/// <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 void Write(IExtendedBinaryWriter writer)
{
writer.WriteOptAscii(Name);
writer.WriteOptAscii(Version);
writer.WriteOpt(ReleaseDateTicks);
writer.WriteOptAscii(Description);
}
public void Write(IExtendedBinaryWriter writer)
{
if (_currentNode != null)
{
_nodes.Add(_currentNode);
}
writer.WriteOptAscii(ReferenceSequence);
writer.WriteOpt(_nodes.Count);
foreach (var node in _nodes)
{
node.Write(writer);
}
writer.WriteOpt(_largeVariants.Count);
if (_largeVariants.Count == 0)
{
return;
}
foreach (var interval in _largeVariants.OrderBy(x => x.Begin).ThenBy(x => x.End))
{
WriteInterval(interval, writer);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.Write(KeyName);
writer.Write(VcfkeyName);
writer.Write(AltAllele);
byte flags = 0;
if (MatchByAllele)
{
flags |= 1;
}
if (IsArray)
{
flags |= 2;
}
writer.Write(flags);
writer.Write(VcfString);
writer.WriteOpt(JsonStrings.Length);
foreach (var jsonString in JsonStrings)
{
writer.Write(jsonString);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOptAscii(Id);
writer.WriteOptAscii(AnnotationType);
writer.WriteOptAscii(SaAltAllele);
writer.Write(IsPositional);
if (StringFields != null)
{
writer.WriteOpt(StringFields.Count);
foreach (var stringField in StringFields)
{
writer.WriteOptAscii(stringField.Key);
writer.WriteOptAscii(stringField.Value);
}
}
else
{
writer.WriteOpt(0);
}
if (BooleanFields != null)
{
writer.WriteOpt(BooleanFields.Count);
foreach (var booleanField in BooleanFields)
{
writer.WriteOptAscii(booleanField);
}
}
else
{
writer.WriteOpt(0);
}
}
private static void WriteIndices <T>(IExtendedBinaryWriter writer, T[] items, IReadOnlyDictionary <T, int> indices)
{
writer.WriteOpt(items.Length);
foreach (var item in items)
{
writer.WriteOpt(GetIndex(item, indices));
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.WriteOpt(CdnaStart);
writer.WriteOpt(CdnaEnd);
writer.WriteOpt(Length);
}
private static void WriteItems <T>(IExtendedBinaryWriter writer, T[] items, Action <T, IExtendedBinaryWriter> writeAction)
{
writer.WriteOpt(items.Length);
foreach (var item in items)
{
writeAction(item, writer);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.Write((byte)Type);
writer.WriteOpt(Id);
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.WriteOpt(CdnaStart);
writer.WriteOpt(CdnaEnd);
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOptAscii(GlobalMajorAllele);
writer.WriteOpt(DataSources.Length);
foreach (var dataSource in DataSources)
{
dataSource.Write(writer);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.Write(GeneName);
writer.WriteOpt(Annotations.Length);
for (int i = 0; i < Annotations.Length; i++)
{
Annotations[i].Write(writer);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOpt(Chromosome.Index);
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.Write((byte)Type);
// ReSharper disable once ImpureMethodCallOnReadonlyValueField
Id.Write(writer);
}
public void Write(IExtendedBinaryWriter writer)
{
writer.Write(DataSource);
writer.Write(IsArray);
writer.WriteOpt(JsonStrings.Length);
foreach (var jsonString in JsonStrings)
{
writer.Write(jsonString);
}
}
private void WriteMaskedEntries(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_maskedEntries.Length);
foreach (var maskedEntry in _maskedEntries)
{
writer.WriteOpt(maskedEntry.Begin);
writer.WriteOpt(maskedEntry.End);
}
}
private void WriteCytogeneticBands(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_cytogeneticBands.Length);
foreach (var band in _cytogeneticBands)
{
writer.WriteOpt(band.Begin);
writer.WriteOpt(band.End);
writer.WriteOptAscii(band.Name);
}
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOpt(Chromosome.Index);
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.Write(OnReverseStrand);
writer.WriteOptAscii(Symbol);
writer.WriteOpt(HgncId);
// ReSharper disable ImpureMethodCallOnReadonlyValueField
EntrezGeneId.Write(writer);
EnsemblId.Write(writer);
}
internal static void WriteItems <T>(IExtendedBinaryWriter writer, IReadOnlyCollection <T> items, Action <T> writeMethod)
{
if (items == null)
{
writer.WriteOpt(0);
}
else
{
writer.WriteOpt(items.Count);
foreach (var item in items)
{
writeMethod(item);
}
}
writer.Write(CacheConstants.GuardInt);
}
private void WriteBlockOffsets(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_blockPositions.Count);
int oldPosition = 0;
long oldBlockOffset = 0;
foreach (var offset in _blockPositions.OrderBy(x => x.Position))
{
int deltaPosition = offset.Position - oldPosition;
long deltaBlockOffset = offset.Offset - oldBlockOffset;
writer.WriteOpt(deltaPosition);
writer.WriteOpt(deltaBlockOffset);
oldPosition = offset.Position;
oldBlockOffset = offset.Offset;
}
}
/// <summary>
/// writes the cytogenetic bands to the file
/// </summary>
public void Write(IExtendedBinaryWriter writer)
{
var numReferences = _cytogeneticBands.Length;
writer.WriteOpt(numReferences);
for (var refIndex = 0; refIndex < numReferences; refIndex++)
{
var numRefEntries = _cytogeneticBands[refIndex].Length;
writer.WriteOpt(numRefEntries);
foreach (var band in _cytogeneticBands[refIndex])
{
writer.WriteOpt(band.Begin);
writer.WriteOpt(band.End);
writer.WriteOptAscii(band.Name);
}
}
}
private static void WriteIntervals <T>(IExtendedBinaryWriter writer, IReadOnlyCollection <IntervalArray <T> > intervalArrays,
Action <T> writeMethod)
{
writer.WriteOpt(intervalArrays.Count);
foreach (var intervalArray in intervalArrays)
{
if (intervalArray == null)
{
writer.WriteOpt(0);
continue;
}
writer.WriteOpt(intervalArray.Array.Length);
foreach (var interval in intervalArray.Array)
{
writeMethod(interval.Value);
}
}
writer.Write(CacheConstants.GuardInt);
}
private void WriteBuffer(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_buffer.Length);
writer.Write(_buffer);
}
public void Write(IExtendedBinaryWriter writer)
{
writer.Write((byte)_id);
writer.Write(_version);
writer.Write(_info);
}
private void WriteMetadata(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_sequenceOffset);
writer.WriteOpt(_numBases);
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.WriteOptAscii(Bases);
}
internal void Write(IExtendedBinaryWriter writer)
{
writer.Write(_info);
writer.Write(_contents);
}
public void Write(IExtendedBinaryWriter writer) => throw new System.NotImplementedException();
public void Write(IExtendedBinaryWriter writer, int peptideIndex)
{
CodingRegion.Write(writer);
ProteinId.Write(writer);
writer.WriteOpt(peptideIndex);
}
private static void WriteInterval(Interval <long> interval, IExtendedBinaryWriter writer)
{
writer.WriteOpt(interval.Begin);
writer.WriteOpt(interval.End);
writer.WriteOpt(interval.Value);
}
public void Write(IExtendedBinaryWriter writer)
{
writer.WriteOpt(_start);
writer.WriteOpt(_end - _start);
writer.WriteOpt(FileLocation);
}
public static void Write(this IInterval interval, IExtendedBinaryWriter writer)
{
writer.WriteOpt(interval.Start);
writer.WriteOpt(interval.End);
}
