--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam.sh	Wed Oct 19 08:34:43 2022 +0000
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+inputBam=$1
+outputBam=$2
+
+samtools view -h "$inputBam" | awk -v OFS="\t" '{
+    # Process only non header lines
+    if(!($1~/^@/)){
+        # SAM flag is field 2
+        n=$2
+        # Change only the second in pair flag is 128
+        d=128
+        q=(n-n%d)/d+(n<0)
+        if(q%2==1){
+            # Evaluate the strand reverse strand flag is 16
+            d=16
+            q=(n-n%d)/d+(n<0)
+            if(q%2==1){
+                # It is reverse it is now forward
+                $2-=16
+            }else{
+                # It is forward it is now reverse
+                $2+=16
+            }
+        }
+    }
+    print
+}' | samtools view -b - > "$outputBam"
\ No newline at end of file