public LocalizationRecord(string value = "", string hint = "",
Source source = Source.Code, PairStatus status = PairStatus.New, string context = "")
{
Value = value;
Hint = hint;
Status = status;
Source = source;
this.context = context;
}
public static ReadPair GetPair(string cigar1, string cigar2, uint mapq1 = 30, uint mapq2 = 30, PairStatus pairStatus = PairStatus.Paired, bool singleReadOnly = false, int nm = 0, int read2Offset = 0, int?nm2 = null, string name = null, string basesRaw = "AAAGTTTTCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", int read1Position = 99, string read1Bases = null, string read2Bases = null)
{
int nmRead2 = nm2 ?? nm;
var tagUtils = new TagUtils();
if (nm >= 0)
{
tagUtils.AddIntTag("NM", nm);
}
var cigarAln1 = new CigarAlignment(cigar1);
var qualities1 = new List <byte>();
for (int i = 0; i < cigarAln1.GetReadSpan(); i++)
{
qualities1.Add(30);
}
//var basesRaw = "AAAGTTTTCCCCCCCCCCCC";
var alignment = new BamAlignment
{
Name = name ?? "hi:1:2:3:4:5:6",
RefID = 1,
Position = read1Position,
Bases = read1Bases ?? basesRaw.Substring(0, (int)cigarAln1.GetReadSpan()),
CigarData = cigarAln1,
Qualities = qualities1.ToArray(),
MapQuality = mapq1
};
alignment.TagData = tagUtils.ToBytes();
if (!singleReadOnly)
{
alignment.SetIsProperPair(true);
alignment.MateRefID = 1;
}
var pair = new ReadPair(alignment);
if (!singleReadOnly)
{
alignment.SetIsMateUnmapped(false);
var tagUtils2 = new TagUtils();
if (nmRead2 >= 0)
{
tagUtils2.AddIntTag("NM", nmRead2);
}
var cigarAln2 = new CigarAlignment(cigar2);
var qualities2 = new List <byte>();
for (int i = 0; i < cigarAln2.GetReadSpan(); i++)
{
qualities2.Add(30);
}
var alignment2 = new BamAlignment
{
Name = "hi:1:2:3:4:5:6",
RefID = 1,
Position = read1Position + read2Offset,
Bases = read2Bases ?? basesRaw.Substring(read2Offset, (int)cigarAln2.GetReadSpan()),
CigarData = cigarAln2,
Qualities = qualities2.ToArray(),
MapQuality = mapq2
};
alignment2.MateRefID = pair.Read1.RefID;
alignment2.SetIsProperPair(true);
alignment2.SetIsSecondMate(true);
alignment2.SetIsReverseStrand(true);
alignment2.TagData = tagUtils2.ToBytes();
pair.AddAlignment(alignment2);
}
pair.PairStatus = pairStatus;
return(pair);
}
static void AddToStorage(SortedDictionary <string, LocalizationRecord> storage,
string key, string value, string hint, Source source, PairStatus status, string context)
{
if (string.IsNullOrEmpty(hint))
{
hint = "Empty";
}
if (storage.ContainsKey(key))
{
var hintOld = storage[key].Hint;
if (hintOld == "Empty" && hint != "Empty")
{
storage[key].Hint = hint;
}
else if (hintOld != hint && hint != "Empty")
{
UnityEngine.Debug.LogError($"Key {key} hint \"{hint}\" from {context} is not same as hint \"{hintOld}\" from {storage[key].context}");
}
return;
}
storage.Add(key, new LocalizationRecord(value, hint, source, status, context));
}
public void ClearRemoved()
{
Status &= ~PairStatus.PairRemoved;
}
public void SetFinal()
{
Status |= PairStatus.PairFinal;
}
public void SetRemoved()
{
Status |= PairStatus.PairRemoved;
}
public void ClearBuffered()
{
Status &= ~PairStatus.PairBuffered;
}
public void SetBuffered()
{
Status |= PairStatus.PairBuffered;
}
private static StatementPair GetCorrespondingPairByStatementPairs(StatementPair pair1, StatementPair pair2, StatementPair pair3, Conclusion conclusion)
{
PairStatus status = GetPairResultStatus(pair1, pair2, pair3);
switch (status)
{
case PairStatus.AllAreInvalid: //==>All pair results are invalid
return(null);
case PairStatus.AllAreValid: //==>All pair results are valid
if (CheckCorrespondingPairs(conclusion, pair1.ResultStatement)) //Checking First Pair
{
return(pair1);
}
