/// <summary>
/// Gets the paired reads type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="libraryInfo">Library information.</param>
/// <param name="useInsertLengthOfReads">
/// If this flag is set to true then insert length will be calculated from read1 and read2,
/// else InsertLength in spcified paired read will be used.
/// </param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, CloneLibraryInformation libraryInfo, bool useInsertLengthOfReads)
{
if (pairedRead == null)
{
throw new ArgumentNullException("pairedRead");
}
if (libraryInfo == null)
{
throw new ArgumentNullException("libraryInfo");
}
return(GetPairedReadType(pairedRead, libraryInfo.MeanLengthOfInsert, libraryInfo.StandardDeviationOfInsert, useInsertLengthOfReads));
}
/// <summary>
/// Gets the paired reads type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="libraryName">library name.</param>
/// <param name="useInsertLengthOfReads">
/// If this flag is set to true then insert length will be calculated from read1 and read2,
/// else InsertLength in spcified paired read will be used.
/// </param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, string libraryName, bool useInsertLengthOfReads)
{
if (pairedRead == null)
{
throw new ArgumentNullException("pairedRead");
}
if (string.IsNullOrEmpty(libraryName))
{
throw new ArgumentNullException("libraryName");
}
CloneLibraryInformation libraryInfo = CloneLibrary.Instance.GetLibraryInformation(libraryName);
if (libraryInfo == null)
{
throw new ArgumentOutOfRangeException("libraryName");
}
return(GetPairedReadType(pairedRead, libraryInfo, useInsertLengthOfReads));
}
/// <summary>
/// Gets the paired reads type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="meanLengthOfInsert">Mean of the insertion length.</param>
/// <param name="standardDeviationOfInsert">Standard deviation of insertion length.</param>
/// <param name="useInsertLengthOfReads">
/// If this flag is set to true then insert length will be calculated from read1 and read2,
/// else InsertLength in spcified paired read will be used.
/// By default this will be set to false.
/// </param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, float meanLengthOfInsert, float standardDeviationOfInsert, bool useInsertLengthOfReads)
{
if (pairedRead == null)
{
throw new ArgumentNullException("pairedRead");
}
if (pairedRead._alignedSequences.Count > 2)
{
return(PairedReadType.MultipleHits);
}
if (useInsertLengthOfReads)
{
return(GetPairedReadType(pairedRead.Read1, pairedRead.Read2, meanLengthOfInsert, standardDeviationOfInsert));
}
else
{
PairedReadType type = GetPairedReadType(pairedRead.Read1, pairedRead.Read2, meanLengthOfInsert, standardDeviationOfInsert);
if (type == PairedReadType.Normal || type == PairedReadType.LengthAnomaly)
{
int insertLength = pairedRead.InsertLength;
// µ + 3σ
float upperLimit = meanLengthOfInsert + (3 * standardDeviationOfInsert);
// µ - 3σ
float lowerLimit = meanLengthOfInsert - (3 * standardDeviationOfInsert);
if (insertLength > upperLimit || insertLength < lowerLimit)
{
type = PairedReadType.LengthAnomaly;
}
else
{
type = PairedReadType.Normal;
}
}
return(type);
}
}
/// <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);
}
/// <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 type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="meanLengthOfInsert">Mean of the insertion length.</param>
/// <param name="standardDeviationOfInsert">Standard deviation of insertion length.</param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, float meanLengthOfInsert, float standardDeviationOfInsert)
{
return(GetPairedReadType(pairedRead, meanLengthOfInsert, standardDeviationOfInsert, false));
}
/// <summary>
/// Gets the paired reads type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="libraryInfo">Library information.</param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, CloneLibraryInformation libraryInfo)
{
return(GetPairedReadType(pairedRead, libraryInfo, false));
}
/// <summary>
/// Gets the paired reads type.
/// </summary>
/// <param name="pairedRead">Paired read.</param>
/// <param name="libraryName">library name.</param>
public static PairedReadType GetPairedReadType(PairedRead pairedRead, string libraryName)
{
return(GetPairedReadType(pairedRead, libraryName, false));
}