org.seqdoop.hadoop_bam

Class BAMRecordWriter<K>

java.lang.Object

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

org.seqdoop.hadoop_bam.BAMRecordWriter<K>

Direct Known Subclasses:

KeyIgnoringBAMRecordWriter

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

A base RecordWriter for BAM 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
BAMRecordWriter(OutputStream output, htsjdk.samtools.SAMFileHeader header, boolean writeHeader)
BAMRecordWriter(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.
BAMRecordWriter(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

BAMRecordWriter

public BAMRecordWriter(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

BAMRecordWriter

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

Throws:

IOException

BAMRecordWriter

public BAMRecordWriter(OutputStream output,
                       htsjdk.samtools.SAMFileHeader 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,SAMRecordWritable>

Throws:

IOException

writeAlignment

protected void writeAlignment(htsjdk.samtools.SAMRecord rec)
                       throws IOException

Throws:

IOException