public void Merge(ReadStatusCounter other)
{
foreach (var readStatus in other._readStatuses)
{
if (!_readStatuses.ContainsKey(readStatus.Key))
{
_readStatuses.Add(readStatus.Key, readStatus.Value);
}
else
{
_readStatuses[readStatus.Key] += readStatus.Value;
}
}
foreach (var debugReadStatus in other._debugReadStatuses)
{
if (!_debugReadStatuses.ContainsKey(debugReadStatus.Key))
{
_debugReadStatuses.Add(debugReadStatus.Key, debugReadStatus.Value);
}
else
{
_debugReadStatuses[debugReadStatus.Key] += debugReadStatus.Value;
}
}
}
public ReadMerger(int minBasecallQuality, bool allowRescuedInsertionBaseDisagreement, bool useSoftclippedBases, bool nifyDisagreements, ReadStatusCounter statusCounter, bool debug, bool ignoreProbeSoftclips)
{
_minBasecallQuality = minBasecallQuality;
_allowRescuedInsertionBaseDisagreement = allowRescuedInsertionBaseDisagreement;
_useSoftclippedBases = useSoftclippedBases;
_nifyDisagreements = nifyDisagreements;
_statusCounter = statusCounter;
_debug = debug;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
}
public BasicStitcher(int minBaseCallQuality, bool nifyDisagreements = true, bool useSoftclippedBases = true, bool debug = false,
bool nifyUnstitchablePairs = false, bool allowRescuedInsertionBaseDisagreement = false, bool ignoreProbeSoftclips = true, int maxReadLength = 1024)
{
_nifyUnstitchablePairs = nifyUnstitchablePairs;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
_useSoftclippedBases = useSoftclippedBases;
_debug = debug;
_statusCounter = new ReadStatusCounter();
_cigarReconciler = new CigarReconciler(_statusCounter, _useSoftclippedBases, _debug, _ignoreProbeSoftclips, maxReadLength);
_readMerger = new ReadMerger(minBaseCallQuality, allowRescuedInsertionBaseDisagreement, _useSoftclippedBases,
nifyDisagreements, _statusCounter, _debug, _ignoreProbeSoftclips);
}
public BasicStitcher(int minBaseCallQuality, bool nifyDisagreements = true, bool useSoftclippedBases = true, bool debug = false,
bool nifyUnstitchablePairs = false, bool allowRescuedInsertionBaseDisagreement = false, bool ignoreProbeSoftclips = true, int maxReadLength = 1024,
bool ignoreReadsAboveMaxLength = false, uint minMapQuality = 1, bool dontStitchHomopolymerBridge = true, int thresholdNumDisagreeingBases = int.MaxValue)
{
_nifyUnstitchablePairs = nifyUnstitchablePairs;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
_useSoftclippedBases = useSoftclippedBases;
_debug = debug;
_minMapQuality = minMapQuality;
_dontStitchHomopolymerBridge = dontStitchHomopolymerBridge;
_statusCounter = new ReadStatusCounter();
_cigarReconciler = new CigarReconciler(_statusCounter, _useSoftclippedBases, _debug, _ignoreProbeSoftclips, maxReadLength, minBaseCallQuality, ignoreReadsAboveMaxStitchedLength: ignoreReadsAboveMaxLength, nifyDisagreements: nifyDisagreements);
_readMerger = new ReadMerger(minBaseCallQuality, allowRescuedInsertionBaseDisagreement, _useSoftclippedBases,
nifyDisagreements, _statusCounter, _debug, _ignoreProbeSoftclips);
_thresholdNumDisagreeingBases = thresholdNumDisagreeingBases;
}
public CigarReconciler(ReadStatusCounter statusCounter, bool useSoftclippedBases, bool debug, bool ignoreProbeSoftclips, int maxReadLength, bool allowTerminalClipsToSupportOverlappingDels = true)
{
_statusCounter = statusCounter;
_useSoftclippedBases = useSoftclippedBases;
_debug = debug;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
_allowTerminalClipsToSupportOverlappingDels = allowTerminalClipsToSupportOverlappingDels;
var maxStitchedReadLength = maxReadLength * 2 - 1;
_stitchPositions = new StitchedPosition[maxStitchedReadLength];
// For performance reasons, we keep one collection of StitchedPositions and recycle them for each pair we try to stitch
for (var i = 0; i < maxStitchedReadLength; i++)
{
_stitchPositions[i] = new StitchedPosition();
}
}
public void SetStatusCounter(ReadStatusCounter counter)
{
_statusCounter = counter;
}