Rsamtools scanTabix segfault
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heinig • 0
@heinig-9313
Last seen 9.2 years ago
Germany

Hi,

I got a segfault when trying to retrieve data from a tabix indexed file using negative coordinate ranges (happened when resizing a range that was close to the chromosome boundary and then splitting it into smaller parts). I know this not not a sensible thing to do, however it should not cause a segmentation fault. Would it be possible to include a sanity check on the param object to prevent this and return an empty result instead?

Here is some code that should cause the problem with any tabix indexed file:

scanTabix("genotypes.txt.bgz", param=GRanges(seqnames=1, ranges=IRanges(-5, -1)))

Best, Matthias

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Rsamtools_1.16.1     Biostrings_2.32.1    XVector_0.4.0       
[4] GenomicRanges_1.16.4 GenomeInfoDb_1.0.2   IRanges_1.22.10     
[7] BiocGenerics_0.10.0 

loaded via a namespace (and not attached):
[1] bitops_1.0-5   stats4_3.1.2   zlibbioc_1.8.0

rsamtools software error • 834 views
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