Package org.bdgenomics.adam.io
Class FastqInputFormat
- java.lang.Object
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- org.apache.hadoop.mapreduce.InputFormat<K,V>
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- org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>
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- org.bdgenomics.adam.io.FastqInputFormat
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- Direct Known Subclasses:
InterleavedFastqInputFormat
,SingleFastqInputFormat
public abstract class FastqInputFormat extends org.apache.hadoop.mapreduce.lib.input.FileInputFormat<Void,org.apache.hadoop.io.Text>
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Field Summary
Fields Modifier and Type Field Description protected boolean
splittable
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Constructor Summary
Constructors Constructor Description FastqInputFormat()
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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
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Method Detail
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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 classorg.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.
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