org.bdgenomics.adam.io

## Class FastqRecordReader

- java.lang.Object
- - org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>
  - - org.bdgenomics.adam.io.FastqRecordReader

- All Implemented Interfaces:
    Closeable, AutoCloseable

      public abstract class FastqRecordReader
      extends org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>

  A record reader for the interleaved FASTQ format. Reads over an input file and parses interleaved FASTQ read pairs into a single Text output. This is then fed into the FastqConverter, which converts the single Text instance into two AlignmentRecords.

- - ### Field Summary

    Fields
    Modifier and Type | Field and Description
    --- | ---
    `static int` | `DEFAULT_MAX_READ_LENGTH` Default maximum read length, `10,000` bp.
    `protected long` | `end` First index value beyond the slice, i.e.
    `protected boolean` | `isCompressed` True if the underlying data is compressed.
    `protected boolean` | `isSplittable` True if the underlying data is splittable.
    `static String` | `MAX_READ_LENGTH_PROPERTY` Maximum read length property name.
    `protected long` | `pos` Current position in file.

  - ### Constructor Summary

    Constructors
    Modifier | Constructor and Description
    --- | ---
    `protected` | `FastqRecordReader(org.apache.hadoop.conf.Configuration conf, org.apache.hadoop.mapreduce.lib.input.FileSplit split)` Builds a new record reader given a config file and an input split.

  - ### Method Summary

    All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
    Modifier and Type | Method and Description
    --- | ---
    `protected abstract boolean` | `checkBuffer(int bufferLength, org.apache.hadoop.io.Text buffer)` Checks to see whether the buffer is positioned at a valid record.
    `void` | `close()` Close this RecordReader to future operations.
    `Void` | `getCurrentKey()` FASTQ has no keys, so we return null.
    `org.apache.hadoop.io.Text` | `getCurrentValue()` Returns the last interleaved FASTQ record.
    `float` | `getProgress()` How much of the input has the RecordReader consumed?
    `void` | `initialize(org.apache.hadoop.mapreduce.InputSplit split, org.apache.hadoop.mapreduce.TaskAttemptContext context)`
    `protected boolean` | `lowLevelFastqRead(org.apache.hadoop.io.Text readName, org.apache.hadoop.io.Text value)` Parses a read from an interleaved FASTQ file.
    `protected String` | `makePositionMessage()` Produces a debugging message with the file position.
    `protected abstract boolean` | `next(org.apache.hadoop.io.Text value)` Reads from the input split.
    `boolean` | `nextKeyValue()` Seeks ahead in our split to the next key-value pair.
    `protected int` | `positionAtFirstRecord(org.apache.hadoop.fs.FSDataInputStream stream, org.apache.hadoop.io.compress.CompressionCodec codec)` Position the input stream at the start of the first record.
    `static void` | `setMaxReadLength(org.apache.hadoop.conf.Configuration conf, int maxReadLength)` Set the maximum read length property to `maxReadLength`.

    - ### Methods inherited from class java.lang.Object

      `clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

- - ### Field Detail

    - #### DEFAULT_MAX_READ_LENGTH

          public static final int DEFAULT_MAX_READ_LENGTH

      Default maximum read length, `10,000` bp.
      See Also:
        Constant Field Values

    - #### MAX_READ_LENGTH_PROPERTY

          public static final String MAX_READ_LENGTH_PROPERTY

      Maximum read length property name.
      See Also:
        Constant Field Values

    - #### end

          protected long end

      First index value beyond the slice, i.e. slice is in range [start,end).

    - #### pos

          protected long pos

      Current position in file.

    - #### isSplittable

          protected boolean isSplittable

      True if the underlying data is splittable.

    - #### isCompressed

          protected boolean isCompressed

      True if the underlying data is compressed.

