org.seqdoop.hadoop_bam

Class KeyIgnoringBCFRecordWriter<K>

java.lang.Object

org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable>

org.seqdoop.hadoop_bam.BCFRecordWriter<K>

org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter<K>

public class KeyIgnoringBCFRecordWriter<K>
extends BCFRecordWriter<K>

A convenience class that you can use as a RecordWriter for BCF files.

The write function ignores the key, just outputting the VariantContext.

Constructor Summary

Constructors

Constructor and Description
KeyIgnoringBCFRecordWriter(OutputStream output, htsjdk.variant.vcf.VCFHeader header, boolean writeHeader)
KeyIgnoringBCFRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
KeyIgnoringBCFRecordWriter(org.apache.hadoop.fs.Path output, htsjdk.variant.vcf.VCFHeader header, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)

Method Summary

Modifier and Type	Method and Description
void	write(K ignored, VariantContextWritable vc)

Methods inherited from class org.seqdoop.hadoop_bam.BCFRecordWriter

close, setInputHeader, writeRecord

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

KeyIgnoringBCFRecordWriter

public KeyIgnoringBCFRecordWriter(org.apache.hadoop.fs.Path output,
                                  org.apache.hadoop.fs.Path input,
                                  boolean writeHeader,
                                  org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                           throws IOException

Throws:

IOException

KeyIgnoringBCFRecordWriter

public KeyIgnoringBCFRecordWriter(org.apache.hadoop.fs.Path output,
                                  htsjdk.variant.vcf.VCFHeader header,
                                  boolean writeHeader,
                                  org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                           throws IOException

Throws:

IOException

KeyIgnoringBCFRecordWriter

public KeyIgnoringBCFRecordWriter(OutputStream output,
                                  htsjdk.variant.vcf.VCFHeader header,
                                  boolean writeHeader)
                           throws IOException

Throws:

IOException

Method Detail

write

public void write(K ignored,
                  VariantContextWritable vc)

Specified by:

write in class org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable>