public List<PileupCount> Add(SAMAlignedItem item, int count)
{
List<PileupCount> result = null;
if (!item.Locations[0].Seqname.Equals(this.Chromosome))
{
result = Count;
Count = new List<PileupCount>();
}
else if (this.Position != -1)
{
if (item.Pos > this.Count.Last().Position)
{
result = Count;
Count = new List<PileupCount>();
}
else
{
int finishedCount = (int)(item.Pos - this.Position);
if (finishedCount > 0)
{
result = new List<PileupCount>();
result.AddRange(Count.Take(finishedCount));
Count.RemoveRange(0, finishedCount);
}
}
}
string align, refer;
item.GetSequences(out align, out refer);
for (int i = Count.Count; i < align.Length; i++)
{
Count.Add(new PileupCount()
{
Chromosome = item.Locations[0].Seqname,
Position = item.Locations[0].Start + i,
Reference = refer[i]
});
}
for (int i = 0; i < align.Length; i++)
{
var c = align[i];
var dic = Count[i];
int curcount = 0;
if (dic.TryGetValue(c, out curcount))
{
dic[c] = curcount + count;
}
else
{
dic[c] = count;
}
}
return result;
}
public void TestGetGetSequences()
{
SAMAlignedItem item = new SAMAlignedItem();
item.AddLocation(new SAMAlignedLocation(item)
{
Cigar = "5S18M2D19M5S",
Start = 39979942,
MismatchPositions = "18^CA10T8",
Sequence = "aaaaaGTAGTACCAACTGTAAGTCCTTATCTTCATACTTTGTaaaaa"
});
string align, refer;
item.GetSequences(out align, out refer);
Assert.AreEqual("GTAGTACCAACTGTAAGT CCTTATCTTCATACTTTGT", align);
Assert.AreEqual("GTAGTACCAACTGTAAGTCACCTTATCTTCTTACTTTGT", refer);
}
public void Add(SAMAlignedItem item, int count)
{
string align, refer;
item.GetSequences(out align, out refer);
for (int i = 0; i < align.Length; i++)
{
var c = align[i];
var dic = Count[(int)(item.Pos) + i];
int curcount = 0;
if (dic.TryGetValue(c, out curcount))
{
dic[c] = curcount + count;
}
else
{
dic[c] = count;
}
}
}