/// <summary>
/// writes the transcript to the binary writer
/// </summary>
public void Write(IExtendedBinaryWriter writer, Dictionary <IGene, int> geneIndices,
Dictionary <ITranscriptRegion, int> transcriptRegionIndices, Dictionary <IInterval, int> microRnaIndices,
Dictionary <string, int> peptideIndices)
{
// transcript
writer.WriteOpt(Chromosome.Index);
writer.WriteOpt(Start);
writer.WriteOpt(End);
// ReSharper disable once ImpureMethodCallOnReadonlyValueField
Id.Write(writer);
// gene
writer.WriteOpt(GetIndex(Gene, geneIndices));
// encoded data
var encoded = EncodedTranscriptData.GetEncodedTranscriptData(BioType, CdsStartNotFound, CdsEndNotFound,
Source, IsCanonical, SiftIndex != -1, PolyPhenIndex != -1, MicroRnas != null, RnaEdits != null,
Selenocysteines != null, TranscriptRegions != null, Translation != null, StartExonPhase);
encoded.Write(writer);
// transcript regions
if (encoded.HasTranscriptRegions)
{
WriteIndices(writer, TranscriptRegions, transcriptRegionIndices);
}
writer.WriteOpt(NumExons);
// protein function predictions
if (encoded.HasSift)
{
writer.WriteOpt(SiftIndex);
}
if (encoded.HasPolyPhen)
{
writer.WriteOpt(PolyPhenIndex);
}
// translation
if (encoded.HasTranslation)
{
// ReSharper disable once PossibleNullReferenceException
var peptideIndex = GetIndex(Translation.PeptideSeq, peptideIndices);
Translation.Write(writer, peptideIndex);
}
// attributes
if (encoded.HasMirnas)
{
WriteIndices(writer, MicroRnas, microRnaIndices);
}
if (encoded.HasRnaEdits)
{
WriteItems(writer, RnaEdits, (x, y) => x.Write(y));
}
if (encoded.HasSelenocysteines)
{
WriteItems(writer, Selenocysteines, (x, y) => y.WriteOpt(x));
}
}
public static ITranscript Read(BufferedBinaryReader reader,
IDictionary <ushort, IChromosome> chromosomeIndexDictionary, IGene[] cacheGenes,
ITranscriptRegion[] cacheTranscriptRegions, IInterval[] cacheMirnas, string[] cachePeptideSeqs)
{
// transcript
var referenceIndex = reader.ReadOptUInt16();
var start = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var id = CompactId.Read(reader);
// gene
var geneIndex = reader.ReadOptInt32();
var gene = cacheGenes[geneIndex];
// encoded data
var encoded = EncodedTranscriptData.Read(reader);
// transcript regions
var transcriptRegions = encoded.HasTranscriptRegions ? ReadIndices(reader, cacheTranscriptRegions) : null;
ushort numExons = reader.ReadOptUInt16();
// protein function predictions
int siftIndex = encoded.HasSift ? reader.ReadOptInt32() : -1;
int polyphenIndex = encoded.HasPolyPhen ? reader.ReadOptInt32() : -1;
// translation
var translation = encoded.HasTranslation ? DataStructures.Translation.Read(reader, cachePeptideSeqs) : null;
// attributes
var mirnas = encoded.HasMirnas ? ReadIndices(reader, cacheMirnas) : null;
var rnaEdits = encoded.HasRnaEdits ? ReadItems(reader, RnaEdit.Read) : null;
var selenocysteines = encoded.HasSelenocysteines ? ReadItems(reader, x => x.ReadOptInt32()) : null;
return(new Transcript(chromosomeIndexDictionary[referenceIndex], start, end, id, translation,
encoded.BioType, gene, ExonUtilities.GetTotalExonLength(transcriptRegions), encoded.StartExonPhase,
encoded.IsCanonical, transcriptRegions, numExons, mirnas, siftIndex, polyphenIndex,
encoded.TranscriptSource, encoded.CdsStartNotFound, encoded.CdsEndNotFound, selenocysteines, rnaEdits));
}