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August 29, 2015 14:08
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Convert ref format to BED format
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| perl -alne '@starts = split /,/,$F[9]; @ends = split /,/,$F[10]; @sizes = map {$ends[$_] - $starts[$_]} 0..($F[8]-1); @offsets = map {$_ - $F[4]} @starts; $" = ","; print "$F[2]\t$F[4]\t$F[5]\t$F[0]/$F[1]\t0\t$F[3]\t$F[6]\t$F[7]\t0,0,0\t$F[8]\t@sizes\t@offsets"' ref.txt > ref.bed |
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