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);
}
}
}
}
public int Extract()
{
var count = 0;
var interval = _reader.GetNextCustomInterval();
while (interval != null)
{
if (Overlap.Partial(interval.Start, interval.End, _begin, _end))
{
_writer.WriteInterval(interval);
count++;
}
interval = _reader.GetNextCustomInterval();
}
_writer.Dispose();
return(count);
}
public void EndofFile()
{
// read the supplementary annotation file
using (var reader = new CustomIntervalReader(_randomPath))
{
for (var i = 0; i < _totalIntervals; i++)
{
reader.GetNextCustomInterval();
}
var observerdInterval = reader.GetNextCustomInterval();
Assert.Null(observerdInterval);
var observerdInterval2 = reader.GetNextCustomInterval();
Assert.Null(observerdInterval2);
}
}
public void ReadCustomIntervals()
{
var customFile = new FileInfo(Resources.TopPath("chr1.nci"));
var customReader = new CustomIntervalReader(customFile.FullName);
var intervals = new List <VariantAnnotation.DataStructures.CustomInterval>();
var customInterval = customReader.GetNextCustomInterval();
while (customInterval != null)
{
intervals.Add(customInterval);
customInterval = customReader.GetNextCustomInterval();
}
Assert.Equal(11, intervals.Count); // 11 custom intervals were written.
Assert.Equal(2, intervals[0].StringValues.Count);
Assert.Equal(2, intervals[0].NonStringValues.Count);
Assert.Equal("NOC2L", intervals[2].StringValues["gene"]);
}
public MockCustomIntervalProvider(Stream stream, ChromosomeRenamer renamer)
{
var intervals = new List <ICustomInterval>();
using (var reader = new CustomIntervalReader(stream))
{
while (true)
{
var interval = reader.GetNextCustomInterval();
if (interval == null)
{
break;
}
intervals.Add(interval);
}
}
_hasIntervals = intervals.Count > 0;
_intervalForest = IntervalArrayFactory.CreateIntervalArray(intervals, renamer);
}