void ChooseIddc(FastqReader reader, BinaryWriter writer)
{
if (!encodeIds)
{
iddc = new PlaceholderIdGenerator();
return;
}
//@SRX000571_SRR002321.54856271 080226_CMLIVERKIDNEY_0007:8:330:23:135 length=36
Regex sra = new Regex(@"^(@[^.]+\.)\d+\s([\S]+)(?:\d+:){3}\d+.*$", RegexOptions.Singleline);
Regex length = new Regex(@"^.+length=\d+$", RegexOptions.Singleline);
//@HWUSI-EAS627_1:3:1:0:370/1 (or /2)
//@BILLIEHOLIDAY_3_FC30G08AAXX:1:1:0:1966
Regex encode = new Regex(@"^(@[\S]+)(?:\d+:){3}\d+(\/[12])*$", RegexOptions.Singleline);
String id = reader.GetID(0);
Match sraMatch = sra.Match(id);
Match encodeMatch = encode.Match(id);
if (sraMatch.Success) //type 0
{
Match lengthMatch = length.Match(id);
writer.Write(0);
iddc = new SraIdDeCompresser(reader, writer, sraMatch, lengthMatch.Success);
}
else if (encodeMatch.Success) //type 2
{
writer.Write(2);
iddc = new EncodeIdDeCompresser(reader, writer, encodeMatch);
}
else //type 1
{
writer.Write(1);
iddc = new PlainIdDeCompresser(reader, writer);
}
}
void ChooseIddc(EncodedFastqReader reader)
{
if (!encodeIds)
{
iddc = new PlaceholderIdGenerator();
return;
}
int iddcType = reader.Reader.ReadInt32();
if (iddcType == 0)
{
iddc = new SraIdDeCompresser(reader, length);
}
else if (iddcType == 1)
{
iddc = new PlainIdDeCompresser(reader);
}
else if (iddcType == 2)
{
iddc = new EncodeIdDeCompresser(reader);
}
else
{
throw new Exception("Missing header info in compressed file! " + iddcType);
}
}
