/// <summary> /// Step 6: Build scaffolds from contig list and paired reads /// </summary> /// <param name="contigs">List of contigs</param> /// <returns>List of scaffold sequences</returns> protected IList <ISequence> BuildScaffolds(IList <ISequence> contigs) { if (_scaffoldBuilder == null) { // Scaffold Builder is a required module for this method. Set this to default. _scaffoldBuilder = new GraphScaffoldBuilder(); } return(_scaffoldBuilder.BuildScaffold(SequenceReads, contigs, KmerLength, depth: Depth, redundancy: ScaffoldRedundancy)); }
/// <summary> /// Dispose field instances. /// </summary> /// <param name="disposeManaged">If disposeManaged equals true, clean all resources.</param> protected virtual void Dispose(bool disposeManaged) { if (disposeManaged) { if (this.scaffoldBuilder != null) { this.scaffoldBuilder.Dispose(); } this.graph = null; this.sequenceReads = null; this.danglingLinksPurger = null; this.redundantPathsPurger = null; this.contigBuilder = null; this.scaffoldBuilder = null; } }
/// <summary> /// Dispose field instances /// </summary> /// <param name="disposeManaged">If disposeManaged equals true, clean all resources</param> protected virtual void Dispose(bool disposeManaged) { if (disposeManaged) { if (_graph != null) { _graph.Dispose(); } if (_scaffoldBuilder != null) { _scaffoldBuilder.Dispose(); } _graph = null; _sequenceReads = null; _danglingLinksPurger = null; _redundantPathsPurger = null; _contigBuilder = null; _scaffoldBuilder = null; } }