FastqInputFormat (ADAM_2.12: Core 0.34.0 API)

java.lang.Object
- org.apache.hadoop.mapreduce.InputFormat<K,V>
- - org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>
  - - org.bdgenomics.adam.io.FastqInputFormat

Direct Known Subclasses:: InterleavedFastqInputFormat, SingleFastqInputFormat

public abstract class FastqInputFormat
extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>

Nested Class Summary
- Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat
  org.apache.hadoop.mapreduce.lib.input.FileInputFormat.Counter

Field Summary

Fields
Modifier and Type Field Description

protected boolean splittable
- Fields inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat
  DEFAULT_LIST_STATUS_NUM_THREADS, INPUT_DIR, INPUT_DIR_NONRECURSIVE_IGNORE_SUBDIRS, INPUT_DIR_RECURSIVE, LIST_STATUS_NUM_THREADS, NUM_INPUT_FILES, PATHFILTER_CLASS, SPLIT_MAXSIZE, SPLIT_MINSIZE

Constructor Summary

Constructors
Constructor Description

FastqInputFormat()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`isSplitable(org.apache.hadoop.mapreduce.JobContext context, org.apache.hadoop.fs.Path filename)`	Checks to see if the file we are looking at is splittable.

Methods inherited from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat
addInputPath, addInputPathRecursively, addInputPaths, computeSplitSize, getBlockIndex, getFormatMinSplitSize, getInputDirRecursive, getInputPathFilter, getInputPaths, getMaxSplitSize, getMinSplitSize, getSplits, listStatus, makeSplit, makeSplit, setInputDirRecursive, setInputPathFilter, setInputPaths, setInputPaths, setMaxInputSplitSize, setMinInputSplitSize

Methods inherited from class org.apache.hadoop.mapreduce.InputFormat
createRecordReader

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - splittable
```
protected boolean splittable
```
- Constructor Detail
  - FastqInputFormat
```
public FastqInputFormat()
```
- Method Detail
  - isSplitable
```
protected boolean isSplitable(org.apache.hadoop.mapreduce.JobContext context,
                              org.apache.hadoop.fs.Path filename)
```
    Checks to see if the file we are looking at is splittable. A file is splittable if it is: - Uncompressed. - Compressed with the BGZFEnhancedGzipCodec _and_ the underlying stream is a BGZF stream. BGZFEnhancedGzipCodec looks for files with a .gz extension, which means that the codec may be selected if the file is a non-block GZIPed file, and thus is non-splittable. To validate this, we use HTSJDKs in-built mechanism for checking if a stream is a BGZF stream. - Any other splittable codec (e.g., .bgz/BGZFCodec, .bz2/BZip2Codec)
    
    Overrides:
    
    isSplitable in class org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>
    
    Parameters:
    
    context - The job context to get the configuration from.
    
    filename - The path the input file is saved at.
    
    Returns:
    
    Returns false if this file is compressed.