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 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 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 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);
}
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"]);
}
