Fix class "IntegerList.Bits".

The class that I added last week was not storing the correct values at all.
Added unit test "IntegerListTest"

pwiz_tools/Shared/CommonUtil/Collections/IntegerList.cs

@@ -76,16 +76,20 @@ public static ImmutableList<int> FromIntegers(IEnumerable<int> values)
         private class Bits : IntegerList
         {
             private readonly int _count;
-            private readonly BitVector32[] _bits;
+            private readonly int[] _bits;
 
             public Bits(int count, IEnumerable<bool> boolValues)
             {
                 _count = count;
-                _bits = new BitVector32[(count + 31) / 32];
+                _bits = new int[(count + 31) / 32];
                 int index = 0;
                 foreach (var boolValue in boolValues)
                 {
-                    _bits[index / 32][index % 32] = boolValue;
+                    if (boolValue)
+                    {
+                        _bits[index / 32] |= 1 << (index % 32);
+                    }
+                    index++;
                 }
             }
 
@@ -108,7 +112,8 @@ public override int this[int index]
                         throw new IndexOutOfRangeException();
                     }
 
-                    return _bits[index / 32][index % 32] ? 1 : 0;
+                    var mask = 1 << (index % 32);
+                    return 0 == (_bits[index / 32] & mask) ? 0 : 1;
                 }
             }
 

pwiz_tools/Skyline/Test/IntegerListTest.cs

@@ -0,0 +1,63 @@
+/*
+ * Original author: Nicholas Shulman <nicksh .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2025 University of Washington - Seattle, WA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+using System.Collections.Generic;
+using System.Linq;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using pwiz.Common.Collections;
+using pwiz.SkylineTestUtil;
+
+namespace pwiz.SkylineTest
+{
+    [TestClass]
+    public class IntegerListTest : AbstractUnitTest
+    {
+        [TestMethod]
+        public void TestIntegerListFromIntegers()
+        {
+            var bits = IntegerListFromIntegers(Enumerable.Repeat(0, 100).Concat(Enumerable.Repeat(1, 100)));
+            Assert.AreEqual("Bits", bits.GetType().Name);
+            var constantList = IntegerListFromIntegers(Enumerable.Repeat(1000, 100));
+            Assert.IsInstanceOfType(constantList, typeof(ConstantList<int>));
+            var bytes = IntegerListFromIntegers(Enumerable.Range(0, 255));
+            Assert.AreEqual("Bytes", bytes.GetType().Name);
+            var shorts = IntegerListFromIntegers(Enumerable.Range(0, 512));
+            Assert.AreEqual("Shorts", shorts.GetType().Name);
+            IntegerListFromIntegers(Enumerable.Range(99999, 100));
+        }
+
+        private ImmutableList<int> IntegerListFromIntegers(IEnumerable<int> values)
+        {
+            var list = values.ToList();
+            var intList = IntegerList.FromIntegers(list);
+            CollectionAssert.AreEqual(list, intList.ToList());
+            if (list.Count == 0)
+            {
+                Assert.AreSame(ImmutableList.Empty<int>(), intList);
+            }
+
+            if (list.Count > 1 && list.Distinct().Count() == 1)
+            {
+                Assert.IsInstanceOfType(intList, typeof(ConstantList<int>));
+            }
+
+            return intList;
+        }
+    }
+}

pwiz_tools/Skyline/Test/Test.csproj

@@ -175,6 +175,7 @@
     <Compile Include="ElibQuantifiableTransitionTest.cs" />
     <Compile Include="ErrorIfPersistentFilesDirModifiedTest.cs" />
     <Compile Include="FastaSequenceTest.cs" />
+    <Compile Include="IntegerListTest.cs" />
     <Compile Include="LocalizedHtmlTutorialsTest.cs" />
     <Compile Include="LibraryRankedSpectrumInfoTest.cs" />
     <Compile Include="MassListIonsTest.cs" />