public static BitArray DetermineBitArrayOfBasesInput(string input, BidirectionalDictionary<string, BitArray> codecDomain,
Dictionary<Constants.ColumnsFromSkipChars, string> byProductsBySkipChars)
{
BitArray bitArrayOfInput = new BitArray(0);
var inputIndeces = new InputIndeces();
while (inputIndeces.InputCharIndex < input.Length)
{
var inputPart = input.Substring(inputIndeces.InputCharIndex, 1);
if ("^".Equals(inputPart))
{
RecordReadStartingFactAndItsQual(input, byProductsBySkipChars, inputIndeces);
}
else if ("$".Equals(inputPart))
{
RecordReadEndingFact(byProductsBySkipChars, inputIndeces);
}
// It is very important that the case "+" is preceded by case "^" because read mapping quality can contain symbol "+".
else if ("+".Equals(inputPart))
{
RecordExtraNucleotidesFact(input, byProductsBySkipChars, inputIndeces);
}
// It is very important that the case "-" is preceded by case "^" because read mapping quality can contain symbol "-".
else if ("-".Equals(inputPart))
{
RecordMissingNucleotidesFact(input, byProductsBySkipChars, inputIndeces);
}
else
{
bitArrayOfInput = UpdateBitArray(codecDomain, bitArrayOfInput, inputIndeces, inputPart);
}
}
return bitArrayOfInput;
}
/// <summary>
/// This method dockets the read indices which have extra nucleotides after actual position.
/// Note: The read nucleotide value is followed by extra nucleotides signs in this case.
/// but the ReadIndex has already been incremented so it should be handled.
/// E.g.: input: .+2AB, the char '+' is assigned to the read '.'.
/// </summary>
/// <param name="input"></param>
/// <param name="byProductsBySkipChars"></param>
/// <param name="inputIndeces"></param>
private static void RecordExtraNucleotidesFact(string input,
Dictionary<Constants.ColumnsFromSkipChars, string> byProductsBySkipChars, InputIndeces inputIndeces)
{
inputIndeces.InputCharIndex++;
var extraNucleotidesLength = Convert.ToInt32(input.Substring(inputIndeces.InputCharIndex, 1));
inputIndeces.InputCharIndex++;
var extraNucleotides = input.Substring(inputIndeces.InputCharIndex, extraNucleotidesLength);
var extraNucleotidesStore = byProductsBySkipChars[Constants.ColumnsFromSkipChars.ExtraNuc];
var previousReadIndex = inputIndeces.ReadIndex - 1;
byProductsBySkipChars[Constants.ColumnsFromSkipChars.ExtraNuc] = extraNucleotidesStore + previousReadIndex + extraNucleotides + Constants.separator;
inputIndeces.InputCharIndex += extraNucleotidesLength;
}
private static BitArray UpdateBitArray(BidirectionalDictionary<string, BitArray> codecDomain, BitArray bitArrayOfInput, InputIndeces inputIndeces, string inputPart)
{
BitArray bitArrayOfInputPart;
if (codecDomain.Forward.TryGetValue(inputPart, out bitArrayOfInputPart))
{
bitArrayOfInput = AppendBitArray(bitArrayOfInput, bitArrayOfInputPart);
inputIndeces.InputCharIndex++;
inputIndeces.ReadIndex++;
}
else
{
throw new ArgumentException("The input cannot be encoded because it contains invalid part!", inputPart);
}
return bitArrayOfInput;
}
/// <summary>
/// This method dockets the read indices which are started at actual position.
/// Note: The read nucleotide value follow starting sign and read mapping quality in this case.
/// E.g.: input: ,^~. when the input processing reach the char '^' then ReadIndex is 1
/// because the ReadIndex has been incremented after char ',' processing.
/// </summary>
/// <param name="input"></param>
/// <param name="byProductsBySkipChars"></param>
/// <param name="inputIndeces"></param>
private static void RecordReadStartingFactAndItsQual(string input,
Dictionary<Constants.ColumnsFromSkipChars, string> byProductsBySkipChars, InputIndeces inputIndeces)
{
var readStartingSigns = byProductsBySkipChars[Constants.ColumnsFromSkipChars.StartingSigns];
byProductsBySkipChars[Constants.ColumnsFromSkipChars.StartingSigns]
= readStartingSigns + inputIndeces.ReadIndex + Constants.separator;
inputIndeces.InputCharIndex++;
var readMappingQual = input.Substring(inputIndeces.InputCharIndex, 1);
var readMappingQuals = byProductsBySkipChars[Constants.ColumnsFromSkipChars.MappingQual];
byProductsBySkipChars[Constants.ColumnsFromSkipChars.MappingQual] = readMappingQuals + readMappingQual + Constants.separator;
inputIndeces.InputCharIndex++;
}
/// <summary>
/// This method dockets the read indices which are ended at actual position.
/// Note: The read nucleotide value is followed by ending sign in this case
/// but the ReadIndex has already been incremented so it should be handled.
/// E.g.: input: .$, the char '$' is assigned to the read '.'.
/// </summary>
/// <param name="byProductsBySkipChars"></param>
/// <param name="inputIndeces"></param>
private static void RecordReadEndingFact(Dictionary<Constants.ColumnsFromSkipChars, string> byProductsBySkipChars,
InputIndeces inputIndeces)
{
var readEndingSigns = byProductsBySkipChars[Constants.ColumnsFromSkipChars.EndingSigns];
var previousReadIndex = inputIndeces.ReadIndex - 1;
byProductsBySkipChars[Constants.ColumnsFromSkipChars.EndingSigns] = readEndingSigns + previousReadIndex + Constants.separator;
inputIndeces.InputCharIndex++;
}
