org.broadinstitute.hellbender.tools.walkers.realignmentfilter

Class RealignmentArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection

public class RealignmentArgumentCollection
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	bwaMemIndexImage BWA-mem index image created by BwaMemIndexImageCreator
static double	DEFAULT_DROP_RATIO
static int	DEFAULT_MAX_REASONABLE_FRAGMENT_LENGTH
static int	DEFAULT_MIN_ALIGNER_SCORE_DIFFERENCE
static int	DEFAULT_MIN_SEED_LENGTH
static int	DEFAULT_NUM_REGULAR_CONTIGS
static double	DEFAULT_SEED_SPLIT_FACTOR
boolean	dontUseMates Turn off the default mate-aware realignment
double	dropRatio BWA-mem extension drop ratio
int	maxReasonableFragmentLength Maximum fragment length to be considered a reasonable pair alignment
int	minAlignerScoreDifference Minimum difference between best and second-best alignment for a read to be considered well-mapped
int	minSeedLength BWA-mem minimum seed length
int	numRegularContigs Number of regular i.e.
double	splitFactor BWA-mem seed split factor

Constructor Summary

Constructors

Constructor and Description
RealignmentArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MIN_SEED_LENGTH

public static final int DEFAULT_MIN_SEED_LENGTH

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Constant Field Values

DEFAULT_DROP_RATIO

public static final double DEFAULT_DROP_RATIO

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Constant Field Values

DEFAULT_SEED_SPLIT_FACTOR

public static final double DEFAULT_SEED_SPLIT_FACTOR

See Also:

Constant Field Values

DEFAULT_MAX_REASONABLE_FRAGMENT_LENGTH

public static final int DEFAULT_MAX_REASONABLE_FRAGMENT_LENGTH

See Also:

Constant Field Values

DEFAULT_MIN_ALIGNER_SCORE_DIFFERENCE

public static final int DEFAULT_MIN_ALIGNER_SCORE_DIFFERENCE

See Also:

Constant Field Values

DEFAULT_NUM_REGULAR_CONTIGS

public static final int DEFAULT_NUM_REGULAR_CONTIGS

See Also:

Constant Field Values

bwaMemIndexImage

@Argument(fullName="bwa-mem-index-image",
          shortName="index",
          doc="BWA-mem index image")
public java.lang.String bwaMemIndexImage

BWA-mem index image created by BwaMemIndexImageCreator

dontUseMates

@Argument(fullName="dont-use-mates",
          doc="Realign individual reads without using their mates",
          optional=true)
public boolean dontUseMates

Turn off the default mate-aware realignment

maxReasonableFragmentLength

@Argument(fullName="max-reasonable-fragment-length",
          doc="Maximum fragment length to be considered a reasonable pair alignment",
          optional=true)
public int maxReasonableFragmentLength

Maximum fragment length to be considered a reasonable pair alignment

minAlignerScoreDifference

@Argument(fullName="min-aligner-score-difference",
          doc="Minimum difference between best and second-best alignment for a read to be considered well-mapped",
          optional=true)
public int minAlignerScoreDifference

Minimum difference between best and second-best alignment for a read to be considered well-mapped

numRegularContigs

@Argument(fullName="num-regular-contigs",
          doc="Number of regular i.e. non-alt contigs",
          optional=true)
public int numRegularContigs

Number of regular i.e. non-alt contigs

minSeedLength

@Argument(fullName="minimum-seed-length",
          shortName="min-seed-length",
          optional=true,
          doc="Minimum number of matching bases to seed a MEM")
public int minSeedLength

BWA-mem minimum seed length

dropRatio

@Argument(fullName="drop-ratio",
          shortName="drop-ratio",
          doc="Fraction of best MEM extension score below which other extensions are dropped")
public double dropRatio

BWA-mem extension drop ratio

splitFactor

@Argument(fullName="seed-split-factor",
          shortName="split-factor",
          doc="MEMs longer than the minimum seed length times this factor are split and re-seeded.")
public double splitFactor

BWA-mem seed split factor

Constructor Detail

RealignmentArgumentCollection

public RealignmentArgumentCollection()