Package htsjdk.variant.bcf2

Class BCF2Decoder

java.lang.Object
htsjdk.variant.bcf2.BCF2Decoder
public final class BCF2Decoder extends Object

  • Constructor Details

    • BCF2Decoder

      public BCF2Decoder()

    • BCF2Decoder

      protected BCF2Decoder(byte[] recordBytes)
      Create a new decoder ready to read BCF2 data from the byte[] recordBytes, for testing purposes
      Parameters:
      recordBytes -

  • Method Details

    • readNextBlock

      public void readNextBlock(int blockSizeInBytes, InputStream stream)
      Reads the next record from input stream and prepare this decoder to decode values from it
      Parameters:
      stream -

    • skipNextBlock

      public void skipNextBlock(int blockSizeInBytes, InputStream stream)
      Skips the next record from input stream, invalidating current block data
      Parameters:
      stream -

    • getRecordBytes

      public byte[] getRecordBytes()
      Returns the byte[] for the block of data we are currently decoding
      Returns:

    • getBlockSize

      public int getBlockSize()
      The size of the current block in bytes
      Returns:

    • blockIsFullyDecoded

      public boolean blockIsFullyDecoded()

    • setRecordBytes

      public void setRecordBytes(byte[] recordBytes)
      Use the recordBytes[] to read BCF2 records from now on
      Parameters:
      recordBytes -

    • decodeTypedValue

      public final Object decodeTypedValue() throws IOException
      Throws:
      IOException

    • decodeTypedValue

      public final Object decodeTypedValue(byte typeDescriptor) throws IOException
      Throws:
      IOException

    • decodeTypedValue

      public final Object decodeTypedValue(byte typeDescriptor, int size) throws IOException
      Throws:
      IOException

    • decodeSingleValue

      public final Object decodeSingleValue(BCF2Type type) throws IOException
      Throws:
      IOException

    • decodeNumberOfElements

      public final int decodeNumberOfElements(byte typeDescriptor) throws IOException
      Throws:
      IOException

    • decodeInt

      public final int decodeInt(byte typeDescriptor, int missingValue) throws IOException
      Decode an int from the stream. If the value in the stream is missing, returns missingValue. Requires the typeDescriptor indicate an inline single element event
      Parameters:
      typeDescriptor -
      Returns:
      Throws:
      IOException

    • decodeInt

      public final int decodeInt(BCF2Type type) throws IOException
      Throws:
      IOException

    • decodeIntArray

      public final int[] decodeIntArray(int size, BCF2Type type, int[] maybeDest) throws IOException
      Low-level reader for int[] Requires a typeDescriptor so the function knows how many elements to read, and how they are encoded. If size == 0 => result is null If size > 0 => result depends on the actual values in the stream -- If the first element read is MISSING, result is null (all values are missing) -- Else result = int[N] where N is the first N non-missing values decoded
      Parameters:
      maybeDest - if not null we'll not allocate space for the vector, but instead use the externally allocated array of ints to store values. If the size of this vector is < the actual size of the elements, we'll be forced to use freshly allocated arrays. Also note that padded int elements are still forced to do a fresh allocation as well.
      Returns:
      see description
      Throws:
      IOException

    • decodeIntArray

      public final int[] decodeIntArray(byte typeDescriptor, int size) throws IOException
      Throws:
      IOException

    • readBlockSize

      public final int readBlockSize(InputStream inputStream) throws IOException
      Read the size of the next block from inputStream
      Parameters:
      inputStream -
      Returns:
      Throws:
      IOException

    • readTypeDescriptor

      public final byte readTypeDescriptor() throws IOException
      Throws:
      IOException