org.seqdoop.hadoop_bam

Class KeyIgnoringVCFRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.VCFRecordWriter<K>

org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter<K>

public class KeyIgnoringVCFRecordWriter<K>
extends VCFRecordWriter<K>

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

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

Constructor Summary

Constructors

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

close, createVariantContextWriter, setInputHeader, writeRecord

Methods inherited from class java.lang.Object

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

Constructor Detail

KeyIgnoringVCFRecordWriter

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

Throws:

IOException

KeyIgnoringVCFRecordWriter

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

Throws:

IOException

KeyIgnoringVCFRecordWriter

public KeyIgnoringVCFRecordWriter(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>