Package htsjdk.samtools.util

Class FastLineReader

java.lang.Object
htsjdk.samtools.util.FastLineReader
All Implemented Interfaces:
Closeable, AutoCloseable
public class FastLineReader extends Object implements Closeable
Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance. Implementation detail: All public methods must leave the input buffer in a non-empty state, unless at EOF.

  • Constructor Details

    • FastLineReader

      public FastLineReader(InputStream in)

  • Method Details

    • eof

      public boolean eof()
      Returns:
      true if input is exhausted

    • atEoln

      public boolean atEoln()
      Returns:
      peeks at the next byte in the stream and returns true if it is CR or LF. Returns false if EOF or next byte is not CR or LF.

    • skipNewlines

      public boolean skipNewlines()
      Advance over any EOLN chars (CR or LF)
      Returns:
      true if saw one or more CR or LFs

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable

    • getByte

      public byte getByte()
      Returns:
      Next byte from the input. Do not call if at EOF.

    • peekByte

      public byte peekByte()
      Returns:
      Next byte from the input, without advancing over that byte. Do not call if at EOF.

    • readToEndOfOutputBufferOrEoln

      public int readToEndOfOutputBufferOrEoln(byte[] outputBuffer, int startOutputIndex)
      Read from input until input is exhausted, EOLN is seen, or output buffer is filled
      Parameters:
      outputBuffer - where to put bytes read
      startOutputIndex - where to start putting bytes read
      Returns:
      number of bytes read