// ReSharper disable once UnusedParameter.Local
private static void CheckString(IExtendedBinaryReader reader, string expectedString)
{
string s = reader.ReadAsciiString();
Assert.NotNull(s);
Assert.Equal(expectedString.Length, s.Length);
Assert.Equal(expectedString, s);
}
public static IGene Read(IExtendedBinaryReader reader, IDictionary <ushort, IChromosome> indexToChromosome)
{
ushort referenceIndex = reader.ReadOptUInt16();
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);
return(new Gene(indexToChromosome[referenceIndex], start, end, onReverseStrand, symbol, hgncId, entrezId, ensemblId));
}
public static IAnnotatedGene Read(IExtendedBinaryReader reader)
{
var geneName = reader.ReadAsciiString();
var annotationLength = reader.ReadOptInt32();
var annotations = new IGeneAnnotationSource[annotationLength];
for (int i = 0; i < annotationLength; i++)
{
annotations[i] = GeneAnnotationSource.Read(reader);
}
return(geneName == NullGene ? null : new AnnotatedGene(geneName, annotations));
}
public static IGeneAnnotationSource Read(IExtendedBinaryReader reader)
{
var dataSource = reader.ReadAsciiString();
var isArray = reader.ReadBoolean();
var jsonStringLength = reader.ReadOptInt32();
var jsonStrings = new string[jsonStringLength];
for (int i = 0; i < jsonStringLength; i++)
{
jsonStrings[i] = reader.ReadString();
}
return(new GeneAnnotationSource(dataSource, jsonStrings, isArray));
}
private JasixIndex(IExtendedBinaryReader reader) : this()
{
var version = reader.ReadOptInt32();
if (version != JasixCommons.Version)
{
throw new InvalidDataException($"Invalid Jasix version: Observed {version}, expected{JasixCommons.Version}");
}
HeaderLine = reader.ReadAsciiString();
var count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
var chrIndex = new JasixChrIndex(reader);
_chrIndices[chrIndex.ReferenceSequence] = chrIndex;
}
}
public JasixChrIndex(IExtendedBinaryReader reader) : this("")
{
ReferenceSequence = reader.ReadAsciiString();
var count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
_nodes.Add(new JasixNode(reader));
}
var intervalCount = reader.ReadOptInt32();
if (intervalCount == 0)
{
return;
}
for (var i = 0; i < intervalCount; i++)
{
_largeVariants.Add(ReadInterval(reader));
}
_intervalArray = new IntervalArray <long>(_largeVariants.ToArray());
}