options(stringsAsFactors=FALSE)
args <- commandArgs(T)
clipSupportFile <- args[1]
detailFile <- args[2]
species <- args[3]

flag <- 'Yes'
flagNo <- 'No'
bed <- read.table(clipSupportFile, sep = '\t')
clipSupport <- paste(bed[, 4], bed[, 2] + 1, bed[, 3], sep = '|')
details <- read.table(detailFile, sep = '\t')
rownames(details) <- paste(details[, 1], details[, 2], details[, 3], sep = '|')
if(species=="hg38"){
details[clipSupport, 7] <- flag
details[is.na(details[, 7]), 7] <- flagNo
details <- as.data.frame(details)
details <- details[order(details[, 7], details[, 4], details[, 5], details[, 6], decreasing = T),]
}else if(species=="mm10"){
details[clipSupport, 8] <- flag
details[is.na(details[, 8]), 8] <- flagNo
details <- as.data.frame(details)
details <- details[order(details[, 8], details[, 4], details[, 5], details[, 6],  details[, 7] , decreasing = T),]
}
# sort
write.table(details, file=detailFile, sep = '\t', quote = F, col.names = F, row.names = F)