/// <summary>
/// returns a 2-bit sequence corresponding to the specified name
/// </summary>
public void GetCompressedSequence(string ensemblReferenceName)
{
var indexEntry = GetIndexEntry(ensemblReferenceName);
if (indexEntry == null)
{
return;
}
// jump to that offset
_stream.Position = indexEntry.FileOffset;
// set the data
var numBufferBytes = CompressedSequence.GetNumBufferBytes(indexEntry.NumBases);
_compressedSequence.Set(indexEntry.NumBases, _reader.ReadBytes(numBufferBytes), indexEntry.MaskedEntries, indexEntry.SequenceOffset);
}
// constructor
public CompressedSequenceTests()
{
_compressedSequence = new CompressedSequence();
// create the following sequence: NNATGTTTCCACTTTCTCCTCATTAGANNNTAACGAATGGGTGATTTCCCTAN
var buffer = new byte[] { 14, 42, 93, 169, 150, 122, 204, 11, 211, 224, 35, 169, 91, 0 };
var maskedIntervals = new IntervalArray <MaskedEntry> .Interval[3];
maskedIntervals[0] = new IntervalArray <MaskedEntry> .Interval(0, 1, new MaskedEntry(0, 1));
maskedIntervals[1] = new IntervalArray <MaskedEntry> .Interval(27, 29, new MaskedEntry(27, 29));
maskedIntervals[2] = new IntervalArray <MaskedEntry> .Interval(52, 52, new MaskedEntry(52, 52));
var maskedIntervalArray = new IntervalArray <MaskedEntry>(maskedIntervals);
_compressedSequence.Set(NumBases, buffer, maskedIntervalArray);
}
