htsjdk.samtools.util

Class ProgressLogger

java.lang.Object

htsjdk.samtools.util.ProgressLogger

All Implemented Interfaces:

ProgressLoggerInterface

public class ProgressLogger
extends java.lang.Object
implements ProgressLoggerInterface

Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.

Constructor Summary

Constructors

Constructor and Description
ProgressLogger(Log log) Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
ProgressLogger(Log log, int n) Construct a progress logger with the desired log and frequency and the verb "Processed".
ProgressLogger(Log log, int n, java.lang.String verb) Construct a progress logger.
ProgressLogger(Log log, int n, java.lang.String verb, java.lang.String noun) Construct a progress logger.

Method Summary

Methods

Modifier and Type	Method and Description
long	getCount() Returns the count of records processed.
long	getElapsedSeconds() Returns the number of seconds since progress tracking began.
boolean	record(SAMRecord... recs) Records multiple SAMRecords and triggers logging if necessary.
boolean	record(SAMRecord rec) Records that a given record has been processed and triggers logging if necessary.
boolean	record(java.lang.String chrom, int pos)

Methods inherited from class java.lang.Object

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

Constructor Detail

ProgressLogger

public ProgressLogger(Log log,
              int n,
              java.lang.String verb,
              java.lang.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,
              java.lang.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 Detail

record

public boolean record(java.lang.String chrom,
             int pos)

Specified by:

record in interface ProgressLoggerInterface

record

public boolean record(SAMRecord rec)

Records that a given record has been processed and triggers logging if necessary.

Specified by:

record in interface ProgressLoggerInterface

Returns:

boolean true if logging was triggered, false otherwise

record

public boolean record(SAMRecord... recs)

Records multiple SAMRecords and triggers logging if necessary.

Specified by:

record in interface ProgressLoggerInterface

getCount

public long getCount()

Returns the count of records processed.

getElapsedSeconds

public long getElapsedSeconds()

Returns the number of seconds since progress tracking began.