Package htsjdk.samtools.util

Class ProgressLogger

java.lang.Object
htsjdk.samtools.util.AbstractProgressLogger
htsjdk.samtools.util.ProgressLogger
All Implemented Interfaces:
ProgressLoggerInterface
public class ProgressLogger extends AbstractProgressLogger
Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.

  • Constructor Details

    • ProgressLogger

      public ProgressLogger(Log log, int n, String verb, String noun)
      Construct a progress logger.
      Parameters:
      log - the Log object to write outputs to
      n - the frequency with which to output (i.e. every N records)
      verb - the verb to log, e.g. "Processed, Read, Written".
      noun - the noun to use when logging, e.g. "Records, Variants, Loci"

    • ProgressLogger

      public ProgressLogger(Log log, int n, String verb)
      Construct a progress logger.
      Parameters:
      log - the Log object to write outputs to
      n - the frequency with which to output (i.e. every N records)
      verb - the verb to log, e.g. "Processed, Read, Written".

    • ProgressLogger

      public ProgressLogger(Log log, int n)
      Construct a progress logger with the desired log and frequency and the verb "Processed".
      Parameters:
      log - the Log object to write outputs to
      n - the frequency with which to output (i.e. every N records)

    • ProgressLogger

      public ProgressLogger(Log log)
      Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
      Parameters:
      log - the Log object to write outputs to

  • Method Details

    • log

      protected void log(String... message)
      Description copied from class: AbstractProgressLogger
      Log a message to whatever logger is being used
      Specified by:
      log in class AbstractProgressLogger
      Parameters:
      message - a message to be logged by the logger (recommended output level is INFO or the equivalent)