[BioC] Rsamtools BAM File Opening Takes Long Time

[Dario Strbenac]

Hello,

I'm trying to open a connection to a BAM file and it takes 16 minutes just to open the connection.

Here is a small example :

library(Rsamtools)
fName <- "http://genomesavant.com/savant//data/examples/pulmonary.bam"
> system.time(file <- open(BamFile(fName)))
   user  system elapsed 
   0.09    0.02  989.95

There is a pulmonary.bam.bai file in the same server directory.

Does anyone else have web-accessible BAM files to test this out on ?

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
[1] Rsamtools_1.6.3     Biostrings_2.22.0   GenomicRanges_1.6.4 IRanges_1.12.5     
[5] RCurl_1.6-10.1      bitops_1.0-4.1     

loaded via a namespace (and not attached):
[1] BSgenome_1.22.0    rtracklayer_1.14.0 tools_2.14.0       XML_3.4-2.2       
[5] zlibbioc_1.0.0    

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