public void Add(string chr, int start, int end, long fileLoc)
{
if (!_chrIndices.ContainsKey(chr))
{
_chrIndices[chr] = new JasixChrIndex(chr);
}
_chrIndices[chr].Add(start, end, fileLoc);
}
public void Add(string chr, int start, int end, long fileLoc, string chrSynonym = null)
{
if (!string.IsNullOrEmpty(chrSynonym))
{
_synonymToChrName[chrSynonym] = chr;
}
if (_chrIndices.TryGetValue(chr, out var chrIndex))
{
chrIndex.Add(start, end, fileLoc);
}
else
{
_chrIndices[chr] = new JasixChrIndex(chr);
_chrIndices[chr].Add(start, end, fileLoc);
}
}
private JasixIndex(IExtendedBinaryReader reader) : this()
{
var version = reader.ReadOptInt32();
if (version != JasixCommons.Version)
{
throw new InvalidDataException($"Invalid Jasix version: Observed {version}, expected{JasixCommons.Version}");
}
HeaderLine = reader.ReadAsciiString();
var count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
var chrIndex = new JasixChrIndex(reader);
_chrIndices[chrIndex.ReferenceSequence] = chrIndex;
}
}
public JasixIndex(Stream stream) : this()
{
_stream = stream;
using (var reader = new ExtendedBinaryReader(stream))
{
int version = reader.ReadOptInt32();
if (version != JasixCommons.Version)
{
throw new InvalidDataException($"Invalid Jasix version: Observed {version}, expected{JasixCommons.Version}");
}
int count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
var chrIndex = new JasixChrIndex(reader);
_chrIndices[chrIndex.ReferenceSequence] = chrIndex;
}
int synonymCount = reader.ReadOptInt32();
for (var i = 0; i < synonymCount; i++)
{
string synonym = reader.ReadAsciiString();
string indexName = reader.ReadAsciiString();
_synonymToChrName[synonym] = indexName;
}
int sectionCount = reader.ReadOptInt32();
for (var i = 0; i < sectionCount; i++)
{
string sectionName = reader.ReadAsciiString();
long begin = reader.ReadOptInt64();
long end = reader.ReadOptInt64();
_sectionRanges[sectionName] = new FileRange(begin, end);
}
}
}
