Package org.broadinstitute.hellbender.utils.runtime

Class ProgressLogger

java.lang.Object
htsjdk.samtools.util.AbstractProgressLogger
org.broadinstitute.hellbender.utils.runtime.ProgressLogger
All Implemented Interfaces:
htsjdk.samtools.util.ProgressLoggerInterface
public class ProgressLogger extends htsjdk.samtools.util.AbstractProgressLogger
Facilitate consistent logging output when progressing through a stream of SAM records. Implements the SAMTools public htsjdk.samtools.util.AbstractProgressLogger interface to enable integration with SAMWriters.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ProgressLogger(org.apache.logging.log4j.Logger logger)
    Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
    ProgressLogger(org.apache.logging.log4j.Logger logger, int n)
    Construct a progress logger with the desired log and frequency and the verb "Processed".
    ProgressLogger(org.apache.logging.log4j.Logger logger, int n, String verb)
    Construct a progress logger.
    ProgressLogger(org.apache.logging.log4j.Logger logger, int n, String verb, String noun)
    Construct a progress logger.

  • Method Summary

    Modifier and Type
    Method
    Description
    protected void
    log(String... message)
    Log a message to whatever logger is being used

    Methods inherited from class htsjdk.samtools.util.AbstractProgressLogger

    getCount, getElapsedSeconds, log, record, record, record, record, reset

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ProgressLogger

      public ProgressLogger(org.apache.logging.log4j.Logger logger, int n, String verb, String noun)
      Construct a progress logger.
      Parameters:
      logger - the Logger object to write output 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(org.apache.logging.log4j.Logger logger, int n, String verb)
      Construct a progress logger.
      Parameters:
      logger - the Logger 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(org.apache.logging.log4j.Logger logger, int n)
      Construct a progress logger with the desired log and frequency and the verb "Processed".
      Parameters:
      logger - the Logger object to write outputs to
      n - the frequency with which to output (i.e. every N records)

    • ProgressLogger

      public ProgressLogger(org.apache.logging.log4j.Logger logger)
      Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
      Parameters:
      logger - the Logger object to write outputs to

  • Method Details

    • log

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