C D E F G I L M N O P S

## C

checkBuffer(int, Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Checks to see whether the buffer is positioned at a valid record.
close() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Close this RecordReader to future operations.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat
  Creates the new record reader that underlies this input format.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat
  Creates the new record reader that underlies this input format.

## D

DEFAULT_MAX_READ_LENGTH - Static variable in class org.bdgenomics.adam.io.FastqRecordReader
  Default maximum read length, `10,000` bp.

## E

end - Variable in class org.bdgenomics.adam.io.FastqRecordReader
  First index value beyond the slice, i.e.

## F

FastqInputFormat - Class in org.bdgenomics.adam.io
FastqInputFormat() - Constructor for class org.bdgenomics.adam.io.FastqInputFormat
FastqRecordReader - Class in org.bdgenomics.adam.io
  A record reader for the interleaved FASTQ format.
FastqRecordReader(Configuration, FileSplit) - Constructor for class org.bdgenomics.adam.io.FastqRecordReader
  Builds a new record reader given a config file and an input split.

## G

getCurrentKey() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  FASTQ has no keys, so we return null.
getCurrentValue() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Returns the last interleaved FASTQ record.
getProgress() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  How much of the input has the RecordReader consumed?

## I

initialize(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.FastqRecordReader
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
isCompressed - Variable in class org.bdgenomics.adam.io.FastqRecordReader
  True if the underlying data is compressed.
isSplitable(JobContext, Path) - Method in class org.bdgenomics.adam.io.FastqInputFormat
  Checks to see if the file we are looking at is splittable.
isSplittable - Variable in class org.bdgenomics.adam.io.FastqRecordReader
  True if the underlying data is splittable.

## L

lowLevelFastqRead(Text, Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Parses a read from an interleaved FASTQ file.

## M

makePositionMessage() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Produces a debugging message with the file position.
MAX_READ_LENGTH_PROPERTY - Static variable in class org.bdgenomics.adam.io.FastqRecordReader
  Maximum read length property name.

## N

next(Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Reads from the input split.
nextKeyValue() - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Seeks ahead in our split to the next key-value pair.

## O

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

## P

pos - Variable in class org.bdgenomics.adam.io.FastqRecordReader
  Current position in file.
positionAtFirstRecord(FSDataInputStream, CompressionCodec) - Method in class org.bdgenomics.adam.io.FastqRecordReader
  Position the input stream at the start of the first record.

## S

setMaxReadLength(Configuration, int) - Static method in class org.bdgenomics.adam.io.FastqRecordReader
  Set the maximum read length property to `maxReadLength`.
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
splittable - Variable in class org.bdgenomics.adam.io.FastqInputFormat

C D E F G I L M N O P S

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