[Bioc-sig-seq] scanBam Error

[Dario Strbenac]

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

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