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Forgot to pass correct parameters to calcPhasingProbsForWindowDistances() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4851 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-12-16 01:58:06 +00:00
parent 2b0dc8625c
commit a5e1854b3a
1 changed files with 2 additions and 2 deletions
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4
R/phasing/calcPhasingProbsForWindowDistances.R
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@ -1,4 +1,4 @@
calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, FILE_NAME = NULL) { calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, meanDepth, nReadsToPhase, L, Fm, Fs, FILE_NAME = NULL) {
WINDOW_SIZES = 2:MAX_WINDOW_SIZE WINDOW_SIZES = 2:MAX_WINDOW_SIZE
phaseProbsPositionWindow = matrix(data = NA, nrow=length(distances), ncol=length(WINDOW_SIZES)) phaseProbsPositionWindow = matrix(data = NA, nrow=length(distances), ncol=length(WINDOW_SIZES))
@ -33,7 +33,7 @@ calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, FILE_
windowDistances = distances[useDistancesRange] windowDistances = distances[useDistancesRange]
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="")) 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=""))
p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Im, Is) p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Fm, Fs)
print(paste("phase prob: ", p, sep="")) print(paste("phase prob: ", p, sep=""))
phaseProbsPositionWindow[i, j] = p phaseProbsPositionWindow[i, j] = p
} }