/// <summary>
/// Gets the paired reads when SAMAligned sequences are in memory.
/// </summary>
/// <param name="meanLengthOfInsert">Mean of the insert length.</param>
/// <param name="standardDeviationOfInsert">Standard deviation of insert length.</param>
/// <param name="calculate">If this flag is set then mean and standard deviation will
/// be calculated from the paired reads instead of specified.</param>
/// <returns>List of paired read.</returns>
private IList <PairedRead> GetInMemoryPairedReads(float meanLengthOfInsert, float standardDeviationOfInsert, bool calculate = false)
{
// Dictionary helps to get the information at one pass of alinged sequence list.
Dictionary <string, PairedRead> pairedReads = new Dictionary <string, PairedRead>();
double sum = 0;
int count = 0;
for (int i = 0; i < QuerySequences.Count; i++)
{
PairedRead pairedRead;
SAMAlignedSequence read = QuerySequences[i];
if ((read.Flag & SAMFlags.PairedRead) == SAMFlags.PairedRead)
{
if (pairedReads.TryGetValue(read.QName, out pairedRead))
{
if (pairedRead.Read2 == null || pairedRead.Read1 == null)
{
if (pairedRead.Read2 == null)
{
pairedRead.Read2 = read;
}
else
{
pairedRead.Read1 = read;
}
pairedRead.PairedType = PairedRead.GetPairedReadType(pairedRead.Read1, pairedRead.Read2, meanLengthOfInsert, standardDeviationOfInsert);
if (pairedRead.PairedType == PairedReadType.Normal || pairedRead.PairedType == PairedReadType.LengthAnomaly)
{
pairedRead.InsertLength = PairedRead.GetInsertLength(pairedRead.Read1, pairedRead.Read2);
if (calculate)
{
sum += pairedRead.InsertLength;
count++;
}
}
}
else
{
pairedRead.InsertLength = 0;
if (calculate)
{
sum -= pairedRead.InsertLength;
count--;
}
pairedRead.Reads.Add(read);
pairedRead.PairedType = PairedReadType.MultipleHits;
}
}
else
{
pairedRead = new PairedRead();
if (!string.IsNullOrEmpty(read.RName) && !read.RName.Equals("*"))
{
pairedRead.Read1 = read;
}
else
{
pairedRead.Read2 = read;
}
pairedRead.PairedType = PairedReadType.Orphan;
pairedRead.InsertLength = 0;
pairedReads.Add(read.QName, pairedRead);
}
}
}
List <PairedRead> allreads = pairedReads.Values.ToList();
pairedReads = null;
if (calculate && count > 0)
{
UpdateType(allreads, sum, count);
}
return(allreads);
}
/// <summary>
/// Gets the paired reads when DV is enabled.
/// </summary>
/// <param name="meanLengthOfInsert">Mean of the insert length.</param>
/// <param name="standardDeviationOfInsert">Standard deviation of insert length.</param>
/// <param name="calculate">If this flag is set then mean and standard deviation will
/// be calculated from the paired reads instead of specified.</param>
/// <returns>List of paired read.</returns>
private IList <PairedRead> GetDVAwarePairedReads(float meanLengthOfInsert, float standardDeviationOfInsert, bool calculate = false)
{
// Dictionary helps to get the information at one pass of alinged sequence list.
Dictionary <string, DVEnabledPairedRead> pairedReads = new Dictionary <string, DVEnabledPairedRead>();
double sum = 0;
int count = 0;
for (int i = 0; i < QuerySequences.Count; i++)
{
DVEnabledPairedRead pairedRead;
SAMAlignedSequence read = QuerySequences[i];
if ((read.Flag & SAMFlags.PairedRead) == SAMFlags.PairedRead)
{
if (pairedReads.TryGetValue(read.QName, out pairedRead))
{
if (pairedRead.Index2 == -1 || pairedRead.Index1 == -1)
{
if (pairedRead.Index2 == -1)
{
pairedRead.Index2 = i;
}
else
{
pairedRead.Index1 = i;
}
// For best performace,
// 1. BAM/SAM file should be sorted by reads name.
// 2. If sorted on mapping position then give unmapped read a coordinate (generally the coordinate of the mapped mate)
// for sorting/indexing purposes only.
pairedRead.PairedType = PairedRead.GetPairedReadType(pairedRead.Read1, pairedRead.Read2, meanLengthOfInsert, standardDeviationOfInsert);
if (pairedRead.PairedType == PairedReadType.Normal || pairedRead.PairedType == PairedReadType.LengthAnomaly)
{
pairedRead.InsertLength = PairedRead.GetInsertLength(pairedRead.Read1, pairedRead.Read2);
if (calculate)
{
sum += pairedRead.InsertLength;
count++;
}
}
}
else
{
pairedRead.InsertLength = 0;
if (calculate)
{
sum -= pairedRead.InsertLength;
count--;
}
pairedRead.ReadIndexes.Add(i);
pairedRead.PairedType = PairedReadType.MultipleHits;
}
}
else
{
pairedRead = new DVEnabledPairedRead(QuerySequences);
if (!string.IsNullOrEmpty(read.RName) && !read.RName.Equals("*"))
{
pairedRead.Index1 = i;
}
else
{
pairedRead.Index2 = i;
}
pairedRead.PairedType = PairedReadType.Orphan;
pairedRead.InsertLength = 0;
pairedReads.Add(read.QName, pairedRead);
}
}
}
List <PairedRead> allreads = pairedReads.Values.ToList <PairedRead>();
pairedReads = null;
if (calculate && count > 0)
{
UpdateType(allreads, sum, count);
}
return(allreads);
}