48 lines
2.2 KiB
R
48 lines
2.2 KiB
R
calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, meanDepth, nReadsToPhase, L, Fm, Fs, FILE_NAME = NULL) {
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WINDOW_SIZES = 2:MAX_WINDOW_SIZE
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phaseProbsPositionWindow = matrix(data = NA, nrow=length(distances), ncol=length(WINDOW_SIZES))
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for (i in 1:length(distances)) {
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# Try to phase (i+1)-st position [relative to i] using varying window sizes:
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for (j in 1:length(WINDOW_SIZES)) {
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windowSize = WINDOW_SIZES[j]
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remainingSize = windowSize - 2 # exlcude i, i+1
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numOnLeft = i - 1
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numOnRight = (length(distances) + 1) - (i + 2) + 1
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if (numOnLeft <= numOnRight) {
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halfToUse = floor(remainingSize / 2) # skimp on the left [floor], and be generous with the right side
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useOnLeft = min(halfToUse, numOnLeft)
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useOnRight = min(remainingSize - useOnLeft, numOnRight)
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}
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else {
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halfToUse = ceiling(remainingSize / 2) # be generous with the right side [ceiling]
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useOnRight = min(halfToUse, numOnRight)
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useOnLeft = min(remainingSize - useOnRight, numOnLeft)
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}
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startInd = i - useOnLeft # go left from position i
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stopInd = i + 1 + useOnRight # go right from position i + 1
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usePositionRange = seq(from=startInd, to=stopInd, by=1)
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useDistancesRange = seq(from=startInd, to=stopInd-1, by=1) # since there are N-1 distances between N consecutive positions
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phaseIndex = which(usePositionRange == i+1)
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if (length(phaseIndex) != 1) stop("NO phaseIndex!")
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windowDistances = distances[useDistancesRange]
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print(paste("Try to phase position ", i+1, " [relative to ", i, "] using positions: (", paste(usePositionRange, collapse=", "), "), windowDistances= (", paste(windowDistances, collapse=", "), "), [phaseIndex= ", phaseIndex, ", i=", i, "]", sep=""))
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p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Fm, Fs)
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print(paste("phase prob: ", p, sep=""))
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phaseProbsPositionWindow[i, j] = p
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}
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if (!is.null(FILE_NAME)) {
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save(list = ls(all=TRUE), file = paste(FILE_NAME, ".RData", sep=""))
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}
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}
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list(phaseProbsPositionWindow=phaseProbsPositionWindow, WINDOW_SIZES=WINDOW_SIZES)
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}
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