public override void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants)
{
var aligned = aln==null ? "FALSE" : "TRUE";
var end = String.Join (",", read.MutationsTested.ToString (), read.MutationsApplied.ToString (),
read.ProcessingTimeMS.ToString (), read.Barcode1.ToString(),
read.Barcode2.ToString ());
string start = String.Join (",", read.Movie, read.HoleNumber.ToString (),
read.SnrA.ToString (), read.SnrC.ToString (), read.SnrG.ToString (),
read.SnrT.ToString (), aligned, read.ReadQuality.ToString (),
read.AvgZscore.ToString (), read.Sequence.Count.ToString (), read.NumPasses.ToString (),
read.ReadCountSuccessfullyAdded.ToString(), read.ReadCountBadZscore.ToString(),
read.ReadCountAlphaBetaMismatch.ToString(),
read.ReadCountOther.ToString());
if (aln == null) {
start = start + ",NA,NA,NA,NA,NA,NA," + end;
} else {
var indels = variants.Count (z => z.Type == VariantType.INDEL);
var snps = variants.Count (z => z.Type == VariantType.SNP);
var total = variants.Count;
var length = aln.AlignedSAMSequence.RefEndPos - aln.AlignedSAMSequence.Pos;
start = start + "," + String.Join (",", length.ToString (), aln.AlignedSAMSequence.Pos, total.ToString (), indels.ToString (), snps.ToString (),
aln.AlignedSAMSequence.RName, end );
}
SW.WriteLine (start);
}
public override void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants)
{
if (variants == null) {
return;
}
foreach (var v in variants) {
incorrectCounts [v.QV]++;
if (v.Type == VariantType.SNP) {
snpErrorCounts [v.QV]++;
} else {
var id = v as IndelVariant;
if (id.InsertionOrDeletion == IndelType.Deletion) {
deletionErrorCounts [v.QV]++;
} else if (id.InsertionOrDeletion == IndelType.Insertion) {
insertionErrorCounts [v.QV]++;
}
}
}
var refseq = aln.AlignedRefSeq;
var qseq = aln.AlignedQuerySeq as QualitativeSequence;
for (int i = 0; i < refseq.Count; i++) {
if (refseq [i] == qseq [i]) {
correctCounts [qseq.GetQualityScore (i)]++;
}
}
}
public override void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants)
{
int i = 1;
foreach (var v in read.ZScores) {
var s = String.Join (",", read.Movie, read.HoleNumber, i.ToString (), v.ToString ());
SW.WriteLine (s);
i++;
}
}
public override void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants)
{
var prefix = String.Join (",",
read.Movie,
read.HoleNumber.ToString ());
SW.WriteLine (prefix + ",A," + read.SnrA);
SW.WriteLine (prefix + ",C," + read.SnrC);
SW.WriteLine (prefix + ",G," + read.SnrG);
SW.WriteLine (prefix + ",T," + read.SnrT);
}
public IEnumerable<ISequence> Parse(Stream stream)
{
FastQParser fqp = new FastQParser ();
foreach (var seq in fqp.Parse (stream)) {
var name = seq.ID;
var sp = name.Split ('/');
var movie = sp [0];
var hole = sp [1];
SAMAlignedSequence sam = new SAMAlignedSequence ();
sam.QuerySequence = seq;
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "sn", Value = "f,0,0,0,0" });
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "rs", Value = "f,0,0,0,0,0,0" });
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "zs", Value = "f,0,0,0,0,0,0" });
PacBioCCSRead read = new PacBioCCSRead (sam) {
AvgZscore = Single.NaN,
HoleNumber = Convert.ToInt32 (hole),
Movie = movie
};
yield return read;
}
}
public override void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants)
{
if (variants == null) {
return;
}
foreach (var v in variants) {
var common = String.Join (",", read.Movie, read.HoleNumber.ToString (), v.RefName,
v.StartPosition.ToString (), v.Length.ToString (), v.Type.ToString (), v.QV.ToString (), v.AtEndOfAlignment.ToString ());
var snp = v as SNPVariant;
string unique;
if (snp != null) {
unique = String.Join (",", snp.RefBP, snp.AltBP, "NA,NA,NA,NA,NA");
} else {
var indel = v as IndelVariant;
unique = string.Join (",", "NA,NA", indel.InsertionOrDeletion.ToString (),
indel.InHomopolymer.ToString (), indel.InsertedOrDeletedBases.ToString (),
indel.HomopolymerLengthInReference.ToString (), indel.HomopolymerBase);
}
SW.WriteLine (common + "," + unique);
}
}
public abstract void ConsumeCCSRead(PacBioCCSRead read, BWAPairwiseAlignment aln, List<Variant> variants);