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

Class HadoopBamUtils

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
public class HadoopBamUtils extends Object

  • Constructor Summary

    Constructors
    Constructor
    Description
    HadoopBamUtils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static htsjdk.samtools.SamFileHeaderMerger
    getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf)
    Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
    static void
    mergeInto(OutputStream out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.conf.Configuration conf, String commandName)
    Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
    static void
    mergeSAMInto(org.apache.hadoop.fs.Path out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.seqdoop.hadoop_bam.SAMFormat format, org.apache.hadoop.conf.Configuration conf, String commandName)
    Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • HadoopBamUtils

      public HadoopBamUtils()

  • Method Details

    • getSAMHeaderMerger

      public static htsjdk.samtools.SamFileHeaderMerger getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf) throws IOException
      Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY. The sort order of the result is set according to the last call to setHeaderMergerSortOrder, or otherwise to "unsorted". The result is cached locally to prevent it from being recomputed too often.
      Parameters:
      conf - Hadoop configuration
      Returns:
      a SamFileHeaderMerger object
      Throws:
      IOException - if an error occurs while getting the Header

    • mergeSAMInto

      public static void mergeSAMInto(org.apache.hadoop.fs.Path out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.seqdoop.hadoop_bam.SAMFormat format, org.apache.hadoop.conf.Configuration conf, String commandName) throws IOException
      Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header. Outputs progress reports if commandName is non-null.
      Parameters:
      out - output file
      directory - directory
      basePrefix - base prefix
      basePostfix - base postfix
      format - SAM format
      conf - Hadoop configuration
      commandName - command name
      Throws:
      IOException - if an error occurs while merging

    • mergeInto

      public static void mergeInto(OutputStream out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.conf.Configuration conf, String commandName) throws IOException
      Merges the files in the given directory that have names given by getMergeableWorkFile() into out. Outputs progress reports if commandName is non-null.
      Parameters:
      out - output file
      directory - directory
      basePrefix - base prefix
      basePostfix - base postfix
      conf - Hadoop configuration
      commandName - command name
      Throws:
      IOException - if an error occurs while merging