org.seqdoop.hadoop_bam

Class VCFRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.VCFRecordWriter<K>

Direct Known Subclasses:

KeyIgnoringVCFRecordWriter

public abstract class VCFRecordWriter<K>
extends org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable>

A base RecordWriter for VCF.

Handles the output stream, writing the header if requested, and provides the writeRecord(htsjdk.variant.variantcontext.VariantContext) function for subclasses.

Constructor Summary

Constructors

Constructor and Description
VCFRecordWriter(OutputStream output, htsjdk.variant.vcf.VCFHeader header, boolean writeHeader)
VCFRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx) A VCFHeader is read from the input Path.
VCFRecordWriter(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	close(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
protected htsjdk.variant.variantcontext.writer.VariantContextWriter	createVariantContextWriter(org.apache.hadoop.conf.Configuration conf, OutputStream out)
void	setInputHeader(htsjdk.variant.vcf.VCFHeader header) Used for lazy decoding of genotype data.
protected void	writeRecord(htsjdk.variant.variantcontext.VariantContext vc)

Methods inherited from class org.apache.hadoop.mapreduce.RecordWriter

write

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFRecordWriter

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

A VCFHeader is read from the input Path.

Throws:

IOException

VCFRecordWriter

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

Throws:

IOException

VCFRecordWriter

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

Throws:

IOException

Method Detail

createVariantContextWriter

protected htsjdk.variant.variantcontext.writer.VariantContextWriter createVariantContextWriter(org.apache.hadoop.conf.Configuration conf,
                                                                                               OutputStream out)

close

public void close(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
           throws IOException

Specified by:

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

Throws:

IOException

setInputHeader

public void setInputHeader(htsjdk.variant.vcf.VCFHeader header)

Used for lazy decoding of genotype data. Of course, each input record may have a different header, but we currently only support one header here... This is in part due to the fact that it's not clear what the best solution is.

writeRecord

protected void writeRecord(htsjdk.variant.variantcontext.VariantContext vc)