/// <summary>
/// Calls the variants.
///
/// Should only be used internally as assumptions are made that the alignments are left-aligned and fulfill certain criteria.
/// </summary>
/// <returns>The variants.</returns>
/// <param name="refSeq">Reference seq.</param>
/// <param name="querySeq">Query seq.</param>
/// <param name="originallyReverseComplemented">If set to <c>true</c> the query sequence was originally reverse complemented. (this affects QV value scoring)</param>
internal static List <Variant> CallVariants(byte[] refSeq, BPandQV[] querySeq, bool originallyReverseComplemented)
{
if (originallyReverseComplemented)
{
AlignmentUtils.ReverseQVValuesForHomopolymers(querySeq);
}
List <Variant> variants = new List <Variant>();
// Now call variants.
var gap = DnaAlphabet.Instance.Gap;
int i = 0;
int refPos = 0;
int queryPos = 0;
while (i < refSeq.Length)
{
if (refSeq[i] == gap)
{
int len = AlignmentUtils.GetGapLength(i, refSeq);
var nextBasePos = (i + len);
// Should alway be true as we don't end in gaps
Debug.Assert(nextBasePos < refSeq.Length);
var hplenAndChar = determineHomoPolymerLength(nextBasePos, refSeq);
var bases = getBases(querySeq, i, len);
var newVariant = new IndelVariant(refPos - 1, len, bases, IndelType.Insertion,
hplenAndChar.Item2, hplenAndChar.Item1,
(i == 0 || (i + len + hplenAndChar.Item1) >= refSeq.Length));
newVariant.QV = querySeq[queryPos].QV;
variants.Add(newVariant);
i += len;
queryPos += len;
}
else if (querySeq[i].BP == gap)
{
int len = AlignmentUtils.GetGapLength(i, querySeq);
var bases = getBases(refSeq, i, len);
var hplenAndChar = determineHomoPolymerLength(i, refSeq);
var newVariant = new IndelVariant(refPos - 1, len, bases,
IndelType.Deletion, hplenAndChar.Item2,
hplenAndChar.Item1, (i == 0 || (i + len + hplenAndChar.Item1) >= refSeq.Length));
/* An insertion mutation occurs BEFORE pos, so normally we get the next base
* or the last one if it's a reverse complemented alignment. However, this is not true if
* it is a homopolymer because what would have been the previous position is the next position
* after left aligning and reversing the position of the QV value.
*
* Consider the following
* --*- -*--
* A-TA --> TA-T
* AGTA TACT
*
* However,
* --*-- --*--
* A-TTA ----> T-AAT
* ATTTA TAAAT
*
*/
if ((i + len) < querySeq.Length)
{
var qc_pos = originallyReverseComplemented ? i - 1 : i + len;
if (newVariant.InHomopolymer)
{
qc_pos = i + len;
}
newVariant.QV = querySeq[qc_pos].QV;
}
variants.Add(newVariant);
i += len;
refPos += len;
}
else
{
if (querySeq[i].BP != refSeq[i])
{
var newVariant = new SNPVariant(refPos, (char)querySeq[i].BP, (char)refSeq[i], (i == 0 || i == (refSeq.Length - 1)));
newVariant.QV = querySeq [queryPos].QV;
variants.Add(newVariant);
}
i++; refPos++; queryPos++;
}
}
return(variants);
}
/// <summary>
/// Calls the variants.
///
/// Should only be used internally as assumptions are made that the alignments are left-aligned and fulfill certain criteria.
/// </summary>
/// <returns>The variants.</returns>
/// <param name="refSeq">Reference seq.</param>
/// <param name="querySeq">Query seq.</param>
/// <param name="originallyReverseComplemented">If set to <c>true</c> the query sequence was originally reverse complemented. (this affects QV value scoring)</param>
internal static List<Variant> CallVariants(byte[] refSeq, BPandQV[] querySeq, bool originallyReverseComplemented)
{
if (originallyReverseComplemented) {
AlignmentUtils.ReverseQVValuesForHomopolymers (querySeq);
}
List<Variant> variants = new List<Variant>();
// Now call variants.
var gap = DnaAlphabet.Instance.Gap;
int i = 0;
int refPos = 0;
while( i < refSeq.Length)
{
if (refSeq[i] == gap)
{
int len = AlignmentUtils.GetGapLength(i, refSeq);
var nextBasePos = (i + len);
// Should alway be true as we don't end in gaps
Debug.Assert (nextBasePos < refSeq.Length);
var hplenAndChar = determineHomoPolymerLength (nextBasePos, refSeq);
var bases = getBases(querySeq, i, len);
var newVariant = new IndelVariant(refPos - 1, len, bases, IndelType.Insertion,
hplenAndChar.Item2, hplenAndChar.Item1,
(i == 0 || (i + len + hplenAndChar.Item1) >= refSeq.Length));
newVariant.QV = querySeq[i].QV;
variants.Add(newVariant);
i += len;
}
else if (querySeq[i].BP == gap)
{
int len = AlignmentUtils.GetGapLength(i, querySeq);
var bases = getBases(refSeq, i, len);
var hplenAndChar = determineHomoPolymerLength (i, refSeq);
var newVariant = new IndelVariant(refPos - 1, len, bases,
IndelType.Deletion, hplenAndChar.Item2,
hplenAndChar.Item1, (i == 0 || (i + len + hplenAndChar.Item1) >= refSeq.Length));
/* An insertion mutation occurs BEFORE pos, so normally we get the next base
* or the last one if it's a reverse complemented alignment. However, this is not true if
* it is a homopolymer because what would have been the previous position is the next position
* after left aligning and reversing the position of the QV value.
*
* Consider the following
* --*- -*--
* A-TA --> TA-T
* AGTA TACT
*
* However,
* --*-- --*--
* A-TTA ----> T-AAT
* ATTTA TAAAT
*
*/
if ((i + len ) < querySeq.Length) {
var qc_pos = originallyReverseComplemented ? i - 1 : i + len;
if (newVariant.InHomopolymer) {
qc_pos = i + len;
}
newVariant.QV = querySeq[qc_pos].QV;
}
variants.Add(newVariant);
i += len;
refPos += len;
}
else
{
if (querySeq[i].BP != refSeq[i])
{
var newVariant = new SNPVariant(refPos, (char) querySeq[i].BP, (char)refSeq[i], (i ==0 || i == (refSeq.Length -1)));
newVariant.QV = querySeq [i].QV;
variants.Add(newVariant);
}
i++; refPos++;
}
}
return variants;
}