/// <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;
        }
Exemplo n.º 2
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 /// <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;
     }
 }
Exemplo n.º 3
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        /// <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;
        }
Exemplo n.º 4
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        /// <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;
        }
Exemplo n.º 5
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        /// <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;
        }
Exemplo n.º 6
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 /// <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;
     }
 }
Exemplo n.º 7
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        /// <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;
        }