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

Class Utils

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
public final class Utils extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    HEADERMERGER_INPUTS_PROPERTY
     
    static final String
    WORK_FILENAME_PROPERTY
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    Utils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    configureSampling(org.apache.hadoop.fs.Path workDir, String outName, org.apache.hadoop.conf.Configuration conf)
    Configure sampling.
    static void
    correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r, org.apache.hadoop.conf.Configuration conf)
    Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
    static String
    getArgv0()
     
    static org.apache.hadoop.fs.Path
    getMergeableWorkFile(org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String extension)
    Returns a name that mergeInto() will recognize as a file to be merged.
    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 String
    getStringencyOptHelp()
    Get stringency option help
    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.
    static void
    printWrapped(PrintStream out, String str)
    Print wrapped.
    static void
    printWrapped(PrintStream out, String str, int indent)
    Print wrapped.
    static void
    printWrapped(PrintStream out, String str, int indent, int wrapAt)
    Print wrapped.
    static void
    setArgv0Class(Class<?> cl)
    Set the arg0 class.
    static void
    setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf, htsjdk.samtools.SAMFileHeader.SortOrder order)
    Set Header merger order.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • Utils

      public Utils()

  • Method Details

    • printWrapped

      public static void printWrapped(PrintStream out, String str)
      Print wrapped.
      Parameters:
      out - print stream
      str - string to write

    • printWrapped

      public static void printWrapped(PrintStream out, String str, int indent)
      Print wrapped.
      Parameters:
      out - print stream
      str - string to write
      indent - indentation

    • printWrapped

      public static void printWrapped(PrintStream out, String str, int indent, int wrapAt)
      Print wrapped.
      Parameters:
      out - print stream
      str - string to write
      indent - indentation
      wrapAt - position to wrap

    • getArgv0

      public static String getArgv0()

    • setArgv0Class

      public static void setArgv0Class(Class<?> cl)
      Set the arg0 class.
      Parameters:
      cl - the class to set

    • configureSampling

      public static void configureSampling(org.apache.hadoop.fs.Path workDir, String outName, org.apache.hadoop.conf.Configuration conf) throws IOException
      Configure sampling.
      Parameters:
      workDir - work directory
      outName - output name
      conf - Hadoop configuration
      Throws:
      IOException - if an error occurs while configuring the sampling

    • getMergeableWorkFile

      public static org.apache.hadoop.fs.Path getMergeableWorkFile(org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String extension)
      Returns a name that mergeInto() will recognize as a file to be merged.

      The filename is the value of WORK_FILENAME_PROPERTY surrounded by basePrefix and basePostfix, followed by the part number and with the given extension.

      Parameters:
      directory - the directory
      basePrefix - base prefix
      basePostfix - base postfix
      ctx - task context
      extension - the extension
      Returns:
      a Path

    • 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 - out stream
      directory - directory
      basePrefix - base prefix
      basePostfix - base postfix
      conf - Hadoop configuration
      commandName - command name
      Throws:
      IOException - if an error occurs while merging

    • setHeaderMergerSortOrder

      public static void setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf, htsjdk.samtools.SAMFileHeader.SortOrder order)
      Set Header merger order.
      Parameters:
      conf - Hadoop configuration
      order - order to use

    • 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

    • correctSAMRecordForMerging

      public static void correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r, org.apache.hadoop.conf.Configuration conf) throws IOException
      Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
      Parameters:
      r - SAM record
      conf - Hadoop configuration
      Throws:
      IOException - if an error occurs

    • 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 - out stream
      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

    • getStringencyOptHelp

      public static String getStringencyOptHelp()
      Get stringency option help
      Returns:
      a string with the help