public JasixNode(IExtendedBinaryReader reader)
{
_start = reader.ReadOptInt32();
//on disk we will store the end as an offset to save space
_end = _start + reader.ReadOptInt32();
FileLocation = reader.ReadOptInt64();
}
private static IntervalArray <T>[] ReadIntervals <T>(IExtendedBinaryReader reader, Func <T> readMethod) where T : IInterval
{
var numRefSeqs = reader.ReadOptInt32();
var intervalArrays = new IntervalArray <T> [numRefSeqs];
for (int refSeqIndex = 0; refSeqIndex < numRefSeqs; refSeqIndex++)
{
var numItems = reader.ReadOptInt32();
if (numItems == 0)
{
continue;
}
var intervals = new Interval <T> [numItems];
for (int i = 0; i < numItems; i++)
{
var item = readMethod();
intervals[i] = new Interval <T>(item.Start, item.End, item);
}
intervalArrays[refSeqIndex] = new IntervalArray <T>(intervals);
}
CheckGuard(reader);
return(intervalArrays);
}
public static IInterval Read(IExtendedBinaryReader reader)
{
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
return(new Interval(start, end));
}
private static Interval <long> ReadInterval(IExtendedBinaryReader reader)
{
var begin = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var position = reader.ReadOptInt64();
return(new Interval <long>(begin, end, position));
}
public static CompactId Read(IExtendedBinaryReader reader)
{
var id = (IdType)reader.ReadByte();
var version = reader.ReadByte();
var info = reader.ReadUInt32();
return(new CompactId(id, version, info));
}
// 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);
}
/// <summary>
/// check if the section guard is in place
/// </summary>
internal static void CheckGuard(IExtendedBinaryReader reader)
{
uint observedGuard = reader.ReadUInt32();
if (observedGuard != CacheConstants.GuardInt)
{
throw new InvalidDataException($"Expected a guard integer ({CacheConstants.GuardInt}), but found another value: ({observedGuard})");
}
}
/// <summary>
/// reads the regulatory element data from the binary reader
/// </summary>
public static IRegulatoryRegion Read(IExtendedBinaryReader reader, IDictionary <ushort, IChromosome> chromosomeIndexDictionary)
{
var refIndex = reader.ReadOptUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
var type = (RegulatoryRegionType)reader.ReadByte();
var id = CompactId.Read(reader);
return(new RegulatoryRegion(chromosomeIndexDictionary[refIndex], start, end, id, type));
}
internal static T[] ReadItems <T>(IExtendedBinaryReader reader, Func <T> readMethod)
{
var numItems = reader.ReadOptInt32();
var items = new T[numItems];
for (int i = 0; i < numItems; i++)
{
items[i] = readMethod();
}
CheckGuard(reader);
return(items);
}
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));
}
private static T[] ReadIndices <T>(IExtendedBinaryReader reader, T[] cachedItems)
{
int numItems = reader.ReadOptInt32();
var items = new T[numItems];
for (int i = 0; i < numItems; i++)
{
var index = reader.ReadOptInt32();
items[i] = cachedItems[index];
}
return(items);
}
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;
}
}
private void ReadBlockOffsets(IExtendedBinaryReader reader)
{
var numEntries = reader.ReadOptInt32();
_blockOffsets = new ISaIndexOffset[numEntries];
int oldPosition = 0;
int oldBlockOffset = 0;
for (int i = 0; i < numEntries; i++)
{
var deltaPosition = reader.ReadOptInt32();
var deltaBlockOffset = reader.ReadOptInt32();
var position = oldPosition + deltaPosition;
var blockOffset = oldBlockOffset + deltaBlockOffset;
_blockOffsets[i] = new SaIndexOffset(position, blockOffset);
oldPosition = position;
oldBlockOffset = blockOffset;
}
}
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());
}
