org.seqdoop.hadoop_bam

Class BCFRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.BCFRecordWriter<K>

Direct Known Subclasses:

KeyIgnoringBCFRecordWriter

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

A base RecordWriter for compressed BCF.

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
BCFRecordWriter(OutputStream output, htsjdk.variant.vcf.VCFHeader header, boolean writeHeader)
BCFRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx) A VCF header is read from the input Path, which should refer to a VCF or BCF file.
BCFRecordWriter(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)
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

BCFRecordWriter

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

A VCF header is read from the input Path, which should refer to a VCF or BCF file.

Throws:

IOException

BCFRecordWriter

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

Throws:

IOException

BCFRecordWriter

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

Throws:

IOException

Method Detail

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)