Hi again,
Seems the problematic entry had a negative QUAL (-2147480064), which
looks very suspicious. Need to go upstream and look for the source of that.
I have no idea why negative QUAL causes a segfault and whether it would
make sense with a more gracious exit. I have attached the problematic
entry, if you are want to test further.
Cheers,
Peter
On 05/27/2016 01:55 PM, Peter Johansson wrote:
Hi,
I get a segfault when I run 'bcftools stats'. Not sure if it's a bug or
incorrect input data. This is with bcftools 1.3.1 with htslib 1.3.1
The command is:
bcftools stats --fasta-ref /usr/local/share/genomes/human_g1k_v37.fasta
KI006.anno.vcf.gz
I get the backtrace below:
Program received signal SIGSEGV, Segmentation fault.
#0 0x00000000004109cc in do_indel_stats (reader=0x742a40, reader=0x742a40,
stats=0x711010, args=0x711010) at vcfstats.c:625
#1 do_vcf_stats (args=0x711010) at vcfstats.c:1067
#2 main_vcfstats (argc=<optimized out>, argv=<optimized out>)
at vcfstats.c:1583
#3 0x00007ffff7103b15 in __libc_start_main () from /lib64/libc.so.6
#4 0x000000000040ce81 in _start ()
Any idea how to track down the problem is welcome.
Thanks,
Peter
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GL000220.1 119477 . TTCTTTC T -2.14748e+09 PASS INDEL;AnnoRegion=intergenic;AnnoGene=NONE:NONE GT:PL:DP:AD 0/0:.,.,.:76:0,25,12,3,3,1,1,2,7,4,2,7,3,1,2,1,1,1 0/0:.,.,.:86:1,23,14,2,1,2,0,0,15,16,4,2,4,0,0,0,1,1
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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