mhap2partial.sh

#!/usr/bin/env bash

awk '
  {printf "%d\t", $1 + 1} #Aiid
  {printf "%d\t", $2 + 1} #Biid
  {if ($5 == $9) {        # orient
    printf "f\t"
  } else {
    printf "r\t"
  }}
  {printf "%d\t", $6}     #Abgn
  {printf "%d\t", $7}     #Aend
  {if ($5 == $9) {        # orient
    {printf "%d\t", $10}    #Bbgn
    {printf "%d\t", $11}    #Bend
  } else {
    {printf "%d\t", $11}    #Bbgn
    {printf "%d\t", $10}    #Bend
  }}
  {printf "%f\t", (1-$3)/2}   #erate
  {printf "\n"}
'