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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
 
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