public void WriteInterval(DataStructures.CustomInterval interval)
{
if (interval.IsEmpty())
{
// marks the last interval
_writer.WriteOpt(interval.Start);
_writer.WriteOpt(interval.End);
_writer.WriteOpt(0); // for the null string dictionary
_writer.WriteOpt(0); // for the null non-string dictionary
return;
}
if (interval.ReferenceName != _referenceName)
{
throw new Exception(
$"Unexpected interval in custom interval writer.\nExpected reference name: {_referenceName}, observed reference name: {interval.ReferenceName}");
}
if (interval.Type != _intervalType)
{
throw new Exception(
$"Unexpected interval in custom interval writer.\nExpected interval type: {_intervalType}, observed interval type: {interval.Type}");
}
_writer.WriteOpt(interval.Start);
_writer.WriteOpt(interval.End);
if (interval.StringValues != null)
{
_writer.WriteOpt(interval.StringValues.Count);
foreach (var keyVal in interval.StringValues)
{
_writer.WriteOptUtf8(keyVal.Key);
_writer.WriteOptUtf8(keyVal.Value);
}
}
else
{
_writer.WriteOpt(0);
}
if (interval.NonStringValues != null)
{
_writer.WriteOpt(interval.NonStringValues.Count);
foreach (var keyVal in interval.NonStringValues)
{
_writer.WriteOptUtf8(keyVal.Key);
_writer.WriteOptUtf8(keyVal.Value);
}
}
else
{
_writer.WriteOpt(0);
}
_count++;
}
public DataStructures.CustomInterval GetNextCustomInterval()
{
if (_reachedEnd)
{
return(null);
}
var chromosome = _referenceName;
var type = _intervalType;
var start = _reader.ReadOptInt32();
var end = _reader.ReadOptInt32();
var interval = new DataStructures.CustomInterval(chromosome, start, end, type, null, null);
if (interval.IsEmpty())
{
_reachedEnd = true;
return(null);
}
var stringDictCount = _reader.ReadOptInt32();
if (stringDictCount > 0)
{
interval.StringValues = new Dictionary <string, string>(stringDictCount);
for (var i = 0; i < stringDictCount; i++)
{
var key = _reader.ReadUtf8String();
var val = _reader.ReadUtf8String();
interval.StringValues.Add(key, val);
}
}
var nonStringDictCount = _reader.ReadOptInt32();
if (nonStringDictCount > 0)
{
interval.NonStringValues = new Dictionary <string, string>(nonStringDictCount);
for (var i = 0; i < nonStringDictCount; i++)
{
var key = _reader.ReadUtf8String();
var val = _reader.ReadUtf8String();
interval.NonStringValues.Add(key, val);
}
}
return(interval);
}
