public Chain(Stream stream)
{
this.chainRecords = new List <ChainRecord>();
StreamReader sr = new StreamReader(stream);
while (!sr.EndOfStream)
{
this.chainRecords.Add(ChainRecord.createChainRecord(sr: sr));
}
this.chainRecords = this.chainRecords.Where(x => x != null).ToList();
}
public static ChainRecord createChainRecord(StreamReader sr)
{
var chainRecord = new ChainRecord();
List <string> header = new List <string>();
while (header.Count < 12 && !sr.EndOfStream)
{
header = sr.ReadLine().Split(null).ToList();
}
if (header.Count < 12)
{
return(null);
}
header.RemoveAt(0);
chainRecord.score = Convert.ToUInt64(header[0]);
chainRecord.tName = header[1];
chainRecord.tSize = Convert.ToInt32(header[2]);
chainRecord.tStrand = header[3];
chainRecord.tStart = Convert.ToInt32(header[4]);
chainRecord.tEnd = Convert.ToInt32(header[5]);
chainRecord.qName = header[6];
chainRecord.qSize = Convert.ToInt32(header[7]);
chainRecord.qStrand = header[8];
chainRecord.qStart = Convert.ToInt32(header[9]);
chainRecord.qEnd = Convert.ToInt32(header[10]);
chainRecord.id = header[11];
chainRecord.chainGaps = new List <ChainGap>();
List <string> gapLine = new List <string>();
while (true)
{
gapLine = sr.ReadLine().Split(null).ToList();
if (gapLine.Count > 1)
{
chainRecord.chainGaps.Add(new ChainGap(size: Convert.ToInt32(gapLine[0]),
dt: Convert.ToInt32(gapLine[1]),
dq: Convert.ToInt32(gapLine[2])));
}
else
{
chainRecord.chainGaps.Add(new ChainGap(size: Convert.ToInt32(gapLine[0]),
dt: 0,
dq: 0));
break;
}
}
return(chainRecord);
}