org.seqdoop.hadoop_bam

Class KeyIgnoringBAMRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.BAMRecordWriter<K>

org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter<K>

public class KeyIgnoringBAMRecordWriter<K>
extends BAMRecordWriter<K>

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

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

Constructor Summary

Constructors

Constructor and Description
KeyIgnoringBAMRecordWriter(OutputStream output, htsjdk.samtools.SAMFileHeader header, boolean writeHeader)
KeyIgnoringBAMRecordWriter(org.apache.hadoop.fs.Path output, org.apache.hadoop.fs.Path input, boolean writeHeader, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
KeyIgnoringBAMRecordWriter(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.BAMRecordWriter

close, writeAlignment

Methods inherited from class java.lang.Object

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

Constructor Detail

KeyIgnoringBAMRecordWriter

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

Throws:

IOException

KeyIgnoringBAMRecordWriter

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

Throws:

IOException

KeyIgnoringBAMRecordWriter

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

Throws:

IOException

Method Detail

write

public void write(K ignored,
                  SAMRecordWritable rec)
           throws IOException

Specified by:

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

Throws:

IOException