private static void Main(string[] args)
{
#if DEBUG
var head1 = new FastQStreamReader("../Data/testfileR1.fastq");
var head2 = new FastQStreamReader("../Data/testfileR2.fastq");
#else
var head1 = new FastQStreamReader("../Data/SoilFenceLib-UNIS_S1_L001_R1_001.fastq");
var head2 = new FastQStreamReader("../Data/SoilFenceLib-UNIS_S1_L001_R2_001.fastq");
#endif
var heads = head1.Zip(head2, (h1, h2) => (Head1: h1, Head2: h2));
var barcodes = BarcodeDatabase.Load("../Data/forward_T_split_map.txt").Result;
var barcodeDict = barcodes.ToDictionary(b => b.BarcodeSequence, b => b);
var primers = barcodes.DistinctBy(b => b.LinkerPrimerSequence)
.Select(b => (new PrimerScanner(b.LinkerPrimerSequence, 1), new PrimerScanner(b.ReversePrimer, 1)))
.ToList();
var timer = new Stopwatch();
timer.Start();
var matches = 0;
var nomatch = 0;
var counter = 0;
var expectedMax = 8413098;
foreach (var head in heads)
//.Select(d => DNAUtil.FindPrimer(d.Head1, d.Head2, primers))
//.Where(m => m.valid))
{
if (!PrimerResult.TryFind(head.Head1, head.Head2, primers, out var value))
{
nomatch++;
continue;
}
counter++;
matches++;
if (counter % 250000 == 0)
{
Console.WriteLine(
$"[{counter * 1.0 / expectedMax:P}] {(matches + nomatch) / (timer.ElapsedMilliseconds / 1000.0)}s/sec");
}
Console.WriteLine(
$"Match: {value.ForwardMatch.Location}/{value.ForwardMatch.Errors} : {value.ReverseMatch.Location}/{value.ReverseMatch.Errors} : {(value.Reversed ? 1 : 0)} : {value.Forward.Header}");
}
timer.Stop();
Console.WriteLine($"Matches: {matches}\nNoMatch: {nomatch}");
Console.WriteLine(
$"Elapsed time: {timer.ElapsedMilliseconds / 1000.0}s, {(matches + nomatch) / (timer.ElapsedMilliseconds / 1000.0)}s/sec");
}
async static Task Main(string[] args)
{
#if DEBUG
var head1 = new FastQStreamReader("../Data/testfileR1.fastq");
var head2 = new FastQStreamReader("../Data/testfileR2.fastq");
#else
var head1 = new FastQStreamReader("../Data/SoilFenceLib-UNIS_S1_L001_R1_001.fastq");
var head2 = new FastQStreamReader("../Data/SoilFenceLib-UNIS_S1_L001_R2_001.fastq");
#endif
var heads = head1.Zip(head2, (h1, h2) => (Head1: h1, Head2: h2));
var barcodes = await BarcodeDatabase.Load("../Data/forward_T_split_map.txt");
var barcodeDict = barcodes.ToDictionary(b => b.BarcodeSequence, b => b);
var primers = barcodes.DistinctBy(b => b.LinkerPrimerSequence)
.Select(b => (new PrimerScanner(b.LinkerPrimerSequence, 1), new PrimerScanner(b.ReversePrimer, 1))).ToList();
var timer = new Stopwatch();
timer.Start();
int matches = 0;
int nomatch = 0;
int counter = 0;
int expectedMax = 8413098;
foreach (var value in heads
.Select(d => DNAUtil.FindPrimer(d.Head1, d.Head2, primers))
.Where(m => m.valid))
{
counter++;
if (counter % 250000 == 0)
{
Console.WriteLine($"[{(counter*1.0)/expectedMax:P}] {(matches+nomatch)/(timer.ElapsedMilliseconds / 1000.0)}s/sec");
}
if (value.valid)
{
//Console.WriteLine($"Matched primer {primer.Primer.Primer} on location {primer.Match.Location}.");
matches++;
}
else
{
//Console.WriteLine($"No match!");
nomatch++;
}
Console.WriteLine($"Match: {value.forwardMatch.Location}/{value.forwardMatch.Errors} : {value.reverseMatch.Location}/{value.reverseMatch.Errors} : {(value.hasBeenReversed ? 1 : 0)} : {value.forward.Header}");
}
timer.Stop();
Console.WriteLine($"Matches: {matches}\nNoMatch: {nomatch}");
Console.WriteLine($"Elapsed time: {timer.ElapsedMilliseconds/1000.0}s, {(matches+nomatch)/(timer.ElapsedMilliseconds / 1000.0)}s/sec");
}
