Package org.broadinstitute.hellbender.tools.walkers.readorientation

Class CollectF1R2CountsArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection

public class CollectF1R2CountsArgumentCollection
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final String	MAX_DEPTH_LONG_NAME
int	maxDepth
static final String	MIN_BASE_QUALITY_LONG_NAME
static final String	MIN_MEDIAN_MQ_LONG_NAME
int	minBaseQuality
int	minMedianMapQual

Constructor Summary

Constructors

Constructor	Description
CollectF1R2CountsArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Details

MIN_MEDIAN_MQ_LONG_NAME

public static final String MIN_MEDIAN_MQ_LONG_NAME

See Also:

• Constant Field Values

MIN_BASE_QUALITY_LONG_NAME

public static final String MIN_BASE_QUALITY_LONG_NAME

See Also:

• Constant Field Values

MAX_DEPTH_LONG_NAME

public static final String MAX_DEPTH_LONG_NAME

See Also:

• Constant Field Values

minMedianMapQual

@Argument(fullName="f1r2-median-mq",
          doc="skip sites with median mapping quality below this value",
          optional=true)
public int minMedianMapQual

minBaseQuality

@Argument(fullName="f1r2-min-bq",
          doc="exclude bases below this quality from pileup",
          optional=true)
public int minBaseQuality

maxDepth

@Argument(fullName="f1r2-max-depth",
          doc="sites with depth higher than this value will be grouped",
          optional=true)
public int maxDepth

Constructor Details

CollectF1R2CountsArgumentCollection

public CollectF1R2CountsArgumentCollection()