示例#1
0
        public void Execute()
        {
            Read read;

            if (_alignmentSource.SourceIsStitched)
            {
                Logger.WriteToLog("Stitched reads detected");
            }

            while ((read = _alignmentSource.GetNextRead()) != null)
            {
                // find candidate variants
                var candidateVariants = _variantFinder.FindCandidates(read, _chrReference.Sequence,
                                                                      _chrReference.Name);

                // track in state manager
                _stateManager.AddCandidates(candidateVariants);
                _stateManager.AddAlleleCounts(read);

                // call anything possible to call
                Call(_alignmentSource.LastClearedPosition);
            }

            Call(); // call everything left

            if (_regionMapper != null)
            {
                _vcfWriter.WriteRemaining(_regionMapper);  // pad any remaining intervals if necessary
            }
            Logger.WriteToLog("Totals: {0} alleles called.  {1} variants collapsed.",
                              _alleleCaller.TotalNumCalled, _alleleCaller.TotalNumCollapsed);
        }
示例#2
0
        public void Execute()
        {
            AlignmentSet alignmentSet;

            while ((alignmentSet = _alignmentSource.GetNextAlignmentSet()) != null)
            {
                // find candidate variants
                var candidateVariants = _variantFinder.FindCandidates(alignmentSet, _chrReference.Sequence,
                                                                      _chrReference.Name);

                // track in state manager
                _stateManager.AddCandidates(candidateVariants);
                _stateManager.AddAlleleCounts(alignmentSet);

                // call anything possible to call
                Call(_alignmentSource.LastClearedPosition);
            }

            Call(); // call everything left

            Logger.WriteToLog("Totals: {0} alleles called.", _numCalledAlleles);
        }