/// <summary>
/// reads the transcript from the binary reader
/// </summary>
public static Transcript Read(ExtendedBinaryReader reader, Gene[] cacheGenes, SimpleInterval[] cacheIntrons,
SimpleInterval[] cacheMirnas, string[] cachePeptideSeqs)
{
// transcript
var referenceIndex = reader.ReadUInt16();
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 = new EncodedTranscriptData(reader.ReadUInt16(), reader.ReadByte());
// exons & introns
var introns = encoded.HasIntrons ? ReadIndices(reader, cacheIntrons) : null;
var cdnaMaps = encoded.HasCdnaMaps ? ReadCdnaMaps(reader) : null;
// protein function predictions
int siftIndex = encoded.HasSift ? reader.ReadOptInt32() : -1;
int polyphenIndex = encoded.HasPolyPhen ? reader.ReadOptInt32() : -1;
// translation
var translation = encoded.HasTranslation ? Translation.Read(reader, cachePeptideSeqs) : null;
// attributes
var mirnas = encoded.HasMirnas ? ReadIndices(reader, cacheMirnas) : null;
return(new Transcript(referenceIndex, start, end, id, encoded.Version, translation, encoded.BioType,
gene, TranscriptUtilities.GetTotalExonLength(cdnaMaps), encoded.StartExonPhase, encoded.IsCanonical,
introns, mirnas, cdnaMaps, siftIndex, polyphenIndex, encoded.TranscriptSource));
}
/// <summary>
/// reads the translation from the binary writer
/// </summary>
public static Translation Read(ExtendedBinaryReader reader, string[] peptideSeqs)
{
var codingRegion = CdnaCoordinateMap.Read(reader);
var proteinId = CompactId.Read(reader);
var proteinVersion = reader.ReadByte();
var peptideIndex = reader.ReadOptInt32();
return(new Translation(codingRegion, proteinId, proteinVersion, peptideSeqs[peptideIndex]));
}
/// <summary>
/// reads the regulatory element data from the binary reader
/// </summary>
public static RegulatoryElement Read(ExtendedBinaryReader reader)
{
var referenceIndex = reader.ReadUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
var type = (RegulatoryElementType)reader.ReadByte();
var id = CompactId.Read(reader);
return(new RegulatoryElement(referenceIndex, start, end, id, type));
}
/// <summary>
/// reads the gene data from the binary reader
/// </summary>
public static Gene Read(ExtendedBinaryReader reader)
{
ushort referenceIndex = reader.ReadUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
bool onReverseStrand = reader.ReadBoolean();
string symbol = reader.ReadAsciiString();
int hgncId = reader.ReadOptInt32();
var entrezId = CompactId.Read(reader);
var ensemblId = CompactId.Read(reader);
int mimNumber = reader.ReadOptInt32();
return(new Gene(referenceIndex, start, end, onReverseStrand, symbol, hgncId, entrezId, ensemblId, mimNumber));
}
