[Bioc-sig-seq] Fastq File size limit in the Short Read Package

[Sirisha Sunkara]

Hi Martin,

Using the ShortRead package, for files > 6.5 Gb size, I seem to be 
running into this error using the readFastq function:

Error in .Call(.read_solexa_fastq, src, withIds) :
  negative length vectors are not allowed

If this is memory related - is there a work-around to working with the 
entire file?

Thank You,
Sirisha

 > sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
[1] C

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

other attached packages:
[1] ShortRead_1.4.0    lattice_0.17-26    BSgenome_1.14.2    
Biostrings_2.14.12
[5] IRanges_1.4.11   

loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1