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close() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Close this RecordReader to future operations.
close() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Close this RecordReader to future operations.
createKey() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Create an object of the appropriate type to be used as a key.
createKey() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Create an object of the appropriate type to be used as a key.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat
 
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat
 
createValue() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Create an object of the appropriate type to be used as a value.
createValue() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Create an object of the appropriate type to be used as a value.

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getCurrentKey() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Added to use mapreduce API.
getCurrentKey() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Added to use mapreduce API.
getCurrentValue() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Added to use mapreduce API.
getCurrentValue() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Added to use mapreduce API.
getPos() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Returns the current position in the input.
getPos() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Returns the current position in the input.
getProgress() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
How much of the input has the RecordReader consumed i.e.
getProgress() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
How much of the input has the RecordReader consumed i.e.

I

initialize(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Added to use mapreduce API.
initialize(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Added to use mapreduce API.
InterleavedFastqInputFormat - Class in org.bdgenomics.adam.io
This class is a Hadoop reader for "interleaved fastq" -- that is, fastq with paired reads in the same file, interleaved, rather than in two separate files.
InterleavedFastqInputFormat() - Constructor for class org.bdgenomics.adam.io.InterleavedFastqInputFormat
 
InterleavedFastqInputFormat.InterleavedFastqRecordReader - Class in org.bdgenomics.adam.io
 
InterleavedFastqInputFormat.InterleavedFastqRecordReader(Configuration, FileSplit) - Constructor for class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
 

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lowLevelFastqRead(Text, Text) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
 
lowLevelFastqRead(Text, Text) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
 

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makePositionMessage() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
 
makePositionMessage() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
 

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next(Text) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Reads the next key/value pair from the input for processing.
next(Text) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Reads the next key/value pair from the input for processing.
nextKeyValue() - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader
Added to use mapreduce API.
nextKeyValue() - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
Added to use mapreduce API.

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org.bdgenomics.adam.io - package org.bdgenomics.adam.io
 

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SingleFastqInputFormat - Class in org.bdgenomics.adam.io
This class is a Hadoop reader for single read fastq.
SingleFastqInputFormat() - Constructor for class org.bdgenomics.adam.io.SingleFastqInputFormat
 
SingleFastqInputFormat.SingleFastqRecordReader - Class in org.bdgenomics.adam.io
 
SingleFastqInputFormat.SingleFastqRecordReader(Configuration, FileSplit) - Constructor for class org.bdgenomics.adam.io.SingleFastqInputFormat.SingleFastqRecordReader
 
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