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 void LoadReads()
{
MySqlCommand cmd = this.CreateCommand();
List <cSequenceRead> lsReads = new List <cSequenceRead>();
cmd.CommandText = "SELECT ID_SEQUENCE_READ, ID_SEQUENCE, QNAME, FLAG, POS, MAPQ, CIGAR, MRNM, MPOS, ISIZE, SEQ, QUAL FROM SEQUENCE_READ WHERE ID_SEQUENCE = @ID_SEQUENCE;";
cmd.Parameters.AddWithValue("@ID_SEQUENCE", this.idSequence);
try
{
this.OpenConnection();
MySqlDataReader dr = cmd.ExecuteReader();
if (dr.HasRows)
{
while (dr.Read())
{
cSequenceRead read = new cSequenceRead
{
idSequenceRead = dr.GetInt64("ID_SEQUENCE_READ"),
QNAME = dr.GetString("QNAME"),
FLAG = dr.GetInt32("FLAG"),
POS = dr.GetInt32("POS"),
MAPQ = dr.GetInt32("MAPQ"),
CIGAR = dr.GetString("CIGAR"),
MRNM = dr.GetInt32("MRNM"),
MPOS = dr.GetInt32("MPOS"),
ISIZE = dr.GetInt32("ISIZE"),
SEQ = dr.GetString("SEQ"),
QUAL = dr.GetString("QUAL")
};
read.GestionINDEL();
lsReads.Add(read);
}
}
this.CloseConnection();
}
catch (Exception ex)
{
this.CloseConnection();
throw;
}
this.Reads = lsReads;
}
private string truncateSequence(cSequenceRead read, bool isDebut)
{
int lng = 0;
if (read.SEQCorrige.Length > 0)
{
lng = this.getLongAmorce(read.SEQCorrige.Length);
}
if (lng == 0)
{
return(read.SEQCorrige);
}
string sequence;
try
{
if (lng > read.SEQCorrige.Length)
{
return(string.Empty);
}
if (!isDebut)
{
sequence = reverseString(reverseString(read.SEQCorrige).Remove(0, lng));
}
else
{
sequence = read.SEQCorrige.Remove(0, lng);
}
return(sequence);
} catch (Exception ex)
{
return(read.SEQCorrige);
}
}
public string truncateSequence(cSequenceRead sequence)
{
return(truncateSequence(sequence, this.FLAG == 99 || this.FLAG == 163));
}
