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0
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 input.1 = args[1]
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4 input.2 = args[2]
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5
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6 fields.1 = args[3]
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7 fields.2 = args[4]
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8
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9 field.1 = args[5]
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10 field.2 = args[6]
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11
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12 output = args[7]
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13
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14 dat1 = read.table(input.1, header=T, sep="\t", quote="", stringsAsFactors=F, fill=T, row.names=NULL)
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15 if(fields.1 != "all"){
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16 fields.1 = unlist(strsplit(fields.1, ","))
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17 dat1 = dat1[,fields.1]
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18 }
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19 dat2 = read.table(input.2, header=T, sep="\t", quote="", stringsAsFactors=F, fill=T, row.names=NULL)
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20 if(fields.2 != "all"){
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21 fields.2 = unlist(strsplit(fields.2, ","))
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22 dat2 = dat2[,fields.2]
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23 }
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24
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25 dat3 = merge(dat1, dat2, by.x=field.1, by.y=field.2)
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26
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27 write.table(dat3, output, sep="\t",quote=F,row.names=F,col.names=T)
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