C G I L M N O S

## C

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.

## G

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

## L

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

## M

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

## N

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.

## O

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

## S

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

C G I L M N O S