#!/usr/bin/env bash

#
# Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved
#
# Before downloading or accessing the software, please read carefully the
# License Agreement available at:
# https://github.com/milaboratory/mixcr/blob/develop/LICENSE
#
# By downloading or accessing the software, you accept and agree to be bound
# by the terms of the License Agreement. If you do not want to agree to the terms
# of the Licensing Agreement, you must not download or access the software.
#
# Start from BAM integration test

assert() {
  expected=$(echo -ne "${2:-}")
  result="$(eval 2>/dev/null $1)" || true
  result="$(sed -e 's/ *$//' -e 's/^ *//' <<<"$result")"
  if [[ "$result" == "$expected" ]]; then
    return
  fi
  result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")"
  [[ -z "$result" ]] && result="nothing" || result="\"$result\""
  [[ -z "$2" ]] && expected="nothing" || expected="\"$2\""
  echo "expected $expected got $result for" "$1"
  exit 1
}

set -euxo pipefail

mixcr analyze --verbose 10x-vdj-tcr-qc-test \
  --species hs \
  --assemble-contigs-by-cells \
  single_cell_vdj_t_subset_R1.fastq.gz \
  single_cell_vdj_t_subset_R2.fastq.gz \
  result

assert "grep 'Off target' result.qc.txt | wc -l" "1"
