private List <cSequence> ExtractFileData(List <cLine> pLsLines)
{
List <cSequence> lsSequences = new List <cSequence>();
List <cSequenceRead> lsSequenceReads = new List <cSequenceRead>();
foreach (cLine line in pLsLines)
{
if (lsSequences.FindAll(item => item.RNAME == line.RNAME).Count == 0)
{
cSequence newSequence = new cSequence();
newSequence.RNAME = line.RNAME;
lsSequences.Add(newSequence);
}
cSequenceRead newRead = new cSequenceRead();
newRead.QNAME = line.QNAME.Trim();
newRead.FLAG = int.Parse(line.FLAG);
newRead.POS = int.Parse(line.POS);
newRead.MAPQ = int.Parse(line.MAPQ);
newRead.CIGAR = line.CIGAR.Trim();
newRead.MPOS = int.Parse(line.MPOS);
newRead.ISIZE = int.Parse(line.ISIZE);
newRead.SEQ = line.SEQ.Trim();
newRead.QUAL = line.QUAL.Trim();
newRead.OPTIONS = new List <cOption>();
foreach (string opt in line.OPTIONS)
{
newRead.OPTIONS.Add(new cOption(opt));
}
if (line.MRNM == "=")
{
//newRead.MRNM = lsSequences.First(item => item.RNAME == line.RNAME).idSequence;
}
else
{
newRead.MRNM = lsSequences.First(item => item.RNAME == line.MRNM).idSequence;
}
if (lsSequences.First(item => item.RNAME == line.RNAME).Reads == null)
{
lsSequences.First(item => item.RNAME == line.RNAME).Reads = new List <cSequenceRead>();
}
newRead.GestionINDEL();
//newRead.GestionAmorces();
lsSequences.First(item => item.RNAME == line.RNAME).Reads.Add(newRead);
}
// lsSequences.ForEach(i => i.Reads.GroupBy(j => j.QNAME));
return(lsSequences);
}
private List <cSequence> LoadSequences(long idIndividu)
{
MySqlCommand cmd = this.CreateCommand();
MySqlDataReader dr;
List <cSequence> lsSequences = new List <cSequence>();
cmd.CommandText = "SELECT ID_SEQUENCE, RNAME FROM SEQUENCE WHERE ID_INDIVIDU = @ID_INDIVIDU;";
cmd.Parameters.AddWithValue("@ID_INDIVIDU", idIndividu);
try
{
this.OpenConnection();
dr = cmd.ExecuteReader();
if (dr.HasRows)
{
while (dr.Read())
{
cSequence seq = new cSequence(dr.GetInt64("ID_SEQUENCE"));
seq.idIndividu = idIndividu;
seq.RNAME = dr.GetString("RNAME");
lsSequences.Add(seq);
}
}
this.CloseConnection();
}
catch (Exception ex)
{
this.CloseConnection();
throw;
}
return(lsSequences);
}
