public ValidationParser(PileupProcessorOptions options, MpileupResult result)
{
_options = options;
_parser = options.GetPileupItemParser(false);
_rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality);
_normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal);
_tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor);
_result = result;
}
public void TestParseInsertionDeletion()
{
var item = new PileupItemParser(0, 0, false, false, false, 3).GetValue(line);
Assert.IsNotNull(item);
Assert.AreEqual(11, item.Samples[0].Count);
//other base are equals to the TestParseNoInsertionDeletion
//The base from insertion
foreach (int i in new int[] { 6, 8 })
{
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][i].Strand);
Assert.AreEqual(AlignedEventType.INSERTION, item.Samples[0][i].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[0][i].Position);
Assert.AreEqual("+2AG", item.Samples[0][i].Event);
Assert.AreEqual(0, item.Samples[0][i].Score);
Assert.AreEqual(0, item.Samples[0][i].ReadMappingQuality);
}
//The base from deletion
foreach (int i in new int[] { 7, 9 })
{
Assert.AreEqual(StrandType.REVERSE, item.Samples[0][i].Strand);
Assert.AreEqual(AlignedEventType.DELETION, item.Samples[0][i].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[0][i].Position);
Assert.AreEqual("-2TC", item.Samples[0][i].Event);
Assert.AreEqual(0, item.Samples[0][i].Score);
Assert.AreEqual(0, item.Samples[0][i].ReadMappingQuality);
}
}
public void TestErrorLine2()
{
var parser = new PileupItemParser(0, 0, true, true, false, 3);
var errorline = "4\t86101\tG\t47\t,+1c,+1c,+1c.+1C.+1C,+1c..+1C.+1C.+1C,+1c.+1C,+1c.+1C.+1C$.+1C.+1C,+1c.+1C.+1C.+1C,+1c.+1C.+1C.+1C.+1C.+1C.+1C.+1C.+1C.+1C.+1C,+1c.+1C.+1C.+1C.+1C,+1c,+1c,+1c.+1C,+1c,+1c,+1c.+1C.+1C^H,+1c\tBCDCDBDEECBCB?CCEDCECCC>?CA@3CCDACCC>>DBDAA?>@.\t37\t,+1c.+1C,+1c.+1C,+1c.+1C,+1c.+1C.+1C.+1C.+1C.+1C$,,.+1C.+1C.+1C.+1C.+1C.+1C.+1C.+1C.+1C,+1c.+1C,+1c,+1c,+1c,+1c,+1c,+1c.+1C,+1c,+1c,+1c,+1c.+1C\tDCC;>DDC?CD3DD<D5DA=;?DF??BCB<6E=546>";
var item = parser.GetValue(errorline);
Assert.AreEqual(2, item.Samples.Count);
}
public void TestErrorLine()
{
var parser = new PileupItemParser(0, 0, true, true, false, 3);
var errorline = "3\t383725\tT\t27\t....,.,..,.,..,,,........^S,^S,\tIFJI<EHGIHF>GIIHGEIIGH=D@GA\t0\t\t";
var item = parser.GetValue(errorline);
Assert.AreEqual(2, item.Samples.Count);
errorline = "2\t43639\tT\t0\t\t\t37\t<<<<<>><<<<<<><<<<<><<<<<<<<>,,..,,.,\tHHGHHGGDHHFEHEGC9HHBFEBCFHHHEHHHD6HHD";
item = parser.GetValue(errorline);
Assert.AreEqual(2, item.Samples.Count);
}
public void TestParseNoInsertionDeletion()
{
var item = new PileupItemParser(0, 0, true, false, false, 3).GetValue(line);
Assert.IsNotNull(item);
Assert.AreEqual(7, item.Samples[0].Count);
Assert.AreEqual("seq2", item.SequenceIdentifier);
Assert.AreEqual(156, item.Position);
Assert.AreEqual('A', item.Nucleotide);
Assert.AreEqual(2, item.Samples.Count);
Assert.AreEqual(7, item.Samples[0].Count);
Assert.AreEqual(4, item.Samples[1].Count);
//The matched base from end of read
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][0].Strand);
Assert.AreEqual(AlignedEventType.MATCH, item.Samples[0][0].EventType);
Assert.AreEqual(PositionType.END, item.Samples[0][0].Position);
Assert.AreEqual("A", item.Samples[0][0].Event);
Assert.AreEqual('<' - 33, item.Samples[0][0].Score);
