org.seqdoop.hadoop_bam

Class CRAMRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.CRAMRecordWriter<K>

Direct Known Subclasses:

KeyIgnoringCRAMRecordWriter

public abstract class CRAMRecordWriter<K>
extends org.apache.hadoop.mapreduce.RecordWriter<K,SAMRecordWritable>

A base RecordWriter for CRAM records.

Handles the output stream, writing the header if requested, and provides the writeAlignment(htsjdk.samtools.SAMRecord) function for subclasses.

Note that each file created by this class consists of a fragment of a complete CRAM file containing only one or more CRAM containers that do not include a CRAM file header, a SAMFileHeader, or a CRAM EOF container.

Constructor Summary

Constructors

Constructor and Description
CRAMRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx) A SAMFileHeader is read from the input Path.
CRAMRecordWriter(org.apache.hadoop.fs.Path output, htsjdk.samtools.SAMFileHeader 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 void	writeAlignment(htsjdk.samtools.SAMRecord rec)

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

CRAMRecordWriter

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

A SAMFileHeader is read from the input Path.

Throws:

IOException

CRAMRecordWriter

public CRAMRecordWriter(org.apache.hadoop.fs.Path output,
                        htsjdk.samtools.SAMFileHeader header,
                        boolean writeHeader,
                        org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                 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,SAMRecordWritable>

Throws:

IOException

writeAlignment

protected void writeAlignment(htsjdk.samtools.SAMRecord rec)