filter3

#!/usr/bin/env bash

# Usage:
#   zero_small.sh [-t threshold] [-z zero_value] [file]
#
# Examples:
#   zero_small.sh data.csv
#   cat data.csv | zero_small.sh
#   zero_small.sh -t 1e-30 -z 0 data.csv

THRESHOLD="1e-20"
ZERO_VAL="0.0"

while getopts "t:z:" opt; do
  case "$opt" in
    t) THRESHOLD="$OPTARG" ;;
    z) ZERO_VAL="$OPTARG" ;;
  esac
done
shift $((OPTIND - 1))

awk -F'~' -v OFS='~' -v thr="$THRESHOLD" -v zero="$ZERO_VAL" '
{
  for (i = 1; i <= NF; i++) {
    # numeric (incl scientific)
    if ($i ~ /^-?[0-9.]+([eE][-+]?[0-9]+)?$/) {
      val = $i + 0
      if (val != 0 && val < thr && val > -thr) {
        $i = zero
      }
    }
  }
  print
}
' "${1:-/dev/stdin}"