Add integration tests for hictk balance

.github/workflows/codecov.yml

@@ -190,6 +190,7 @@ jobs:
 
       - name: Run integration tests
         run: |
+          test/scripts/hictk_balance.sh build/src/hictk/hictk hic_tools.jar
           test/scripts/hictk_dump_chroms.sh build/src/hictk/hictk
           test/scripts/hictk_dump_bins.sh build/src/hictk/hictk
           test/scripts/hictk_dump_resolutions.sh build/src/hictk/hictk

.github/workflows/macos-ci.yml

@@ -362,6 +362,10 @@ jobs:
           zstd -dcf binaries.tar.zst | tar -xf -
           tar -xf test/data/hictk_test_data.tar.xz
 
+      - name: Test hictk balance
+        run: |
+          test/scripts/hictk_balance.sh bin/hictk hic_tools.jar
+
       - name: Test hictk dump chroms
         run: |
           test/scripts/hictk_dump_chroms.sh bin/hictk

.github/workflows/ubuntu-ci.yml

@@ -415,6 +415,10 @@ jobs:
           zstd -dcf binaries.tar.zst | tar -xf -
           tar -xf test/data/hictk_test_data.tar.xz
 
+      - name: Test hictk balance
+        run: |
+          test/scripts/hictk_balance.sh bin/hictk hic_tools.jar
+
       - name: Test hictk dump chroms
         run: |
           test/scripts/hictk_dump_chroms.sh bin/hictk

test/scripts/hictk_balance.sh

@@ -0,0 +1,147 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+set -e
+set -o pipefail
+set -u
+
+echo "##################################"
+echo "#### hictk balance            ####"
+
+# readlink -f is not available on macos...
+function readlink_py {
+  set -eu
+  python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+}
+
+function check_files_exist {
+  set -eu
+  status=0
+  for f in "$@"; do
+    if [ ! -f "$f" ]; then
+      2>&1 echo "Unable to find test file \"$f\""
+      status=1
+    fi
+  done
+
+  return "$status"
+}
+
+function dump_interactions {
+  set -o pipefail
+  set -eu
+
+  hictk="$1"
+  resolution="$3"
+  f="$2"
+
+  if [[ "$f"  == *.hic ]]; then
+    weight=WEIGHT
+  else
+    weight=weight
+  fi
+
+  "$hictk" dump "$f"                \
+                --balance="$weight" \
+                --resolution        \
+                "$resolution"       |
+                cut -f 3
+}
+
+function absolute_error {
+  set -o pipefail
+  set -eu
+
+  f1="$1"
+  f2="$2"
+
+  # shellcheck disable=SC2016
+  cmd='function abs(v) {
+          return v < 0 ? -v : v
+       }
+       ($2!=$1 && abs($1 - $2) > 1.0e-5) { print $0 }
+       '
+
+  # Fail if the absolute error is > 1.0e-5
+  if paste "$f1" "$f2" | awk -F '\t' "$cmd" | grep . ; then
+    return 1
+  else
+    return 0
+  fi
+}
+
+function compare_matrices {
+  set -o pipefail
+  set -eu
+
+  hictk="$1"
+  resolution="$4"
+  f1="$2"
+  f2="$3"
+
+  2>&1 echo "Comparing $f1 with $f2..."
+  if absolute_error \
+      <(dump_interactions "$hictk" "$f1" "$resolution") \
+      <(dump_interactions "$hictk" "$f2" "$resolution"); then
+    2>&1 echo "Files are identical"
+    return 0
+  else
+    2>&1 echo "Files differ"
+    return 1
+  fi
+}
+
+export function readlink_py
+
+status=0
+
+if [ $# -ne 2 ]; then
+  2>&1 echo "Usage: $0 path_to_hictk juicer_tools.jar"
+  status=1
+fi
+
+hictk_bin="$1"
+juicer_tools_jar="$2"
+
+data_dir="$(readlink_py "$(dirname "$0")/../data/")"
+script_dir="$(readlink_py "$(dirname "$0")")"
+
+ref_cool="$data_dir/cooler/ENCFF993FGR.2500000.cool"
+ref_hic="$data_dir/hic/ENCFF993FGR.hic"
+
+export PATH="$PATH:$script_dir"
+
+if ! check_files_exist "$ref_cool" "$ref_hic" "$juicer_tools_jar"; then
+  exit 1
+fi
+
+outdir="$(mktemp -d -t hictk-tmp-XXXXXXXXXX)"
+trap 'rm -rf -- "$outdir"' EXIT
+
+cp "$ref_cool" "$ref_hic" "$outdir"
+
+"$hictk_bin" balance "$outdir/"*.cool -t $(nproc) --chunk-size=100 --mode=cis --force
+if ! compare_matrices "$hictk_bin" "$outdir/"*.cool "$ref_cool" 2500000; then
+  status=1
+fi
+
+"$hictk_bin" balance "$outdir/"*.hic -t $(nproc) --chunk-size=100 --mode=cis --force --juicer-tools-jar "$juicer_tools_jar"
+if ! compare_matrices "$hictk_bin" "$outdir/"*.hic "$ref_cool" 2500000; then
+  status=1
+fi
+
+"$hictk_bin" balance "$outdir/"*.cool -t $(nproc) --in-memory --mode=cis --force
+if ! compare_matrices "$hictk_bin" "$outdir/"*.cool "$ref_cool" 2500000; then
+  status=1
+fi
+
+if [ "$status" -eq 0 ]; then
+  printf '\n### PASS ###\n'
+else
+  printf '\n### FAIL ###\n'
+fi
+
+exit "$status"