#!/bin/bash -norc

# Public domain notice for all NCBI EDirect scripts is located at:
# https://www.ncbi.nlm.nih.gov/books/NBK179288/#chapter6.Public_Domain_Notice

idx=0
lft=0
rgt=0
stp=0
std=""
scr=""
pfx=""
while IFS=$'\t' read tag val
do
  case "$tag" in
    index )
      idx="$val"
      ;;
    score )
      lft=0
      rgt=0
      scr="$val"
      pfx=""
      printf "\n${scr}\t${idx}\t"
      ;;
    start )
      lft="$val"
      rgt="$lft"
      ;;
    stop )
      stp="$val"
      ;;
    strand )
      std="$val"
      printf "${std}\t"
      ;;
    match )
      rgt=$((rgt + val))
      ;;
    mismatch )
      rgt=$((rgt + val))
      ;;
    genomic-ins )
      if [ "$val" -ge 30 ]
      then
        dec=$(( rgt - 1 ))
        printf "${pfx}${lft}..${dec}"
        lft=$((rgt + val))
        rgt="$lft"
        pfx=","
      else
        rgt=$((rgt + val))
      fi
      ;;
    product-ins )
      ;;
    end )
      dec=$(( rgt - 1 ))
      printf "${pfx}${lft}..${dec}\n"
      lft=0
      rgt=0
      pfx=""
      ;;
    * )
      ;;
  esac
done |
grep '.'
