org.broadinstitute.hellbender.tools.walkers.haplotypecaller

Class AssemblyRegionTrimmerArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmerArgumentCollection

public class AssemblyRegionTrimmerArgumentCollection
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected int	discoverExtension the maximum extent into the full active region extension that we're willing to go in genotyping our events
protected boolean	dontTrimActiveRegions
protected int	ggaExtension
int	indelPadding Include at least this many bases around an event for calling it
int	snpPadding

Constructor Summary

Constructors

Constructor and Description
AssemblyRegionTrimmerArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

dontTrimActiveRegions

@Advanced
 @Argument(fullName="dont-trim-active-regions",
          doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping",
          optional=true)
protected boolean dontTrimActiveRegions

discoverExtension

@Hidden
 @Argument(fullName="max-disc-ar-extension",
          doc="the maximum extent into the full active region extension that we\'re willing to go in genotyping our events for discovery",
          optional=true)
protected int discoverExtension

the maximum extent into the full active region extension that we're willing to go in genotyping our events

ggaExtension

@Hidden
 @Argument(fullName="max-gga-ar-extension",
          doc="the maximum extent into the full active region extension that we\'re willing to go in genotyping our events for GGA mode",
          optional=true)
protected int ggaExtension

indelPadding

@Hidden
 @Argument(fullName="padding-around-indels",
          doc="Include at least this many bases around an event for calling indels",
          optional=true)
public int indelPadding

Include at least this many bases around an event for calling it

snpPadding

@Hidden
 @Argument(fullName="padding-around-snps",
          doc="Include at least this many bases around an event for calling snps",
          optional=true)
public int snpPadding

Constructor Detail

AssemblyRegionTrimmerArgumentCollection

public AssemblyRegionTrimmerArgumentCollection()