/// <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>
/// constructor
/// </summary>
public Transcript(ushort referenceIndex, int start, int end, CompactId id, byte version,
Translation translation, BioType bioType, Gene gene, int totalExonLength, byte startExonPhase,
bool isCanonical, SimpleInterval[] introns, SimpleInterval[] microRnas, CdnaCoordinateMap[] cdnaMaps,
int siftIndex, int polyPhenIndex, TranscriptDataSource transcriptSource) : base(referenceIndex, start, end)
{
Id = id;
Version = version;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
Introns = introns;
MicroRnas = microRnas;
CdnaMaps = cdnaMaps;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
TranscriptSource = transcriptSource;
TotalExonLength = TranscriptUtilities.GetTotalExonLength(cdnaMaps);
}