public static IRnaEdit Read(BufferedBinaryReader reader)
{
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
string bases = reader.ReadAsciiString();
return(new RnaEdit(start, end, bases));
}
public static ICodingRegion Read(BufferedBinaryReader reader)
{
int genomicStart = reader.ReadOptInt32();
int genomicEnd = reader.ReadOptInt32();
int cdnaStart = reader.ReadOptInt32();
int cdnaEnd = reader.ReadOptInt32();
int length = reader.ReadOptInt32();
return(new CodingRegion(genomicStart, genomicEnd, cdnaStart, cdnaEnd, length));
}
public static ITranscriptRegion Read(BufferedBinaryReader reader)
{
TranscriptRegionType type = (TranscriptRegionType)reader.ReadByte();
ushort id = reader.ReadOptUInt16();
int genomicStart = reader.ReadOptInt32();
int genomicEnd = reader.ReadOptInt32();
int cdnaStart = reader.ReadOptInt32();
int cdnaEnd = reader.ReadOptInt32();
return(new TranscriptRegion(type, id, genomicStart, genomicEnd, cdnaStart, cdnaEnd));
}
public static ITranslation Read(BufferedBinaryReader reader, string[] peptideSeqs)
{
var codingRegion = DataStructures.CodingRegion.Read(reader);
var proteinId = CompactId.Read(reader);
var peptideIndex = reader.ReadOptInt32();
var peptideSeq = peptideIndex == -1 ? null : peptideSeqs[peptideIndex];
return(new Translation(codingRegion, proteinId, peptideSeq));
}
private static T[] ReadItems <T>(BufferedBinaryReader reader, Func <BufferedBinaryReader, T> readFunc)
{
int numItems = reader.ReadOptInt32();
var items = new T[numItems];
for (int i = 0; i < numItems; i++)
{
items[i] = readFunc(reader);
}
return(items);
}
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));
}