\name{getFastq}
\alias{getFastq}
\title{Download fastq files associated with input SRA accessions from NCBI SRA ftp site }
\description{
This function will available download fastq files associated with input SRA accessions from NCBI SRA ftp site. 
}
\usage{
getFastq(in_acc, sra_con, destdir, makeDirectory = FALSE, method)
}
\arguments{
  \item{in_acc}{
character vector of SRA accessions and should be of same SRA data type, either one of SRA  submission, SRA study, SRA  sample, SRA  experiment and SRA  run
}
  \item{sra_con}{
Connection to the SRAmetadb SQLite database
}
  \item{destdir}{
Directory where downloaded fastq files are saved
}
  \item{makeDirectory}{
logical, TRUE or FALSE. If TRUE and baseDir does not exists, storedir will be created to save downloaded files, otherwise downloaded fastq files will be saved to current directory. 
}
  \item{method}{Character vector of length 1, passed to the identically
    named argument of \code{\link{download.file}}.}
}
\details{
The function will convert all input SRA accessions to SRA experiment and run accessions and then all available fastq files will be downloaded. Currently files are only downloaded from the NCBI SRA ftp site.
}
\author{
Jack Zhu <zhujack@mail.nih.gov>
}
\section{Warning }{
The size of fastq files in SRA could be very large and downloading multiple ones could take long time and quite some storage space	
}
\seealso{
\code{\link{getFastqInfo}}, \code{\link{listFastq}}
}
\examples{
if(file.exists('SRAmetadb.sqlite')) {

	library(SRAdb)
	sra_dbname <- 'SRAmetadb.sqlite'	
	sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
	
	## Download all available fastq files associated with "SRR000648" and "SRR000657" from NCBI SRA ftp site to current directory
	getFastq (in_acc=c("SRR000648","SRR000657"), sra_con=sra_con, destdir=getwd())

} else {
  	print("use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file and then rerun the example")
}
}