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 Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
