org.seqdoop.hadoop_bam

Class KeyIgnoringSAMRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.SAMRecordWriter<K>

org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter<K>

public class KeyIgnoringSAMRecordWriter<K>
extends SAMRecordWriter<K>

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

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

Constructor Summary

Constructors

Constructor and Description
KeyIgnoringSAMRecordWriter(OutputStream output, htsjdk.samtools.SAMFileHeader header, boolean writeHeader)
KeyIgnoringSAMRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
KeyIgnoringSAMRecordWriter(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	write(K ignored, SAMRecordWritable rec)

Methods inherited from class org.seqdoop.hadoop_bam.SAMRecordWriter

close, writeAlignment

Methods inherited from class java.lang.Object

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

Constructor Detail

KeyIgnoringSAMRecordWriter

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

Throws:

IOException

KeyIgnoringSAMRecordWriter

public KeyIgnoringSAMRecordWriter(org.apache.hadoop.fs.Path output,
                                  htsjdk.samtools.SAMFileHeader header,
                                  boolean writeHeader,
                                  org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                           throws IOException

Throws:

IOException

KeyIgnoringSAMRecordWriter

public KeyIgnoringSAMRecordWriter(OutputStream output,
                                  htsjdk.samtools.SAMFileHeader header,
                                  boolean writeHeader)
                           throws IOException

Throws:

IOException

Method Detail

write

public void write(K ignored,
                  SAMRecordWritable rec)

Specified by:

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