Exemplo n.º 1
0
        private void Call(int?upToPosition = null)
        {
            var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference);

            if (readyBatch == null)
            {
                return;
            }

            if (readyBatch.HasCandidates)
            {
                // evaluate and call variants (including ref calls if producing gvcf)
                var BaseCalledAllelesByPosition = _alleleCaller.Call(readyBatch, _stateManager);

                var BaseCalledAlleles = BaseCalledAllelesByPosition.Values.SelectMany(a => a).ToList();

                // write to vcf
                _vcfWriter.Write(BaseCalledAlleles, _regionMapper);

                if (_biasFileWriter != null)
                {
                    _biasFileWriter.Write(BaseCalledAlleles);
                }
            }

            if (_intervalSet != null && readyBatch.MaxClearedPosition.HasValue)
            {
                _intervalSet.SetCleared(readyBatch.MaxClearedPosition.Value);
            }

            _stateManager.DoneProcessing(readyBatch);
        }
Exemplo n.º 2
0
        private void Call(int?upToPosition = null)
        {
            var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference);

            // map to intervals if needed
            if (_regionMapper != null)
            {
                _regionMapper.Pad(readyBatch, !upToPosition.HasValue);
            }

            if (readyBatch.HasCandidates)
            {
                // evaluate and call variants (including ref calls if producing gvcf)
                var calledVariants = _alleleCaller.Call(readyBatch, _stateManager);

                _numCalledAlleles += calledVariants.Count();

                // write to vcf
                _vcfWriter.Write(calledVariants);

                if (_biasFileWriter != null)
                {
                    _biasFileWriter.Write(calledVariants);
                }
            }

            _stateManager.DoneProcessing(readyBatch);
        }
        private void Call(int?upToPosition = null)
        {
            var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference, _forcedGtAlleles);

            if (readyBatch == null)
            {
                return;
            }

            if (readyBatch.HasCandidates)
            {
                // evaluate and call variants (including ref calls if producing gvcf)
                var BaseCalledAllelesByPosition = _alleleCaller.Call(readyBatch, _stateManager);


                var BaseCalledAlleles = BaseCalledAllelesByPosition.Values.SelectMany(a => a).ToList();



                // write to vcf
                _vcfWriter.Write(BaseCalledAlleles, _regionMapper);

                //always coupled together for simplicty, so no need for two checks.
                if (_writeBiasFiles)
                {
                    _strandBiasFileWriter.Write(BaseCalledAlleles);
                    _ampliconBiasFileWriter.Write(BaseCalledAlleles);
                }
            }

            if (_intervalSet != null && readyBatch.MaxClearedPosition.HasValue)
            {
                _intervalSet.SetCleared(readyBatch.MaxClearedPosition.Value);
            }

            _stateManager.DoneProcessing(readyBatch);
        }