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
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