/// <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;
}
}
