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);