public CustomIntervalExtractor(string inputCustIntervalPath, string outputDir, int begin, int end)
{
_begin = begin;
_end = end;
_reader = new CustomIntervalReader(inputCustIntervalPath);
string outputFileName = outputDir + Path.DirectorySeparatorChar + _reader.GetReferenceName() + '_' + _reader.GetIntervalType()
+ '_' + begin.ToString(CultureInfo.InvariantCulture) + '_' + end.ToString(CultureInfo.InvariantCulture) + ".nci";
Console.WriteLine("Creating custom interval db: " + outputFileName);
_writer = new CustomIntervalWriter(outputFileName, _reader.GetReferenceName(), _reader.GetIntervalType(), _reader.DataVersion);
}
public void ReadAndWriteTests()
{
using (var reader = new CustomIntervalReader(_randomPath))
{
var observedType = reader.GetIntervalType();
var observedRefName = reader.GetReferenceName();
Assert.Equal(_intervalType, observedType);
Assert.Equal("chr1", observedRefName);
for (var i = 0; i < _totalIntervals; i++)
{
var observedInterval = reader.GetNextCustomInterval();
Assert.Equal(_expectedCustomIntervals[i].ReferenceName, observedInterval.ReferenceName);
Assert.Equal(_expectedCustomIntervals[i].Start, observedInterval.Start);
Assert.Equal(_expectedCustomIntervals[i].End, observedInterval.End);
if (i > 0)
{
Assert.Equal(_expectedCustomIntervals[i].StringValues, observedInterval.StringValues);
Assert.Equal(_expectedCustomIntervals[i].NonStringValues, observedInterval.NonStringValues);
}
else
{
Assert.Null(observedInterval.StringValues);
Assert.Null(observedInterval.NonStringValues);
}
}
}
}