/// <summary>
/// Initializes a new instance of the GraphScaffoldBuilder class.
/// </summary>
/// <param name="mapPairedReads">Mapping reads to mate pairs.</param>
/// <param name="readContigMap"> Mapping reads to contigs.</param>
/// <param name="pairedReadFilter">Filtering of mate pairs.</param>
/// <param name="distanceCalculator">Calculation of distance between
/// contigs using mate pairs.</param>
/// <param name="tracePath">Traversal of contig overlap graph.</param>
/// <param name="pathAssembler">Removal of containing paths and removal of overlapping paths.</param>
public GraphScaffoldBuilder(
IMatePairMapper mapPairedReads,
IReadContigMapper readContigMap,
IOrientationBasedMatePairFilter pairedReadFilter,
IDistanceCalculator distanceCalculator,
ITracePath tracePath,
IPathPurger pathAssembler)
{
this.mapPairedReads = mapPairedReads ?? new MatePairMapper();
this.readContigMap = readContigMap ?? new ReadContigMapper();
this.pairedReadFilter = pairedReadFilter ?? new OrientationBasedMatePairFilter();
this.tracePath = tracePath ?? new TracePath();
this.pathAssembler = pathAssembler ?? new PathPurger();
if (null != distanceCalculator)
{
this.distanceCalculator = distanceCalculator;
}
//Hierarchical Scaffolding With Bambus
//by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
//Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.
this.redundancyField = 2;
//Memory and performance optimization.
this.depthField = 10;
}
/// <summary>
/// Dispose field instances.
/// </summary>
/// <param name="disposeManaged">If disposeManaged equals true, clean all resources.</param>
protected virtual void Dispose(bool disposeManaged)
{
if (disposeManaged)
{
this.distanceCalculator = null;
this.mapPairedReads = null;
this.pairedReadFilter = null;
this.pathAssembler = null;
this.readContigMap = null;
this.tracePath = null;
}
}
/// <summary>
/// Initializes a new instance of the GraphScaffoldBuilder class.
/// </summary>
public GraphScaffoldBuilder()
{
this.mapPairedReads = new MatePairMapper();
this.readContigMap = new ReadContigMapper();
this.pairedReadFilter = new OrientationBasedMatePairFilter();
this.tracePath = new TracePath();
this.pathAssembler = new PathPurger();
//Hierarchical Scaffolding With Bambus
//by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
//Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.
this.redundancyField = 2;
//Memory and performance optimization.
this.depthField = 10;
}
/// <summary>
/// Initializes a new instance of the GraphScaffoldBuilder class.
/// </summary>
public GraphScaffoldBuilder()
{
this.mapPairedReads = new MatePairMapper();
this.readContigMap = new ReadContigMapper();
this.pairedReadFilter = new OrientationBasedMatePairFilter();
this.tracePath = new TracePath();
this.pathAssembler = new PathPurger();
//Hierarchical Scaffolding With Bambus
//by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
//Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.
this.redundancyField = 2;
//Memory and performance optimization.
this.depthField = 10;
}
/// <summary>
/// Initializes a new instance of the GraphScaffoldBuilder class.
/// </summary>
/// <param name="mapPairedReads">Mapping reads to mate pairs.</param>
/// <param name="readContigMap"> Mapping reads to contigs.</param>
/// <param name="pairedReadFilter">Filtering of mate pairs.</param>
/// <param name="distanceCalculator">Calculation of distance between
/// contigs using mate pairs.</param>
/// <param name="tracePath">Traversal of contig overlap graph.</param>
/// <param name="pathAssembler">Removal of containing paths and removal of overlapping paths.</param>
public GraphScaffoldBuilder(
IMatePairMapper mapPairedReads,
IReadContigMapper readContigMap,
IOrientationBasedMatePairFilter pairedReadFilter,
IDistanceCalculator distanceCalculator,
ITracePath tracePath,
IPathPurger pathAssembler)
{
this.mapPairedReads = mapPairedReads ?? new MatePairMapper();
this.readContigMap = readContigMap ?? new ReadContigMapper();
this.pairedReadFilter = pairedReadFilter ?? new OrientationBasedMatePairFilter();
this.tracePath = tracePath ?? new TracePath();
this.pathAssembler = pathAssembler ?? new PathPurger();
if (null != distanceCalculator)
{
this.distanceCalculator = distanceCalculator;
}
//Hierarchical Scaffolding With Bambus
//by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
//Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.
this.redundancyField = 2;
//Memory and performance optimization.
this.depthField = 10;
}
/// <summary>
/// Dispose field instances.
/// </summary>
/// <param name="disposeManaged">If disposeManaged equals true, clean all resources.</param>
protected virtual void Dispose(bool disposeManaged)
{
if (disposeManaged)
{
this.distanceCalculator = null;
this.mapPairedReads = null;
this.pairedReadFilter = null;
this.pathAssembler = null;
this.readContigMap = null;
this.tracePath = null;
}
}
/// <summary>
/// Initializes a new instance of the GraphScaffoldBuilder class.
/// </summary>
/// <param name="mapPairedReads">Mapping reads to mate pairs.</param>
/// <param name="readContigMap"> Mapping reads to contigs.</param>
/// <param name="pairedReadFilter">Filtering of mate pairs.</param>
/// <param name="distanceCalculator">Calculation of distance between
/// contigs using mate pairs.</param>
/// <param name="tracePath">Traversal of contig overlap graph.</param>
/// <param name="pathAssembler">Removal of containing paths and removal of overlapping paths.</param>
public GraphScaffoldBuilder(
IMatePairMapper mapPairedReads,
IReadContigMapper readContigMap,
IOrientationBasedMatePairFilter pairedReadFilter,
IDistanceCalculator distanceCalculator,
ITracePath tracePath,
IPathPurger pathAssembler)
{
if (null != mapPairedReads)
{
_mapPairedReads = mapPairedReads;
}
else
{
_mapPairedReads = new MatePairMapper();
}
if (null != readContigMap)
{
_readContigMap = readContigMap;
}
else
{
_readContigMap = new ReadContigMapper();
}
if (null != pairedReadFilter)
{
_pairedReadFilter = pairedReadFilter;
}
else
{
_pairedReadFilter = new OrientationBasedMatePairFilter();
}
if (null != distanceCalculator)
{
_distanceCalculator = distanceCalculator;
}
else
{
_distanceCalculator = new DistanceCalculator();
}
if (null != tracePath)
{
_tracePath = tracePath;
}
else
{
_tracePath = new TracePath();
}
if (null != pathAssembler)
{
_pathAssembler = pathAssembler;
}
else
{
_pathAssembler = new PathPurger();
}
//Hierarchical Scaffolding With Bambus
//by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg
//Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.
_redundancy = 2;
//Memory and performance optimization.
_depth = 10;
}