org.broadinstitute.hellbender.cmdline.argumentcollections

Class OptionalIntervalArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection

org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection

All Implemented Interfaces:

java.io.Serializable

public final class OptionalIntervalArgumentCollection
extends IntervalArgumentCollection

An interval argument class that allows -L to be specified but does not require it.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<java.lang.String>	intervalStrings

Fields inherited from class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection

EXCLUDE_INTERVALS_LONG_NAME, EXCLUDE_INTERVALS_SHORT_NAME, excludeIntervalStrings, INTERVAL_EXCLUSION_PADDING_LONG_NAME, INTERVAL_MERGING_RULE_LONG_NAME, INTERVAL_PADDING_LONG_NAME, INTERVAL_SET_RULE_LONG_NAME, intervalExclusionPadding, intervalMergingRule, intervalPadding, intervalSetRule, traversalParameters

Constructor Summary

Constructors

Constructor and Description
OptionalIntervalArgumentCollection()

Method Summary

Modifier and Type	Method and Description
protected void	addToIntervalStrings(java.lang.String newInterval) Add an extra interval string to the intervals to include.
protected java.util.List<java.lang.String>	getIntervalStrings() Subclasses must provide a -L argument and override this to return the results of that argument.

Methods inherited from class org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection

getIntervalExclusionPadding, getIntervalMergingRule, getIntervalPadding, getIntervals, getIntervalSetRule, getTraversalParameters, intervalsSpecified

Methods inherited from class java.lang.Object

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

Field Detail

intervalStrings

@Argument(fullName="intervals",
          shortName="L",
          suppressFileExpansion=true,
          doc="One or more genomic intervals over which to operate",
          optional=true)
protected final java.util.List<java.lang.String> intervalStrings

Constructor Detail

OptionalIntervalArgumentCollection

public OptionalIntervalArgumentCollection()

Method Detail

getIntervalStrings

protected java.util.List<java.lang.String> getIntervalStrings()

Description copied from class: IntervalArgumentCollection

Subclasses must provide a -L argument and override this to return the results of that argument. The -L argument specifies intervals to include in analysis and has the following semantics It can use samtools-style intervals either explicitly on the command line (e.g. -L 1 or -L 1:100-200) or by loading in a file containing a list of intervals (e.g. -L myFile.intervals). It can be specified multiple times.

Specified by:

getIntervalStrings in class IntervalArgumentCollection

Returns:

string gathered from the command line -L argument to be parsed into intervals to include

addToIntervalStrings

protected void addToIntervalStrings(java.lang.String newInterval)

Description copied from class: IntervalArgumentCollection

Add an extra interval string to the intervals to include. ONLY for testing -- will throw if called after interval parsing has been performed.

Specified by:

addToIntervalStrings in class IntervalArgumentCollection