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Last data update: 2014.03.03

R: Multi-threaded Probabilistic Base Calling

ForkBatch

R Documentation

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,...)
## S4 method for signature 'RolexaRun'
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.

Author(s)

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef

References

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Rolexa)
Error in library(Rolexa) : there is no package called 'Rolexa'
Execution halted