/// <summary>
/// Initializes a new instance of the <see cref="Bio.Variant.IndelVariant"/> class.
/// </summary>
/// <param name="position">Position.</param>
/// <param name="length">Length.</param>
/// <param name="bases">Bases.</param>
/// <param name="insertionOrDeletion">Insertion or deletion.</param>
/// <param name="hpBase">Hp base.</param>
/// <param name="hpLengthInReference">Hp length in reference.</param>
/// <param name="atAlignmentEnd">If set to <c>true</c> at alignment end.</param>
public IndelVariant(int position, int length, string bases, IndelType insertionOrDeletion, char hpBase, int hpLengthInReference, bool atAlignmentEnd = false)
: base(position, atAlignmentEnd)
{
Type = VariantType.INDEL;
InsertionOrDeletion = insertionOrDeletion;
Length = length;
InsertedOrDeletedBases = bases;
HomopolymerBase = hpBase;
HomopolymerLengthInReference = hpLengthInReference;
}
public static void TestLeftAlignmentStep()
{
var refseq = "ACAATAAAAGCGCGCGCGCGTTACGTATAT--ATGGATAT";
var queryseq = "ACAATAA-AGC--GCGC--GTTACGTATATATATGGATAT";
var r = new Sequence(DnaAlphabet.Instance, refseq);
var q = new Sequence(DnaAlphabet.Instance, queryseq);
var aln = new PairwiseSequenceAlignment(r, q);
var pas = new PairwiseAlignedSequence();
pas.FirstSequence = r;
pas.SecondSequence = q;
aln.Add(pas);
var tpl = VariantCaller.LeftAlignIndelsAndCallVariants(aln, true);
// Check the left alignment
aln = tpl.Item1 as PairwiseSequenceAlignment;
var lar = aln.PairwiseAlignedSequences [0].FirstSequence.ConvertToString();
var laq = aln.PairwiseAlignedSequences [0].SecondSequence.ConvertToString();
var exprefseq = "ACAATAAAAGCGCGCGCGCGTTACG--TATATATGGATAT";
var expqueryseq = "ACAAT-AAA----GCGCGCGTTACGTATATATATGGATAT";
Assert.AreEqual(exprefseq, lar);
Assert.AreEqual(expqueryseq, laq);
// And it's hard, so we might as well check the variants
var variants = tpl.Item2;
Assert.AreEqual(3, variants.Count);
string[] bases = new string[] { "A", "GCGC", "TA" };
char[] hpbases = new char[] { 'A', 'G', 'T' };
bool[] inHp = new bool[] { true, false, false };
int[] lengths = new int[] { 1, 4, 2 };
int[] starts = new int[] { 4, 8, 24 };
IndelType[] types = new IndelType[] { IndelType.Deletion, IndelType.Deletion, IndelType.Insertion };
for (int i = 0; i < 3; i++)
{
Assert.AreEqual(VariantType.INDEL, variants [i].Type);
var vi = variants [i] as IndelVariant;
Assert.AreEqual(hpbases[i], vi.HomopolymerBase);
Assert.AreEqual(starts [i], vi.StartPosition);
Assert.AreEqual(lengths [i], vi.Length);
Assert.AreEqual(bases [i], vi.InsertedOrDeletedBases);
Assert.AreEqual(inHp [i], vi.InHomopolymer);
Assert.AreEqual(types [i], vi.InsertionOrDeletion);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="Bio.Variant.IndelVariant"/> class.
/// </summary>
/// <param name="position">Position.</param>
/// <param name="length">Length.</param>
/// <param name="bases">Bases.</param>
/// <param name="insertionOrDeletion">Insertion or deletion.</param>
/// <param name="hpBase">Hp base.</param>
/// <param name="hpLengthInReference">Hp length in reference.</param>
/// <param name="atAlignmentEnd">If set to <c>true</c> at alignment end.</param>
public IndelVariant(int position, int length, string bases, IndelType insertionOrDeletion, char hpBase, int hpLengthInReference, bool atAlignmentEnd = false)
: base (position, atAlignmentEnd)
{
Type = VariantType.INDEL;
InsertionOrDeletion = insertionOrDeletion;
Length = length;
InsertedOrDeletedBases = bases;
HomopolymerBase = hpBase;
HomopolymerLengthInReference = hpLengthInReference;
}
public static void TestLeftAlignmentStep() {
var refseq = "ACAATAAAAGCGCGCGCGCGTTACGTATAT--ATGGATAT";
var queryseq = "ACAATAA-AGC--GCGC--GTTACGTATATATATGGATAT";
var r = new Sequence (DnaAlphabet.Instance, refseq);
var q = new Sequence (DnaAlphabet.Instance, queryseq);
var aln = new PairwiseSequenceAlignment (r, q);
var pas = new PairwiseAlignedSequence ();
pas.FirstSequence = r;
pas.SecondSequence = q;
aln.Add (pas);
var tpl = VariantCaller.LeftAlignIndelsAndCallVariants (aln, true);
// Check the left alignment
aln = tpl.Item1 as PairwiseSequenceAlignment;
var lar = aln.PairwiseAlignedSequences [0].FirstSequence.ConvertToString();
var laq = aln.PairwiseAlignedSequences [0].SecondSequence.ConvertToString();
var exprefseq = "ACAATAAAAGCGCGCGCGCGTTACG--TATATATGGATAT";
var expqueryseq = "ACAAT-AAA----GCGCGCGTTACGTATATATATGGATAT";
Assert.AreEqual (exprefseq, lar);
Assert.AreEqual (expqueryseq, laq);
// And it's hard, so we might as well check the variants
var variants = tpl.Item2;
Assert.AreEqual (3, variants.Count);
string[] bases = new string[] { "A", "GCGC", "TA" };
char[] hpbases = new char[] { 'A', 'G', 'T' };
bool[] inHp = new bool[] { true, false, false };
int[] lengths = new int[] { 1, 4, 2 };
int[] starts = new int[] { 4, 8, 24 };
IndelType[] types = new IndelType[] { IndelType.Deletion, IndelType.Deletion, IndelType.Insertion };
for (int i = 0; i < 3; i++) {
Assert.AreEqual (VariantType.INDEL, variants [i].Type);
var vi = variants [i] as IndelVariant;
Assert.AreEqual (hpbases[i], vi.HomopolymerBase);
Assert.AreEqual (starts [i], vi.StartPosition);
Assert.AreEqual (lengths [i], vi.Length);
Assert.AreEqual (bases [i], vi.InsertedOrDeletedBases);
Assert.AreEqual (inHp [i], vi.InHomopolymer);
Assert.AreEqual (types [i], vi.InsertionOrDeletion);
}
}