else if (CheckCorrespondingPairs(conclusion, pair2.ResultStatement)) //Checking Second Pair
{
return(pair2);
}
else if (CheckCorrespondingPairs(conclusion, pair3.ResultStatement)) //Checking Third Pair
{
return(pair3);
}
return(null);
case PairStatus.FirstPairAloneIsValid: //==> pair1 result alone is valid
if (CheckCorrespondingPairs(conclusion, pair1.ResultStatement)) //Checking First Pair
{
return(pair1);
}
return(null);
case PairStatus.SecondPairAloneIsValid: //==> pair2 result alone is valid
if (CheckCorrespondingPairs(conclusion, pair2.ResultStatement)) //Checking Second Pair
{
return(pair2);
}
return(null);
case PairStatus.ThirdPairAloneIsValid: //==> pair3 result alone is valid
if (CheckCorrespondingPairs(conclusion, pair3.ResultStatement)) //Checking Third Pair
{
return(pair3);
}
return(null);
case PairStatus.FirstAndSecondPairsAreValid: //==> pair1 & pair2 results are valid
if (CheckCorrespondingPairs(conclusion, pair1.ResultStatement)) //Checking First Pair
{
return(pair1);
}
else if (CheckCorrespondingPairs(conclusion, pair2.ResultStatement)) //Checking Second Pair
{
return(pair2);
}
return(null);
case PairStatus.SecondAndThirdPairsAreValid: //==> pair2 & pair3 results are valid
if (CheckCorrespondingPairs(conclusion, pair2.ResultStatement)) //Checking Second Pair
{
return(pair2);
}
else if (CheckCorrespondingPairs(conclusion, pair3.ResultStatement)) //Checking Third Pair
{
return(pair3);
}
return(null);
case PairStatus.FirstAndThirdPairsAreValid: //==> pair1 & pair3 results are valid
if (CheckCorrespondingPairs(conclusion, pair1.ResultStatement)) //Checking First Pair
{
return(pair1);
}
else if (CheckCorrespondingPairs(conclusion, pair3.ResultStatement)) //Checking Third Pair
{
return(pair3);
}
return(null);
}
return(null);
}
public ReadPair TryPair(BamAlignment alignment, PairStatus pairStatus = PairStatus.Unknown)
{
if (_readsProcessed % 100000 == 0)
{
LogStatus(alignment.RefID + ":" + alignment.Position);
}
_readsProcessed++;
LastRefId = alignment.RefID;
var readIndexer = ReadIndexer(alignment);
// Check if this read should be blacklisted
if (ShouldBlacklistReadIndexer(alignment))
{
_blacklistedReads.Add(readIndexer);
}
// If this read is in the blacklist, or is a read that should be "aggressively" skipped, skip the read. If we've already started tracking a mate, remove it from the mate lookup.
if (ShouldSkipAndRemoveWaitingMates(alignment) || _blacklistedReads.Contains(readIndexer))
{
_readsAggressivelySkipped++;
if (_readsWaitingForMate.ContainsKey(readIndexer))
{
_readsWaitingForMate.Remove(readIndexer);
}
return(null);
}
if (ShouldSkipRead(alignment))
{
_readsSkipped++;
return(null);
}
if (!_readsWaitingForMate.ContainsKey(readIndexer))
{
// TODO do we really need to create a new copy here? I think we're already doing it later
_readsWaitingForMate.Add(readIndexer, new ReadPair(alignment, readIndexer, GetReadNumber(alignment))
{
PairStatus = pairStatus
});
return(null);
}
else
{
var readPair = _readsWaitingForMate[readIndexer];
readPair.AddAlignment(alignment, GetReadNumber(alignment));
if (!readPair.IsComplete(_requireSupplementaries) || _pairEvaluator.TreatReadPairAsIncomplete(readPair))
{
return(null);
}
_pairsProcessed++;
// Check pair and either skip or return pair
var shouldSkip = ShouldSkipPair(readPair);
if (!shouldSkip || _removeFailedPairs)
{
_readsWaitingForMate.Remove(readIndexer); // If succeeded, no longer waiting for mate; if failed and we're being strict on failures, remove
}
if (ShouldWhitelistReadIndexer(alignment, shouldSkip))
{
_whitelistedReads.Add(readIndexer);
}
if (shouldSkip)
{
_pairsSkipped++;
}
else
{
_pairsPaired++;
}
return(shouldSkip ? null : readPair);
}
}
