git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128662 bc3139a8-67e5-0310-9ffc-ced21a209358
Wolfgang Kaisers authored on 13/04/2017 15:57:02
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## ## |
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+## Project : seqTools ## |
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+## Created : 26.August.2013 ## |
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+## Author : W. Kaisers ## |
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+## File : trimFastq.r ## |
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+## Content : Functions which work on fastq and fastq and write output ## |
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+## files: trimFastq, writeFai ## |
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+## ## |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## trimFastq: Trimming and discarding reads based on quality values |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+ |
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+trimFastq<-function(infile, outfile="keep.fq.gz", discard="disc.fq.gz", |
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+ qualDiscard=0, qualMask=0, fixTrimLeft=0, fixTrimRight=0, |
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+ qualTrimLeft=0, qualTrimRight=0, qualMaskValue=78, minSeqLen=0) |
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+{
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+ if(!is.character(infile)) |
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+ stop("'infile' must be a string.")
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+ |
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+ if(length(infile) != 1) |
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+ stop("'infile' must have length 1.")
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+ |
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+ if(!file.exists(infile)) |
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+ stop("File 'infile' not found.")
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+ |
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+ if(!is.character(outfile)) |
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+ stop("'outfile' must be character.")
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+ |
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+ if(!is.character(outfile)) |
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+ stop("'discard' (file) must be character.")
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+ |
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+ if(!is.character(discard)) |
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+ stop("'discard' must be character.")
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+ |
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+ if(!is.character(discard)) |
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+ stop("'discard' (file) must be character.")
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+ |
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+ if(!is.numeric(qualDiscard)) |
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+ stop("'qualDiscard' must be numeric.")
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+ |
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+ if(length(qualDiscard)!=1) |
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+ stop("'qualDiscard' must have length 1.")
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+ |
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+ qualDiscard<-as.integer(qualDiscard) |
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+ if( (qualDiscard < 0) || (qualDiscard > 93)) |
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+ stop("'qualDiscard' out of range.")
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+ |
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+ if(!is.numeric(qualMask)) |
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+ stop("'qualMask' must be numeric.")
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+ |
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+ if(length(qualMask) != 1) |
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+ stop("'qualMask' must have length 1.")
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+ |
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+ qualMask<-as.integer(qualMask) |
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+ if( (qualMask < 0) || (qualMask > 93) ) |
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+ stop("'qualMask' out of range.")
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+ |
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+ if(!is.numeric(fixTrimLeft)) |
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+ stop("'fixTrimLeft' must be numeric.")
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+ |
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+ if(length(fixTrimLeft) != 1) |
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+ stop("'fixTrimLeft' must have length 1.")
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+ |
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+ if( (fixTrimLeft < 0) || (fixTrimLeft > 100) ) |
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+ stop("'fixTrimLeft' out of range.")
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+ |
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+ if(!is.numeric(fixTrimRight)) |
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+ stop("'fixTrimRight' must be numeric.")
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+ |
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+ if(length(fixTrimRight) != 1) |
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+ stop("'fixTrimRight' must have length 1.")
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+ |
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+ if( (fixTrimRight < 0) || (fixTrimRight > 100) ) |
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+ stop("'fixTrimRight' out of range.")
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+ |
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+ if(!is.numeric(qualTrimLeft)) |
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+ stop("'qualTrimLeft' must be numeric.")
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+ |
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+ if(length(qualTrimLeft)!= 1) |
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+ stop("'qualTrimLeft' must have length 1.")
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+ qualTrimLeft<-as.integer(qualTrimLeft) |
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+ |
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+ if( (qualTrimLeft < 0) || (qualTrimLeft > 93) ) |
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+ stop("'qualTrimLeft' out of range.")
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+ |
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+ if(!is.numeric(qualTrimRight)) |
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+ stop("'qualTrimRight' must be numeric.")
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+ |
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+ if(length(qualTrimRight) != 1) |
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+ stop("'qualTrimRight' must have length 1.")
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+ qualTrimRight<-as.integer(qualTrimRight) |
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+ |
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+ if( (qualTrimRight < 0) || (qualTrimRight > 93) ) |
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+ stop("'qualTrimRight' out of range.")
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+ |
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+ if(!is.numeric(qualMaskValue)) |
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+ stop("'qualMaskValue' must be numeric.")
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+ |
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+ if(length(qualMaskValue) != 1) |
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+ stop("'qualMaskValue' must have length 1.")
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+ |
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+ if( (qualMaskValue < 0) || (qualMaskValue > 93) ) |
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+ stop("'qualMaskValue' out of range.")
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+ |
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+ if(!is.numeric(minSeqLen)) |
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+ stop("'minSeqLen' must be numeric.")
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+ |
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+ if(length(minSeqLen) != 1) |
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+ stop("'minSeqLen' must have length 1.")
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+ |
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+ if( (minSeqLen < 0) || (minSeqLen > 200) ) |
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+ stop("'minSeqLen' out of range.")
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+ |
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+ val<-as.integer(c( |
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+ fixTrimLeft, |
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+ fixTrimRight, |
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+ qualTrimLeft, |
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+ qualTrimRight, |
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+ qualDiscard, |
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+ qualMask, |
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+ qualMaskValue, |
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+ minSeqLen |
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+ )) |
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+ res<-.Call("trim_fastq", infile, val, c(outfile,discard))
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+ |
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+ bm <- Sys.localeconv()[7] |
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+ message("[trimFastq] ", format(res[1], width=11, big.mark=bm),
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+ " records written to outfile.") |
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+ message("[trimFastq] ", format(res[2], width=11, big.mark=bm),
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+ " records written to discard.") |
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+ return(invisible(res)) |
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+} |
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+ |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |
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+## END OF FILE |
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## |