Mercurial > repos > ldelisle > revertr2orientationinbam

annotate revertR2orientationInBam.sh @ 1:2c86ad672f52 draft default tip

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planemo upload commit 89aa8abdc88aa922cab8d9c5f17078ba1e388339-dirty
author ldelisle
date Wed, 19 Oct 2022 08:34:43 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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1 #!/bin/bash
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2
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3 inputBam=$1
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4 outputBam=$2
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5
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6 samtools view -h "$inputBam" | awk -v OFS="\t" '{
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7 # Process only non header lines
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8 if(!($1~/^@/)){
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9 # SAM flag is field 2
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10 n=$2
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11 # Change only the second in pair flag is 128
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12 d=128
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13 q=(n-n%d)/d+(n<0)
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14 if(q%2==1){
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15 # Evaluate the strand reverse strand flag is 16
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16 d=16
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17 q=(n-n%d)/d+(n<0)
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18 if(q%2==1){
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19 # It is reverse it is now forward
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20 $2-=16
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21 }else{
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22 # It is forward it is now reverse
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23 $2+=16
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24 }
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25 }
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26 }
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27 print
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28 }' | samtools view -b - > "$outputBam"