[BioC] 'Rsamtools' produces segfaults with XS tag

[Misha Kapushesky]

Hi,

I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. 
After some more tinkering - it seems I can't reproduce this on my Mac, 
only on our Linux install. I also just noticed that the released version 
is 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps 
it's a version incompatibility and we managed to install ourselves 
something incompatible? If that's the case, we'll probably try to get a 
more standard install going, and hopefully the problem will go away...

--Misha

On Fri, 13 Aug 2010, Martin Morgan wrote:

> Thanks Misha for the additional hints; I looked at the code and couldn't
> see anything immediately wrong, but if you can provide a (minimal?)  bam
> file displaying the problem that would be helpful. Martin
>
> Misha Kapushesky <ostolop at ebi.ac.uk> writes:
>
>> 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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>>
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>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>