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source(file = "./ClassDefine.R")
Obj <- new("ReadsCheck", list(panelBed = "./example/APL_panel.bed", bamDir = "./example"))
# 1. Merge the panel
Obj <- PanelMerge(Obj)
Obj <- PlotBedHist(Obj)
# 2. Deal with each bam file
for (loop in c(1:length(Obj@bamList))) {
print(loop)
if (Obj@status == 0) {
Obj <- ReadsDepth(Obj, test = T)
}
if (Obj@status == 1) {
Obj <- PlotCountFig(Obj)
}
if (Obj@status == 3) {
Obj <- SingleReadsSummary(Obj)
}
if (Obj@status == 7) {
Obj@status = 0
}
}
if (Obj@currBamNum == length(Obj@bamList) + 1) {
Obj <- AllReadsSummary(Obj)
}
# Obj <- ReadsDepth(Obj, test = T) Obj <- PanelMerge(Obj) Obj <- PlotCountFig(Obj) Obj <-
# PlotBedHist(Obj) Obj <- SingleReadsSummary(Obj) Obj <- AllReadsSummary(Obj)