  - ### Constructor Detail

    - #### FastqRecordReader

          protected FastqRecordReader(org.apache.hadoop.conf.Configuration conf,
                                      org.apache.hadoop.mapreduce.lib.input.FileSplit split)
                               throws IOException

      Builds a new record reader given a config file and an input split.
      Parameters:
        `conf` - The Hadoop configuration object. Used for gaining access to the underlying file system.
        `split` - The file split to read.
      Throws:
        `IOException`

  - ### Method Detail

    - #### setMaxReadLength

          public static void setMaxReadLength(org.apache.hadoop.conf.Configuration conf,
                                              int maxReadLength)

      Set the maximum read length property to `maxReadLength`.
      Parameters:
        `conf` - configuration
        `maxReadLength` - maximum read length, in base pairs (bp)

    - #### checkBuffer

          protected abstract boolean checkBuffer(int bufferLength,
                                                 org.apache.hadoop.io.Text buffer)

      Checks to see whether the buffer is positioned at a valid record.
      Parameters:
        `bufferLength` - The length of the line currently in the buffer.
        `buffer` - A buffer containing a peek at the first line in the current stream.
      Returns:
        Returns true if the buffer contains the first line of a properly formatted FASTQ record.

    - #### positionAtFirstRecord

          protected final int positionAtFirstRecord(org.apache.hadoop.fs.FSDataInputStream stream,
                                                    org.apache.hadoop.io.compress.CompressionCodec codec)
                                             throws IOException

      Position the input stream at the start of the first record.
      Parameters:
        `stream` - The stream to reposition.
      Throws:
        `IOException`

    - #### initialize

          public final void initialize(org.apache.hadoop.mapreduce.InputSplit split,
                                       org.apache.hadoop.mapreduce.TaskAttemptContext context)
                                throws IOException,
                                       InterruptedException

      Specified by:
        `initialize` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Throws:
        `IOException`
        `InterruptedException`

    - #### getCurrentKey

          public final Void getCurrentKey()

      FASTQ has no keys, so we return null.
      Specified by:
        `getCurrentKey` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Returns:
        Always returns null.

    - #### getCurrentValue

          public final org.apache.hadoop.io.Text getCurrentValue()

      Returns the last interleaved FASTQ record.
      Specified by:
        `getCurrentValue` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Returns:
        The text corresponding to the last read pair.

    - #### nextKeyValue

          public final boolean nextKeyValue()
                                     throws IOException,
                                            InterruptedException

      Seeks ahead in our split to the next key-value pair. Triggers the read of an interleaved FASTQ read pair, and populates internal state.
      Specified by:
        `nextKeyValue` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Returns:
        True if reading the next read pair succeeded.
      Throws:
        `IOException`
        `InterruptedException`

    - #### close

          public final void close()
                           throws IOException

      Close this RecordReader to future operations.
      Specified by:
        `close` in interface `Closeable`
      Specified by:
        `close` in interface `AutoCloseable`
      Specified by:
        `close` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Throws:
        `IOException`

    - #### getProgress

          public final float getProgress()

      How much of the input has the RecordReader consumed?
      Specified by:
        `getProgress` in class `org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>`
      Returns:
        Returns a value on [0.0, 1.0] that notes how many bytes we have read so far out of the total bytes to read.

    - #### makePositionMessage

          protected final String makePositionMessage()

      Produces a debugging message with the file position.
      Returns:
        Returns a string containing {filename}:{index}.

    - #### lowLevelFastqRead

          protected final boolean lowLevelFastqRead(org.apache.hadoop.io.Text readName,
                                                    org.apache.hadoop.io.Text value)
                                             throws IOException

      Parses a read from an interleaved FASTQ file. Only reads a single record.
      Parameters:
        `readName` - Text record containing read name. Output parameter.
        `value` - Text record containing full record. Output parameter.
      Returns:
        Returns true if read was successful (did not hit EOF).
      Throws:
        `RuntimeException` - Throws exception if FASTQ record doesn't have proper formatting (e.g., record doesn't start with @).
        `IOException`

    - #### next

          protected abstract boolean next(org.apache.hadoop.io.Text value)
                                   throws IOException

      Reads from the input split.
      Parameters:
        `value` - Text record to write input value into.
      Returns:
        Returns whether this read was successful or not.
      Throws:
        `IOException`
      See Also:
        `lowLevelFastqRead(Text, Text)`

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