Assert.AreEqual(0, item.Samples[0][0].ReadMappingQuality);
//The matched bases from forward strand read
foreach (int i in new int[] { 1, 3 })
{
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][i].Strand);
Assert.AreEqual(AlignedEventType.MATCH, item.Samples[0][i].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[0][i].Position);
Assert.AreEqual("A", item.Samples[0][i].Event);
Assert.AreEqual(0, item.Samples[0][i].ReadMappingQuality);
}
Assert.AreEqual('9' - 33, item.Samples[0][1].Score);
Assert.AreEqual('5' - 33, item.Samples[0][3].Score);
//The matched bases from reverse strand read
foreach (int i in new int[] { 2, 5 })
{
Assert.AreEqual(StrandType.REVERSE, item.Samples[0][i].Strand);
Assert.AreEqual(AlignedEventType.MATCH, item.Samples[0][i].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[0][i].Position);
Assert.AreEqual("A", item.Samples[0][i].Event);
Assert.AreEqual(0, item.Samples[0][i].ReadMappingQuality);
}
Assert.AreEqual('7' - 33, item.Samples[0][2].Score);
Assert.AreEqual(':' - 33, item.Samples[0][5].Score);
//The matched base from start of read
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][4].Strand);
Assert.AreEqual(AlignedEventType.MATCH, item.Samples[0][4].EventType);
Assert.AreEqual(PositionType.START, item.Samples[0][4].Position);
Assert.AreEqual("A", item.Samples[0][4].Event);
Assert.AreEqual(';' - 33, item.Samples[0][4].Score);
Assert.AreEqual('7' - 33, item.Samples[0][4].ReadMappingQuality);
//The insertions and deletions had been ignored
//The mismatched base
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][6].Strand);
Assert.AreEqual(AlignedEventType.MISMATCH, item.Samples[0][6].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[0][6].Position);
Assert.AreEqual("G", item.Samples[0][6].Event);
Assert.AreEqual('<' - 33, item.Samples[0][6].Score);
Assert.AreEqual(0, item.Samples[0][6].ReadMappingQuality);
//The matched bases from forward strand read
foreach (int i in new int[] { 0, 1, 2, 3 })
{
Assert.AreEqual(AlignedEventType.MATCH, item.Samples[1][i].EventType);
Assert.AreEqual(PositionType.MIDDLE, item.Samples[1][i].Position);
Assert.AreEqual("A", item.Samples[1][i].Event);
Assert.AreEqual(0, item.Samples[1][i].ReadMappingQuality);
Assert.AreEqual('<' - 33, item.Samples[1][i].Score);
}
Assert.AreEqual(StrandType.FORWARD, item.Samples[1][0].Strand);
Assert.AreEqual(StrandType.REVERSE, item.Samples[1][1].Strand);
Assert.AreEqual(StrandType.FORWARD, item.Samples[1][2].Strand);
Assert.AreEqual(StrandType.FORWARD, item.Samples[1][3].Strand);
//foreach (var ss in item.Samples[0])
//{
// Console.WriteLine("{0}\t{1}", ss.Base, ss.Score);
//}
}
public void TestParseFilterByBaseMappingQuality()
{
var item = new PileupItemParser(0, 25, true, true, false, 3).GetValue(line);
Assert.IsNotNull(item);
Assert.AreEqual(4, item.Samples[0].Count);
Assert.AreEqual(27, item.Samples[0][0].Score);
Assert.AreEqual("A", item.Samples[0][0].Event);
Assert.AreEqual(26, item.Samples[0][1].Score);
Assert.AreEqual("A", item.Samples[0][1].Event);
Assert.AreEqual(25, item.Samples[0][2].Score);
Assert.AreEqual("A", item.Samples[0][2].Event);
Assert.AreEqual(27, item.Samples[0][3].Score);
Assert.AreEqual("G", item.Samples[0][3].Event);
}
public void TestParseFilterByCount()
{
var item = new PileupItemParser(5, 0, false, false, false, 3).GetValue(line);
Assert.IsNull(item);
}