Hmm,

Very long CIGAR strings used to cause a crash, they ought now to be
caught and trigger an error:

https://github.com/samtools/samtools/pull/39

Peter

On Fri, Oct 31, 2014 at 12:38 PM, Nick Loman <n.j.lo...@bham.ac.uk> wrote:
> Latest build of samtools (1.1) mpileup core dumps with the following file
> (produced with latest BWA and samtools on nanopore data) in -g (BCF) or -v
> (VCF) mode, e.g..
>
> samtools mpileup -Q 0 -f NC_000913.fna -g Ecoli_R73_2D.bam
>
> I wonder if there is some kind of buffer overflow, e.g. with a long CIGAR
> string.
>
> The file is available here:
>
> http://pathogenomics.bham.ac.uk/filedist/nanopore/Ecoli_R73_2D.bam
>
> Any ideas anyone?
>
> GDB backtrace:
> #0  0x00007ffff6ec1bb9 in __GI_raise (sig=sig@entry=6) at
> ../nptl/sysdeps/unix/sysv/linux/raise.c:56
> #1  0x00007ffff6ec4fc8 in __GI_abort () at abort.c:89
> #2  0x0000000000459a1f in skip_aux (s=<optimised out>) at sam.c:1071
> #3  bam_aux_get (b=<optimised out>, tag=<optimised out>) at sam.c:1087
> #4  0x0000000000404e9b in group_smpl (ignore_rg=0, plp=0x6b8150,
> n_plp=0x6b8170, fn=0x7fffffffe350,
>     n=1, buf=0x7fffffffdc50, sm=0x6b8010, m=0x7fffffffdc30) at
> bam_plcmd.c:198
> #5  mpileup (conf=<optimised out>, n=1, fn=0x7fffffffe350) at
> bam_plcmd.c:451
> #6  0x000000000040779c in bam_mpileup (argc=<optimised out>, argv=<optimised
> out>)
>     at bam_plcmd.c:875
> #7  0x00007ffff6eacec5 in __libc_start_main (main=0x403af0 <main>, argc=8,
> argv=0x7fffffffe318,
>     init=<optimised out>, fini=<optimised out>, rtld_fini=<optimised out>,
> stack_end=0x7fffffffe308)
>     at libc-start.c:287
> #8  0x0000000000404051 in _start ()
>
> Cheers
>
>
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