Comparing two n×m matrices I have to do a pairwise compare of a couple of text files. They have the following format:

id_1|errorcode_1|m|data_1_1|data_1_2|...|data_1_m
id_2|errorcode_2|m|data_2_1|data_2_2|...|data_2_m
  .
  .
  .
id_n|errorcode_n|m|data_n_1|data_n_2|...|data_n_m


The columns are ordered, but the rows can be in an arbitrary order. And there are always a couple of data-fields that have to be ignored.

This is my method that I call twice (switching the target and source array). It takes around 20 minutes to execute with two files where n = 16000 and m = 100.

private static string[] GetDifferences( IEnumerable&lt;string&gt; source  
                                      , IEnumerable&lt;string&gt; target  
                                      , IEnumerable&lt;int&gt; ignoredIndices)
{
    var uniqueInSource = new List&lt;string&gt;();

    foreach (var sourceLine in source)
    {
        var found = false;
        var sourceSplit = sourceLine.Split('|').ToList();

        // filter out malformed lines
        if (sourceSplit.Count &gt; 2 &amp;&amp; !int.TryParse(sourceSplit[2], out _))
        {
            continue;
        }

        foreach (var index in ignoredIndices)
        {
            sourceSplit.RemoveAt(index + 3);
        }

        foreach (var targetLine in source)
        {
            var targetSplit = targetLine.Split('|').ToList();

            if (targetSplit.Count &gt; 2 &amp;&amp; !int.TryParse(targetSplit[2], out _))
            {
                continue;
            }

            foreach (var index in ignoredIndices)
            {
                targetSplit.RemoveAt(index + 3);
            }

            if (targetSplit.SequenceEqual(sourceSplit))
            {
                found = true;
                break;
            }
        }

        if (!found)
        {
            uniqueInSource.Add(string.Join("|", sourceLine));
        }
    }

    return uniqueInSource.ToArray();
}


I feel that my approach might be too naive since I think it's somewhere around O(m*n2).
Your method is currently doing three things at a time and repeating the same logic multiple times:


parsing logs-1 (parsing a line)
parsing logs-2 (parsing a line again with the exact same code)
comparing both logs


It would be much easier to optimize and use it if you refactored it into  specialized structures/methods.



You put the first two cases into the static factory method Parse. It'll encapsulate the parsing part so you have implemented it only once. 

Then you need to encapsulate the equality. You do this by implementing the IEquatable&lt;LogLine&gt; interface. You should do this very carefuly because both the Equals and GetHashCode methods are important for the performance.

This new class can now be very easily tested for: equality, parsing and performance.

public class LogLine : IEquatable&lt;LogLine&gt;
{
    public string Errorcode { get; set; }

    public string[] Data { get; set; }

    // add other properties...

    public static LogLine Parse(string log, IEnumerable&lt;int&gt; ignoreColumns)
    {
        // implement parsing
    }

    public bool Equals(LogLine other)
    {
        // implement log equality
    }

    public override bool Equals(object obj)
    {
        return base.Equals(obj as LogLine);
    }

    public override int GetHashCode()
    {
        // implement log hash-code
    }
}


And that's it because you now have a very LINQ-friendly class that you can use like this where you can parse all lines with a simple Select:

// dummies
var logs1 = Enumerable.Empty&lt;string&gt;();
var logs2 = Enumerable.Empty&lt;string&gt;();
var ignoreColumns = Enumerable.Empty&lt;int&gt;();

var logLines1 = logs1.Select(l =&gt; LogLine.Parse(l, ignoreColumns));
var logLines2 = logs2.Select(l =&gt; LogLine.Parse(l, ignoreColumns));


And you can compare them however you like with Except or Intersect or use GroupBy or Distinct or whatever you want. If you use more then a single extension should call .ToList() after each parsing so that you don't parse them multiple times.