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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