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3
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1 #!bin/bash
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2
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3 #purpose: shell script which performs the split option
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4 #author: Ziru Zhou
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5 #date: October, 2012
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6
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7 main()
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8 {
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9 output1="${1}"
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10 output2="${2}"
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11 input="${3}"
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12
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13 $(samtools view -H ${input} > tmp)
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14 linecount=$(samtools view ${input} | wc -l)
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15 half=$(((${linecount} + 1) / 2))
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16 samtools view ${input} | shuf | split -d -l ${half}
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17
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18 $(cat tmp x00 > x00h)
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19 $(cat tmp x01 > x01h)
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20 samtools view -bSo ${output1} x00h
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21 samtools view -bSo ${output2} x01h
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22
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23 rm tmp x00h x01h x00 x01
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24 }
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25 main "${@}"
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