Uses of Class
org.seqdoop.hadoop_bam.SequencedFragment

Packages that use SequencedFragment

Package	Description
org.seqdoop.hadoop_bam

Uses of SequencedFragment in org.seqdoop.hadoop_bam

Methods in org.seqdoop.hadoop_bam that return SequencedFragment

Modifier and Type	Method and Description
SequencedFragment	QseqInputFormat.QseqRecordReader.createValue() Create an object of the appropriate type to be used as a value.
SequencedFragment	FastqInputFormat.FastqRecordReader.createValue() Create an object of the appropriate type to be used as a value.
SequencedFragment	QseqInputFormat.QseqRecordReader.getCurrentValue() Added to use mapreduce API.
SequencedFragment	FastqInputFormat.FastqRecordReader.getCurrentValue() Added to use mapreduce API.

Methods in org.seqdoop.hadoop_bam that return types with arguments of type SequencedFragment

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,SequencedFragment>	QseqInputFormat.createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,SequencedFragment>	FastqInputFormat.createRecordReader(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>	QseqOutputFormat.getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext task)
org.apache.hadoop.mapreduce.RecordWriter<org.apache.hadoop.io.Text,SequencedFragment>	FastqOutputFormat.getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext task)

Methods in org.seqdoop.hadoop_bam with parameters of type SequencedFragment

Modifier and Type	Method and Description
protected boolean	FastqInputFormat.FastqRecordReader.lowLevelFastqRead(org.apache.hadoop.io.Text key, SequencedFragment value)
protected String	FastqOutputFormat.FastqRecordWriter.makeId(SequencedFragment seq)
boolean	QseqInputFormat.QseqRecordReader.next(org.apache.hadoop.io.Text key, SequencedFragment value) Reads the next key/value pair from the input for processing.
boolean	FastqInputFormat.FastqRecordReader.next(org.apache.hadoop.io.Text key, SequencedFragment value) Reads the next key/value pair from the input for processing.
void	QseqOutputFormat.QseqRecordWriter.write(org.apache.hadoop.io.Text ignored_key, SequencedFragment seq)
void	FastqOutputFormat.FastqRecordWriter.write(org.apache.hadoop.io.Text key, SequencedFragment seq)