Mercurial > repos > lldelisle > revertr2orientationinbam
comparison revertR2orientationInBam.sh @ 0:05aa21d39189 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
author | lldelisle |
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date | Wed, 19 Oct 2022 08:50:18 +0000 |
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-1:000000000000 | 0:05aa21d39189 |
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1 #!/bin/bash | |
2 | |
3 inputBam=$1 | |
4 outputBam=$2 | |
5 | |
6 samtools view -h "$inputBam" | awk -v OFS="\t" '{ | |
7 # Process only non header lines | |
8 if(!($1~/^@/)){ | |
9 # SAM flag is field 2 | |
10 n=$2 | |
11 # Change only the second in pair flag is 128 | |
12 d=128 | |
13 q=(n-n%d)/d+(n<0) | |
14 if(q%2==1){ | |
15 # Evaluate the strand reverse strand flag is 16 | |
16 d=16 | |
17 q=(n-n%d)/d+(n<0) | |
18 if(q%2==1){ | |
19 # It is reverse it is now forward | |
20 $2-=16 | |
21 }else{ | |
22 # It is forward it is now reverse | |
23 $2+=16 | |
24 } | |
25 } | |
26 } | |
27 print | |
28 }' | samtools view -b - > "$outputBam" |