// --------------------------------------------------------------------------------
//
// Constructors
//
// --------------------------------------------------------------------------------
/// <summary>
/// create a local-sorting VCF writer, given an inner VCF writer to write to
/// </summary>
/// <param name="innerWriter"> the VCFWriter to write to </param>
/// <param name="takeOwnershipOfInner"> Should this Writer close innerWriter when it's done with it </param>
public SortingVariantContextWriterBase(VariantContextWriter innerWriter, bool takeOwnershipOfInner)
{
this.innerWriter = innerWriter;
this.finishedChromosomes = new SortedSet<string>();
this.takeOwnershipOfInner = takeOwnershipOfInner;
// has to be PriorityBlockingQueue to be thread-safe
this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;
}
public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance) : this(innerWriter, maxCachingStartDistance, false); / / by default, don't own inner
/// <summary>
/// create a local-sorting VCF writer, given an inner VCF writer to write to
/// </summary>
/// <param name="innerWriter"> the VCFWriter to write to </param>
/// <param name="maxCachingStartDistance"> the maximum start distance between records that we'll cache </param>
/// <param name="takeOwnershipOfInner"> Should this Writer close innerWriter when it's done with it </param>
public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, bool takeOwnershipOfInner) : base(innerWriter, takeOwnershipOfInner)
{
this.maxCachingStartDistance = maxCachingStartDistance;
}
public SortingVariantContextWriterBase(VariantContextWriter innerWriter) : this(innerWriter, false); / / by default, don't own inner
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance, bool takeOwnershipOfInner)
{
return(new SortingVariantContextWriter(innerWriter, maxCachingStartDistance, takeOwnershipOfInner));
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, int maxCachingStartDistance)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance)
{
return(sortOnTheFly(innerWriter, maxCachingStartDistance, false));
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance, bool takeOwnershipOfInner)
{
return new SortingVariantContextWriter(innerWriter, maxCachingStartDistance, takeOwnershipOfInner);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, int maxCachingStartDistance)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance)
{
return sortOnTheFly(innerWriter, maxCachingStartDistance, false);
}
