On 22 Aug 2016, at 21:15, Yuelin Zhu <[email protected]> wrote:
> I got Segmentation fault whenever doing bcftools index on the following file:
>
> http://gbnci-abcc.ncifcrf.gov/fileman/temp/1348518/geno.TRA.bcf
[...]
>
> $ bcftools index geno.TRA.bcf
> Segmentation fault
Thanks for the bug report. Your file contains a couple of records with a POS
field of 0:
chrUn_gl000237 0 TRA00075433 N [etc]
chrUn_gl000241 0 TRA00075451 N [etc]
and it is these that is causing bcftools index to crash. If I remove those two
records, the file can be indexed fine.
The VCF spec says that POS=0 indicates that the variant record is in a
telomere. Is it intentional that there are a couple of telomeric entries in
your file, or is this perhaps a bug or artefact of the analysis program in use?
In any case, (1) bcftools index shouldn't crash and (2) if POS=0 is meaningful
and valid in VCF/BCF files, bcftools needs to handle it. So we'll fix this,
and thanks again for the bug report [1].
John
[1] Which I've filed as https://github.com/samtools/htslib/issues/406
--
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.
------------------------------------------------------------------------------
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
