/// <summary>
/// Converts quality scores from fromQualityScore type to toQualityScore type
/// Ex: Phred to Solexa or Solexa to Phred
/// </summary>
/// <param name="fromQualityScoreType">from quality score type.</param>
/// <param name="toQualityScoreType">to quality score type.</param>
/// <param name="qualScores">Quality scores</param>
private static int[] Convert(BaseQualityScoreType fromQualityScoreType, BaseQualityScoreType toQualityScoreType, int[] qualScores)
{
long count = qualScores.GetLongLength();
int[] result = new int[count];
if (fromQualityScoreType == toQualityScoreType)
{
Helper.Copy(qualScores, result, qualScores.GetLongLength());
}
else
{
if (fromQualityScoreType == BaseQualityScoreType.PhredBaseQualityScore)
{
for (long i = 0; i < count; i++)
{
result[i] = ConvertPhredToSolexa(qualScores[i]);
}
}
else
{
for (long i = 0; i < count; i++)
{
result[i] = ConvertSolexaToPhred(qualScores[i]);
}
}
}
return result;
}
/// <summary>
/// Converts quality score from fromQualityScore type to toQualityScore type
/// Ex: Phred to Solexa or Solexa to Phred
/// </summary>
/// <param name="fromQualityScoreType">from quality score type.</param>
/// <param name="toQualityScoreType">to quality score type.</param>
/// <param name="qualScore">Quality score</param>
private static int Convert(BaseQualityScoreType fromQualityScoreType, BaseQualityScoreType toQualityScoreType, int qualScore)
{
int result;
if (fromQualityScoreType == toQualityScoreType)
{
result = qualScore;
}
else
{
if (fromQualityScoreType == BaseQualityScoreType.PhredBaseQualityScore)
{
result = ConvertPhredToSolexa(qualScore);
}
else
{
result = ConvertSolexaToPhred(qualScore);
}
}
return result;
}
