne - Switzerland >> Tel. +41 21 6936869 >> ---------------------------------------------- >> >> >> ------------------------------------------------------------------------------ >> >> >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> _______________________________________________ >> Samtools-help mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/samtools-help >> -- Claudio Alberti ---------------------------------------------- http://gramm.epfl.ch EPFL SCI STI MM ELG 140 (ELG Building) Station 11 CH-1015 Lausanne - Switzerland Tel. +41 21 6936869 ---------------------------------------------- ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
