org.seqdoop.hadoop_bam

Class SAMRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.SAMRecordWriter<K>

Direct Known Subclasses:

KeyIgnoringSAMRecordWriter

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

A base RecordWriter for SAM records.

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

Constructor Summary

Constructors

Constructor and Description
SAMRecordWriter(OutputStream output, htsjdk.samtools.SAMFileHeader header, boolean writeHeader)
SAMRecordWriter(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.
SAMRecordWriter(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

SAMRecordWriter

public SAMRecordWriter(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

SAMRecordWriter

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

Throws:

IOException

SAMRecordWriter

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

Throws:

IOException

Method Detail

close

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

Specified by:

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

writeAlignment

protected void writeAlignment(htsjdk.samtools.SAMRecord rec)