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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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