public void Randomize(string population)
{
var random = new Random();
var newSNPToGenotypeMap = new Dictionary <string, SNPGenotype>();
foreach (var pair in SNPDatabaseManager.localDatabase.snpToInfoMap)
{
// Chose a random genotype, weighted according to the specified population frequency.
var randomFraction = random.NextDouble();
foreach (var genotypeInfo in pair.Value.genotypes)
{
// Determine the frequency for this genotype in the specified population.
var populationFrequency = 1.0 / (double)pair.Value.genotypes.Length;
if (genotypeInfo.populationFrequencies.ContainsKey(population))
{
populationFrequency = genotypeInfo.populationFrequencies[population];
}
// Randomly decide whether to use this genotype.
if (randomFraction > populationFrequency)
{
randomFraction -= populationFrequency;
}
else
{
var newValue = new SNPGenotype();
newValue.genotype = genotypeInfo.genotype;
newValue.orientation = pair.Value.orientation;
newSNPToGenotypeMap.Add(pair.Key, newValue);
break;
}
}
}
snpToGenotypeMap = newSNPToGenotypeMap;
}
public static SNPGenotype Read(BinaryReader reader)
{
var result = new SNPGenotype();
result.orientation = (Orientation)reader.ReadByte();
result.genotype = DiploidGenotype.Read(reader);
return(result);
}
public static SNPGenotype ReadLegacy(BinaryReader reader)
{
var result = new SNPGenotype();
var legacyGenotype = DiploidGenotype.Read(reader);
var legacyOrientation = reader.ReadByte();
result.orientation = Orientation.Plus;
result.genotype = DiploidGenotype.Read(reader);
return(result);
}
public void AddSNPValue(string id, SNPGenotype value)
{
// Always store the SNP value with the lower-case SNP ID.
id = id.ToLowerInvariant();
if (snpToGenotypeMap.ContainsKey(id))
{
// If there SNP value is already in the database, ensure this data doesn't conflict with it.
SNPGenotype oldValue = snpToGenotypeMap[id];
Debug.Assert(oldValue.Equals(value));
}
else
{
// Add the SNP value to the database.
snpToGenotypeMap.Add(id, value);
}
}
public IndividualGenomeDatabase Read()
{
// Initialize the database.
var database = new IndividualGenomeDatabase();
// Read the table of SNP genotypes.
tableReader.Read(
delegate(string[] columns)
{
if (columns.Length == 4)
{
// Parse a column of this format: rs# chromosome position genotype
var snpId = columns[0];
var snpValue = new SNPGenotype();
snpValue.genotype = DNA.StringToDiploidGenotype(columns[3]);
snpValue.orientation = Orientation.Plus;
// Add the SNP genotype to the database.
database.AddSNPValue(snpId, snpValue);
}
});
return(database);
}
public IndividualGenomeDatabase Read()
{
// Initialize the database.
var database = new IndividualGenomeDatabase();
// Read the table of SNP genotypes.
tableReader.Read(
delegate(string[] columns)
{
if (columns.Length == 6)
{
// Parse a column of this format: rs4477212,A/G,1,72017,+,AA
var snpId = columns[0];
var snpValue = new SNPGenotype();
snpValue.genotype = DNA.StringToDiploidGenotype(columns[5]);
snpValue.orientation = DNA.StringToOrientation(columns[4]);
// Add the SNP genotype to the database.
database.AddSNPValue(snpId, snpValue);
}
});
return(database);
}
public static GenomeLoadResult Load(Stream stream, string password, ref IndividualGenomeDatabase outResult)
{
var reader = new BinaryReader(stream);
// Read the file magic and version.
char[] fileMagic = reader.ReadChars(referenceFileMagic.Length);
// If the file doesn't have the expected magic header, abort and return an error.
bool bFileHasMagic = Utilities.ArrayCompare(fileMagic, referenceFileMagic);
bool bFileHasLegacyMagic = Utilities.ArrayCompare(fileMagic, referenceFileMagicLegacy);
if (!bFileHasMagic && !bFileHasLegacyMagic)
{
return(GenomeLoadResult.UnrecognizedFile);
}
// The encryption system doesn't handle short passwords gracefully, so extend them to 16 characters with spaces.
password = password.PadRight(16, ' ');
// Read the saved password hash from the file, and compare it to the hash of the password we're trying to load with.
// This can't be done by saving some magic header inside the encrypted part of the file, as the CryptoStream will crash when decrypting with the wrong password.
byte[] passwordASCII = ASCIIEncoding.ASCII.GetBytes(password);
byte[] passwordHash = (new SHA512Managed()).ComputeHash(passwordASCII);
byte[] savedPasswordHash = reader.ReadBytes(passwordHash.Length);
if (!Utilities.ArrayCompare(passwordHash, savedPasswordHash))
{
return(GenomeLoadResult.IncorrectPassword);
}
// Read the initialization vector.
byte[] initializationVector = reader.ReadBytes(16);
// Create a decrypting stream to read the encrypted data from the file.
reader = new BinaryReader(
new CryptoStream(
stream,
Rijndael.Create().CreateDecryptor(
ASCIIEncoding.ASCII.GetBytes(password),
initializationVector),
CryptoStreamMode.Read));
// Create the genome database that's about to be loaded.
outResult = new IndividualGenomeDatabase();
outResult.password = password;
// Read SNPs until the end of the file.
while (stream.Position < stream.Length)
{
// Read a SNP ID and value pair, and add them to the database.
var Key = reader.ReadString();
SNPGenotype Genotype;
if (bFileHasLegacyMagic)
{
Genotype = SNPGenotype.ReadLegacy(reader);
}
else
{
Genotype = SNPGenotype.Read(reader);
}
outResult.AddSNPValue(Key, Genotype);
}
return(GenomeLoadResult.Success);
}
