Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli

Class CLIMergingAnySAMOutputFormat<K>

java.lang.Object
org.apache.hadoop.mapreduce.OutputFormat<K,V>
org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat<K>
public class CLIMergingAnySAMOutputFormat<K> extends org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>
Like a KeyIgnoringAnySAMOutputFormat, but sets the SAMFileHeader to Utils.getSAMHeaderMerger().getMergedHeader() and allows the output directory (the "work directory") to exist.

  • Nested Class Summary

    Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

    org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.Counter

  • Field Summary

    Fields inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

    COMPRESS, COMPRESS_CODEC, COMPRESS_TYPE, OUTDIR

  • Constructor Summary

    Constructors
    Constructor
    Description
    CLIMergingAnySAMOutputFormat()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)
     
    org.apache.hadoop.fs.Path
    getDefaultWorkFile(org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String ext)
     
    org.apache.hadoop.mapreduce.RecordWriter<K,org.seqdoop.hadoop_bam.SAMRecordWritable>
    getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext context)
     

    Methods inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

    getCompressOutput, getOutputCommitter, getOutputCompressorClass, getOutputPath, getPathForWorkFile, getUniqueFile, getWorkOutputPath, setCompressOutput, setOutputCompressorClass, setOutputPath

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • CLIMergingAnySAMOutputFormat

      public CLIMergingAnySAMOutputFormat()

  • Method Details

    • getRecordWriter

      public org.apache.hadoop.mapreduce.RecordWriter<K,org.seqdoop.hadoop_bam.SAMRecordWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext context) throws IOException
      Specified by:
      getRecordWriter in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>
      Throws:
      IOException

    • getDefaultWorkFile

      public org.apache.hadoop.fs.Path getDefaultWorkFile(org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String ext) throws IOException
      Overrides:
      getDefaultWorkFile in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>
      Throws:
      IOException

    • checkOutputSpecs

      public void checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)
      Overrides:
      checkOutputSpecs in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>