Rolexa (version 1.28.0)

ForkBatch: Multi-threaded Probabilistic Base Calling

Description

Performs multi-threaded base calling on a collection of intensity files generated by the Solexa image analysis software

Usage

ForkBatch(run=Rolexa.env,path,outpath="./",prefix="rs_",nthreads=3,nfiles=2,lane=1,tiles=1:100,...)
"OneBatch"(run,path,lane,tiles,outpath,prefix)
OneBatch(run,...)

Arguments

run

a RolexaRun object defining the run parameters

path

a SolexaPath object defining providing the input paths

outpath

the path to the output directory

prefix

output file prefix, see SaveResults

nthreads

number of threads to use

nfiles

number of input files to concatenate in one batch

lane

the lane number to analyze

tiles

a subset of tiles to read

...

further arguments passed to the RolexaRun constructor

Details

The function ForkBatch runs through the list of input files, concatenates them by batches of nfiles, then calls OneBatch in each of the nthreads threads until all batches have been processed. Each batch results are passed to FilterResults and saved in an output file inside outpath.

References

Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431

See Also

CombineFastQ, CombineReads and SaveResults

Examples

path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
## Not run: 
# #This will take some time to complete:
# library(fork)
# ForkBatch(run=rolenv,path=path,tiles=1)
# ## End(Not run)