public void InitializeReadMap()
{
if (FqReadMap == null)
{
FqReadMap = HashFastq.deserializeHashmap();
}
}
/// <summary>
/// Constructs the sequencer specific read map by calling the HashFastq class to deserialize it from memory.
/// After it is constructed the same class is used to calculate relavent quality scores for each of the nucleotide/quality
/// pairings.
/// </summary>
/// <param name="sequencerType"></param>
/// <returns></returns>
public Dictionary <int, FqNucleotideRead> ConstructSequencerSpecificReadMap(String sequencerType)
{
if (FqReadMap == null)
{
FqReadMap = HashFastq.deserializeHashmap();
}
if (isMapConstructed == false)
{
this.SequencerType = sequencerType;
FqReadMap = HashFastq.calculateHashQualities(SequencerType, FqReadMap);
isMapConstructed = true;
}
return(FqReadMap);
}
public static void serializeFastqHashmap()
{
Dictionary <int, FqNucleotideRead> hashmap = HashFastq.createHashMap();
try
{
using (Stream stream = File.Open(@FQ_FILE_MAP_SERIALIZING_NAME, FileMode.Create))
{
BinaryFormatter bin = new BinaryFormatter();
bin.Serialize(stream, hashmap);
}
}
catch (IOException e)
{
Console.Write("Creation of serialized fastq Fq_FILE_MAP failed \n");
Console.Write(e.StackTrace);
}
}
/// <summary>
/// Calculates the sequencer specific quality scores for each component
/// </summary>
public override void calculateMapQualities()
{
Fq_FILE_MAP = HashFastq.calculateHashQualities(sequencerType, Fq_FILE_MAP);
}
