Got it, thanks (to both Johns)! Works fine if I don't specify the filename.
Derek On Tue, 7 Oct 2014, John Marshall wrote: > On 7 Oct 2014, at 00:08, Derek M. <[email protected]> > wrote: >> I've installed samtools-1.1 and htslib-1.1. >> [...] >> $ samtools index SRR794854.bam SRR794854.bai >> Samtools-htslib-API: bam_index_build2() not yet implemented >> Aborted (core dumped) > > bam_index_build2() is an entry point to the indexing code that lets you > specify the filename for the BAI file, and for boring reasons it doesn't yet > exist in the htslib version of the code [1]. Making an index with samtools's > default filename works fine however: > > $ samtools index SRR794854.bam > > followed by renaming it if other parts of your pipeline are wedded to the > other index filename convention: > > $ mv -f SRR794854.bam.bai SRR794854.bai > > Apologies for the inconvenience... we aim to re-enable specifying the > filename at some point, but the fix is somewhat invasive so hasn't bubbled to > the top of the priority list as yet. > > John > > [1] This is https://github.com/samtools/samtools/issues/199 > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
