Example usage for org.apache.hadoop.mapreduce RecordReader subclass-usage

Introduction

In this page you can find the example usage for org.apache.hadoop.mapreduce RecordReader subclass-usage.

Usage

From source file org.bgi.flexlab.gaea.data.mapreduce.input.fastq.FastqRecordReader.java

public class FastqRecordReader extends RecordReader<Text, Text> {
    public final static String READ_NAME_TYPE = "read.name.type";

    private FastqBasicReader reader = null;
    private Text key = null;
    private Text value = null;

From source file org.bgi.flexlab.gaea.data.mapreduce.input.sam.GaeaSamRecordReader.java

public class GaeaSamRecordReader extends RecordReader<LongWritable, SamRecordWritable> {
    private LongWritable key = new LongWritable();
    private SamRecordWritable record = new SamRecordWritable();

    private FSDataInputStream input;
    private SAMRecordIterator iterator;

From source file org.bgi.flexlab.gaea.data.mapreduce.input.vcf.VCFRecordReader.java

public class VCFRecordReader extends RecordReader<LongWritable, VariantContextWritable> {
    private Configuration conf;

    private VCFCodec codec = new VCFCodec();
    private AsciiLineReaderIterator it;
    private AsciiLineReader reader;

From source file org.bigsolr.hadoop.SolrRecordReader.java

public class SolrRecordReader extends RecordReader<NullWritable, SolrRecord>
        implements org.apache.hadoop.mapred.RecordReader<NullWritable, SolrRecord> {

    private int currentDoc = 0;
    private int numDocs;
    private SolrRecord record;

From source file org.broadinstitute.sting.gatk.hadoop.BAMRecordReader.java

/**
 * The key is the bitwise OR of the reference sequence ID in the upper 32 bits
 * and the 0-based leftmost coordinate in the lower.
 */
public class BAMRecordReader extends RecordReader<LongWritable, SAMRecordWritable> {
    private final LongWritable key = new LongWritable();

From source file org.broadinstitute.sting.gatk.hadoop.ContigRecordReader.java

/**
 * The key is the bitwise OR of the reference sequence ID in the upper 32 bits
 * and the 0-based leftmost coordinate in the lower.
 */
public class ContigRecordReader extends RecordReader<LongWritable, SAMRecordWritable> {
    private final LongWritable key = new LongWritable();

From source file org.broadinstitute.sting.gatk.hadoop.hadoopsrc.LineRecordReader.java

/**
 * Treats keys as offset in file and value as line.
 */
public class LineRecordReader extends RecordReader<LongWritable, Text> {

    private long start;

From source file org.broadinstitute.sting.gatk.hadoop.LociRecordReader.java

public class LociRecordReader extends RecordReader<LongWritable, Text> {
    private final LongWritable key = new LongWritable();
    private final Text record = new Text();

    private BlockCompressedInputStream bci;
    private BAMRecordCodec codec;

From source file org.broadinstitute.sting.gatk.hadoop.NLineXRecordReader.java

public class NLineXRecordReader extends RecordReader<LongWritable, Text> {

    private LongWritable key = new LongWritable();
    private Text value = new Text();

    private long end;

From source file org.broadinstitute.sting.gatk.hadoop.WholeFileRecordReader.java

public class WholeFileRecordReader extends RecordReader<LongWritable, Text> {
    private final LongWritable key = new LongWritable();
    private final Text record = new Text();

    private boolean called = false;
    private Path file;