private static bool isVCFStream(Stream stream, string MAGIC_HEADER_LINE)
{
try {
byte[] buff = new byte[MAGIC_HEADER_LINE.Length];
stream.Read(buff, 0, MAGIC_HEADER_LINE.Length);
return(buff.SequenceEqual(VCFUtils.StringToBytes(MAGIC_HEADER_LINE)));
// String firstLine = new String(buff);
// return firstLine.startsWith(MAGIC_HEADER_LINE);
} catch { // (Exception e)
return(false);
} finally {
stream.Close();
}
}
/// <param name="test"> bases to test against
/// </param>
/// <returns> true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles </returns>
public bool BasesMatch(string test)
{
return(BasesMatch(VCFUtils.StringToBytes(test.ToUpper())));
}
public static bool AcceptableAlleleBases(string bases, bool allowNsAsAcceptable)
{
return(AcceptableAlleleBases(VCFUtils.StringToBytes(bases), allowNsAsAcceptable));
}
/// <seealso cref= Allele(byte[], boolean)
/// </seealso>
/// <param name="bases"> bases representing an allele </param>
/// <param name="isRef"> is this the reference allele? </param>
public static Allele Create(string bases, bool isRef)
{
return(Create(VCFUtils.StringToBytes(bases), isRef));
}
/// <param name="bases"> bases representing an allele </param>
/// <returns> true if the bases represent the well formatted allele </returns>
public static bool AcceptableAlleleBases(string bases)
{
return(AcceptableAlleleBases(VCFUtils.StringToBytes(bases), true));
}
