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