Package htsjdk.samtools

Class Bin

    • Constructor Detail

      • Bin

        public Bin​(int referenceSequence,
           int binNumber)

    • Method Detail

      • getReferenceSequence

        protected int getReferenceSequence()

      • getBinNumber

        public int getBinNumber()

      • equals

        public boolean equals​(Object other)
        See whether two bins are equal. If the ref seq and the bin number are equal, assume equality of the chunk list.
        Overrides:
        equals in class Object
        Parameters:
        other - The other Bin to which to compare this.
        Returns:
        True if the two bins are equal. False otherwise.

      • hashCode

        public int hashCode()
        Compute a unique hash code for the given reference sequence and bin number.
        Overrides:
        hashCode in class Object
        Returns:
        A unique hash code.

      • containsChunks

        public boolean containsChunks()
        Returns whether the bin currently contains chunks.
        Returns:
        True if the bin has chunks, false otherwise.

      • compareTo

        public int compareTo​(Bin other)
        Compare two bins to see what ordering they should appear in.
        Specified by:
        compareTo in interface Comparable<Bin>
        Parameters:
        other - Other bin to which this bin should be compared.
        Returns:
        -1 if this < other, 0 if this == other, 1 if this > other.

      • addInitialChunk

        public void addInitialChunk​(Chunk newChunk)
        Adds the first chunk to the bin

      • addChunk

        public void addChunk​(Chunk newChunk)
        Adds a chunk to the bin (may be the first chunk or a later one).
        Parameters:
        newChunk - the chunk to add

      • setChunkList

        public void setChunkList​(List<Chunk> list)
        Sets the chunks associated with this bin

      • getChunkList

        public List<Chunk> getChunkList()
        Gets the list of chunks associated with this bin.
        Returns:
        the chunks in this bin. If no chunks are associated, an empty list will be returned.

      • setLastChunk

        public void setLastChunk​(Chunk c)
        Optimization to keep lastChunk instead of iterating over all chunks repeatedly

      • getLastChunk

        public Chunk getLastChunk()
        Warning: Currently only valid during index building, not when reading existing index, (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
        Returns:
        the last Chunk of the chunkList