[Bioc-sig-seq] scanBam Error

[Martin Morgan]

On 12/12/2010 08:00 PM, Dario Strbenac wrote:
> Hello,
> 

> I'm having trouble reading in a BAM file when "seq" is one of the
strings passed to the what argument of ScanBamParam. If it's not, then
the the reading completes successfully. I don't understand what the
error means. It is :
> 
> Error in .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) : 
>   INTEGER() can only be applied to a 'integer', not a 'closure'
> 
> The traceback is :
> 
>> traceback()
> 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
> 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param)
> 2: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE), 
>        param = ScanBamParam(reverseComplement = TRUE, what = c("rname", 
>            "strand", "pos", "seq")))
> 1: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE), 
>        param = ScanBamParam(reverseComplement = TRUE, what = c("rname", 
>            "strand", "pos", "seq")))
> 
> and the environment is :
> 
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252    
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] Rsamtools_1.2.1     Biostrings_2.18.0   GenomicRanges_1.2.0 IRanges_1.8.2      
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0

Hi Dario -- this is some kind of error in Rsamtools' C code, but I'm not
able to reproduce it on my end so can't track it down. Is there any way
of producing and sharing with me an example file that has this problem?

One thing (not causing the bug) in your traceback is that 'flag' should
be an argument to ScanBamParam; as it is I think it is being silently
ignored.

Martin

> 
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
> 
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