extractCoverageFromVcf fixed version

[shajoezhu]

extractCoverageFromVcf<-function (vcfName, ADFieldIndex = 2) 
{
    h <- function(w) {
        if (any(grepl("gzfile connection", w))) 
            invokeRestart("muffleWarning")
    }
    gzf = gzfile(vcfFile, open = "rb")
    skipNum = 0
    line = withCallingHandlers(readLines(gzf, n = 1), warning = h)
    while (length(line) > 0) {
        if (grepl("##", line)) {
            skipNum = skipNum + 1
        }
        else {
            break
        }
        line = withCallingHandlers(readLines(gzf, n = 1), warning = h)
    }
    close(gzf)
    vcf = read.table(gzfile(vcfName), skip = skipNum, header = T, 
        comment.char = "", stringsAsFactors = FALSE, check.names = FALSE)
    sampleName = names(vcf)[10]
    tmp = vcf[[sampleName]]
    field = strsplit(as.character(tmp), ":")
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    tmpCov = strsplit(as.character(tmpCovStr), ",")
    indexOfCheckingCov.logic = (lapply(tmpCov,'length') != 2)
    chrom = vcf[,1]
    pos = vcf[,2]
    if ( sum(indexOfCheckingCov.logic) > 0 ){
        cat("Drop markers at", which(indexOfCheckingCov.logic),"\n")
        tmpCov = tmpCov[!indexOfCheckingCov.logic]
        chrom = chrom[!indexOfCheckingCov.logic]
        pos = pos[!indexOfCheckingCov.logic]
    }
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    return(data.frame(CHROM = chrom, POS = pos, refCount = refCount, 
        altCount = altCount))
}

[shajoezhu]

This is a hack to filter out the site that vcf sample field doesn't have the second field AD