protected override List <T> DoBuild <T>(string fileName, out List <QueryInfo> totalQueries)
{
var result = new List <T>();
_format = _options.GetSAMFormat();
totalQueries = new List <QueryInfo>();
using (var sr = SAMFactory.GetReader(fileName, true))
{
int count = 0;
int waitingcount = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
count++;
if (count % 1000 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
var parts = line.Split('\t');
var qname = parts[SAMFormatConst.QNAME_INDEX];
var qi = new QueryInfo(qname);
totalQueries.Add(qi);
SAMFlags flag = (SAMFlags)int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
if (!_filter.AcceptFlags(flag))
{
continue;
}
var mismatchCount = _format.GetNumberOfMismatch(parts);
var seq = parts[SAMFormatConst.SEQ_INDEX];
qi.Mismatch = mismatchCount;
qi.Length = seq.Length;
//too many mismatchs
if (!_filter.AcceptMismatch(mismatchCount))
{
continue;
}
if (!_filter.AcceptQueryName(qname))
{
continue;
}
if (!_filter.AcceptLength(seq.Length))
{
continue;
}
var cigar = parts[SAMFormatConst.CIGAR_INDEX];
if (!_filter.AcceptCigar(cigar))
{
continue;
}
var seqname = parts[SAMFormatConst.RNAME_INDEX].StringAfter("chr");
var start = int.Parse(parts[SAMFormatConst.POS_INDEX]);
var end = SAMUtils.ParseEnd(start, cigar);
bool isReversed = flag.HasFlag(SAMFlags.QueryOnReverseStrand);
char strand;
if (isReversed)
{
strand = '-';
}
else
{
strand = '+';
}
var sam = new T();
var loc = new SAMAlignedLocation(sam)
{
Seqname = seqname,
Start = start,
End = end,
Strand = strand,
};
if (!_filter.AcceptLocus(loc))
{
continue;
}
if (isReversed)
{
seq = SequenceUtils.GetReverseComplementedSequence(seq);
}
sam.Qname = qname;
sam.Sequence = seq;
loc.AlignmentScore = _format.GetAlignmentScore(parts);
loc.Cigar = cigar;
loc.NumberOfMismatch = mismatchCount;
loc.MismatchPositions = _format.GetMismatchPositions(parts);
if (_format.HasAlternativeHits)
{
_format.ParseAlternativeHits(parts, sam);
}
result.Add(sam);
waitingcount++;
if (waitingcount % 100 == 0)
{
Progress.SetMessage("{0} feature reads from {1} reads", waitingcount, count);
}
}
}
return(result);
}
protected override List <T> DoBuild <T>(string fileName, out List <QueryInfo> totalQueries)
{
var result = new List <T>();
_format = _options.GetSAMFormat();
totalQueries = new List <QueryInfo>();
using (var sr = SAMFactory.GetReader(fileName, true))
{
int count = 0;
int waitingcount = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
if (count % 1000 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (count % 100000 == 0 && count > 0)
{
Progress.SetMessage("{0} candidates from {1} reads", waitingcount, count);
}
count++;
var qname = line.StringBefore("\t");
//Console.WriteLine("line = {0}", line);
//Console.WriteLine("query = {0}", qname);
var qi = new QueryInfo(qname);
totalQueries.Add(qi);
var parts = line.Split('\t');
SAMFlags flag = (SAMFlags)int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
//unmatched
if (flag.HasFlag(SAMFlags.UnmappedQuery))
{
continue;
}
//too many mismatchs
var mismatchCount = _format.GetNumberOfMismatch(parts);
var seq = parts[SAMFormatConst.SEQ_INDEX];
qi.Mismatch = mismatchCount;
qi.Length = seq.Length;
qi.NoPenaltyMutation = 0;
if (_options.T2cAsNoPenaltyMutation)
{
}
if (mismatchCount > _options.MaximumMismatch)
{
continue;
}
if (!AcceptQueryName(qname))
{
continue;
}
//too short
if (seq.Length < _options.MinimumReadLength)
{
continue;
}
//too long
if (seq.Length > _options.MaximumReadLength)
{
continue;
}
var cigar = parts[SAMFormatConst.CIGAR_INDEX];
////insertion/deletion
//if (cigar.Any(m => m == 'I' || m == 'D'))
//{
// continue;
//}
bool isReversed = flag.HasFlag(SAMFlags.QueryOnReverseStrand);
char strand;
if (isReversed)
{
strand = '-';
seq = SequenceUtils.GetReverseComplementedSequence(seq);
}
else
{
strand = '+';
}
var score = _format.GetAlignmentScore(parts);
var sam = new T()
{
Qname = qname,
Sequence = seq
};
var seqname = parts[SAMFormatConst.RNAME_INDEX];
var loc = new SAMAlignedLocation(sam)
{
Seqname = seqname,
Start = int.Parse(parts[SAMFormatConst.POS_INDEX]),
Strand = strand,
Cigar = cigar,
NumberOfMismatch = mismatchCount,
AlignmentScore = score,
MismatchPositions = _format.GetMismatchPositions(parts)
};
loc.ParseEnd(sam.Sequence);
sam.AddLocation(loc);
if (_format.HasAlternativeHits)
{
_format.ParseAlternativeHits(parts, sam);
}
result.Add(sam);
waitingcount++;
}
Progress.SetMessage("Finally, there are {0} candidates from {1} reads", waitingcount, count);
}
return(result);
}
