A C D E F G I L M N O P S
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All Classes All Packages
A
- ADD_LIST_ELEMENT_RECORDS - Static variable in class org.apache.parquet.avro.AvroSchemaConverter
- AvroSchemaConverter - Class in org.apache.parquet.avro
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Converts an Avro schema into a Parquet schema, or vice versa.
- AvroSchemaConverter() - Constructor for class org.apache.parquet.avro.AvroSchemaConverter
- AvroSchemaConverter(Configuration) - Constructor for class org.apache.parquet.avro.AvroSchemaConverter
C
- checkBuffer(int, Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Checks to see whether the buffer is positioned at a valid record.
- close() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Close this RecordReader to future operations.
- convert(Schema) - Method in class org.apache.parquet.avro.AvroSchemaConverter
- convert(MessageType) - Method in class org.apache.parquet.avro.AvroSchemaConverter
- createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.InterleavedFastqInputFormat
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Creates the new record reader that underlies this input format.
- createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.bdgenomics.adam.io.SingleFastqInputFormat
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Creates the new record reader that underlies this input format.
D
- DEFAULT_MAX_READ_LENGTH - Static variable in class org.bdgenomics.adam.io.FastqRecordReader
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Default maximum read length,
10,000
bp.
E
- end - Variable in class org.bdgenomics.adam.io.FastqRecordReader
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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
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A record reader for the interleaved FASTQ format.
- FastqRecordReader(Configuration, FileSplit) - Constructor for class org.bdgenomics.adam.io.FastqRecordReader
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Builds a new record reader given a config file and an input split.
G
- getCurrentKey() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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FASTQ has no keys, so we return null.
- getCurrentValue() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Returns the last interleaved FASTQ record.
- getNonNull(Schema) - Static method in class org.apache.parquet.avro.AvroSchemaConverter
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Given a schema, check to see if it is a union of a null type and a regular schema, and then return the non-null sub-schema.
- getProgress() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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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
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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
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True if the underlying data is compressed.
- isSplitable(JobContext, Path) - Method in class org.bdgenomics.adam.io.FastqInputFormat
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Checks to see if the file we are looking at is splittable.
- isSplittable - Variable in class org.bdgenomics.adam.io.FastqRecordReader
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True if the underlying data is splittable.
L
- lowLevelFastqRead(Text, Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Parses a read from an interleaved FASTQ file.
M
- makePositionMessage() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Produces a debugging message with the file position.
- MAX_READ_LENGTH_PROPERTY - Static variable in class org.bdgenomics.adam.io.FastqRecordReader
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Maximum read length property name.
N
- next(Text) - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Reads from the input split.
- nextKeyValue() - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Seeks ahead in our split to the next key-value pair.
O
- org.apache.parquet.avro - package org.apache.parquet.avro
- org.bdgenomics.adam.io - package org.bdgenomics.adam.io
P
- pos - Variable in class org.bdgenomics.adam.io.FastqRecordReader
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Current position in file.
- positionAtFirstRecord(FSDataInputStream, CompressionCodec) - Method in class org.bdgenomics.adam.io.FastqRecordReader
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Position the input stream at the start of the first record.
S
- setMaxReadLength(Configuration, int) - Static method in class org.bdgenomics.adam.io.FastqRecordReader
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Set the maximum read length property to
maxReadLength
. - SingleFastqInputFormat - Class in org.bdgenomics.adam.io
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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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