qualityTrimming

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## Quality Trimming of FASTQ Reads ##
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## Author: Thomas Girke
## Last update: May 30, 2016
## Usage of below function combined with preprocessReads form systemPipeR:
# qcTrim <- "qualityTrimming(fq, phred_cutoff=20, cutoff_occurrences=1, N_cutoff=1, minreadlength=100)"
# preprocessReads(args=args, Fct=qcTrim, batchsize=100000, overwrite=TRUE, compress=TRUE)

## Arguments: 
        ## phred_cutoff: min Phred score to trigger tail trimming 
        ## cutoff_occurences: min number of Phred score cutoff violations to trigger tail trimming
        ## N_cutoff: after tail trimming reads with >=N_cutoff Ns are entirely removed
        ## minreadlength: reads below the assigned length threshold are removed

qualityTrimming <- function(fq, phred_cutoff, cutoff_occurrences, N_cutoff, minreadlength) {
  	fq <- trimTails(fq, k=cutoff_occurrences, a=rawToChar(as.raw(phred_cutoff+33)), successive=FALSE)
  	fq <- fq[width(fq)>=minreadlength] # Read length filter
  	filter <- compose(nFilter(threshold=N_cutoff))
  	fq <- fq[filter(fq)]
  	return(fq)
}