public void TestConstructorWithByteArray()
{
byte[] sequenceData = new byte[6];
sequenceData[0] = (byte)'C';
sequenceData[1] = (byte)'A';
sequenceData[2] = (byte)'A';
sequenceData[3] = (byte)'G';
sequenceData[4] = (byte)'C';
sequenceData[5] = (byte)'T';
byte[] qualityScores = new byte[6];
qualityScores[0] = 65;
qualityScores[1] = 65;
qualityScores[2] = 65;
qualityScores[3] = 65;
qualityScores[4] = 110;
qualityScores[5] = 125;
string expectedSequence = "CAAGCT";
QualitativeSequence qualitativeSequence = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Illumina_v1_3, sequenceData, qualityScores);
string actual = "";
foreach (byte bt in qualitativeSequence)
{
actual += (char)bt;
}
Assert.AreEqual(expectedSequence, actual);
Assert.AreEqual(qualitativeSequence.Alphabet, Alphabets.DNA);
Assert.AreEqual(qualitativeSequence.Count, 6);
//
// Test for indexer
Assert.AreEqual(qualitativeSequence[0], (byte)'C');
Assert.AreEqual(qualitativeSequence[1], (byte)'A');
Assert.AreEqual(qualitativeSequence[2], (byte)'A');
Assert.AreEqual(qualitativeSequence[3], (byte)'G');
Assert.AreEqual(qualitativeSequence[4], (byte)'C');
Assert.AreEqual(qualitativeSequence[5], (byte)'T');
int index = 0;
foreach (byte qualityScore in qualitativeSequence.GetEncodedQualityScores())
{
Assert.AreEqual(qualityScores[index++], qualityScore);
}
}
/// <summary>
/// Convert quality values to string array
/// </summary>
/// <param name="sequence">Sequence which has the quality values</param>
/// <param name="maxColumns">Max number of columns to write to</param>
/// <returns>string array with quality values</returns>
public static string[,] FastQQualityValuesToRange(QualitativeSequence sequence, int maxColumns)
{
var qualityScoreArray = sequence.GetEncodedQualityScores();
long rowCount = (int)Math.Ceiling((decimal)qualityScoreArray.Length / (decimal)maxColumns);
long columnCount = sequence.Count > maxColumns ? maxColumns : sequence.Count;
string[,] rangeData = new string[rowCount, columnCount];
int count = 0;
for (int row = 0; row < rowCount; row++)
{
for (int col = 0; col < columnCount && count < qualityScoreArray.Length; col++, count++)
{
rangeData[row, col] = (qualityScoreArray[count]).ToString(CultureInfo.InvariantCulture);
}
}
return rangeData;
}