#!/bin/bash

set -e

INPUT=testdata/four_reads.pe.fastq;
reads_not_trimmed=$(./target/debug/fasten_trim < $INPUT )
original_reads=$(cat $INPUT)
if [ "$reads_not_trimmed" != "$original_reads" ]; then
  echo "ERROR running fasten_trim with no trimming options, ie not trimming and keeping output the same as input."
  exit 1
fi

onebase=$(./target/debug/fasten_trim --first-base 3 --last-base 4 < testdata/four_reads.pe.fastq | perl -lane 'print if($i++ % 4 == 1);' |awk 'NR > 1 { printf "_"; } { printf $1; } END { printf "\n"; }')
shouldbe="T_T_G_A_C_A_C_A"
if [ "$onebase" != "$shouldbe" ]; then
  echo "ERROR trimming to the third base"
  exit 1
fi

last_read_length=$(./target/debug/fasten_trim --first-base 53 < testdata/four_reads.pe.fastq | ./target/debug/fasten_metrics --each-read | tail -n 1 | cut -f 2)
if [ "$last_read_length" -ne 47 ]; then
  echo "ERROR trimming to the last 47 bp of the reads"
  exit 1
fi

echo "$0 passed";