[BioC] 'Rsamtools' produces segfaults with XS tag

[Misha Kapushesky]

Hi,

I can add more detail to this - the same problem:

> library( "Rsamtools" )
...
> tags <- c("NM", "MD", "XA", "XS","NS")
> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam"
> and_bam = scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags))

*** caught segfault ***
address 0x2b3449beb8cd, cause 'invalid permissions'

Traceback:
1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param)
3: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))
4: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))

This error goes away if we don't include "XS" in tags, also if we use 
version 1.0.0 of Rsamtools. Any ideas?

The sessionInfo() output is below. Thanks in advance!

--Misha

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
[1] C

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

other attached packages:
[1] Rsamtools_1.1.11    Biostrings_2.16.9   GenomicRanges_1.0.7
[4] IRanges_1.6.11      svMisc_0.9-57       JavaGD_0.5-2
[7] rJava_0.8-4

loaded via a namespace (and not attached):
[1] Biobase_2.8.0


On Thu, 12 Aug 2010, Andrew Tikhonov wrote:

> Dear Biocore Team,
>
> 	We've got a problem where 'Rsamtools' produces segfaults and 
> core-dumps when reading a .bam file using the "XS" tag. We have a faulty .bam 
> and the list or R commands to reproduce it. Could you please point us to 
> someone who we may discuss this matter with and, if possible, fix the 
> problem.
>
> 	Thanks a lot in advance.
>
> Regards,
> Andrew
>
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