Class Utils


  • public final class Utils
    extends Object
    • Constructor Detail

      • Utils

        public Utils()
    • Method Detail

      • printWrapped

        public static void printWrapped​(PrintStream out,
                                        String str,
                                        int indent)
      • printWrapped

        public static void printWrapped​(PrintStream out,
                                        String str,
                                        int indent,
                                        int wrapAt)
      • getArgv0

        public static String getArgv0()
      • setArgv0Class

        public static void setArgv0Class​(Class<?> cl)
      • configureSampling

        public static void configureSampling​(org.apache.hadoop.fs.Path workDir,
                                             String outName,
                                             org.apache.hadoop.conf.Configuration conf)
                                      throws IOException
        Throws:
        IOException
      • 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.
      • 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.
        Throws:
        IOException
      • setHeaderMergerSortOrder

        public static void setHeaderMergerSortOrder​(org.apache.hadoop.conf.Configuration conf,
                                                    htsjdk.samtools.SAMFileHeader.SortOrder order)
      • 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.
        Throws:
        IOException
      • 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().
        Throws:
        IOException
      • 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.
        Throws:
        IOException
      • getStringencyOptHelp

        public static String getStringencyOptHelp()