picard.analysis

Class JumpingLibraryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.JumpingLibraryMetrics

public class JumpingLibraryMetrics
extends htsjdk.samtools.metrics.MetricBase

High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".

Field Summary

Fields

Modifier and Type	Field and Description
long	CHIMERIC_PAIRS The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
long	FRAGMENTS The number of fragments in the SAM file
long	JUMP_DUPLICATE_PAIRS The number of outward-facing pairs that are duplicates
double	JUMP_DUPLICATE_PCT The percentage of outward-facing pairs that are marked as duplicates
long	JUMP_LIBRARY_SIZE The estimated library size for outward-facing pairs
double	JUMP_MEAN_INSERT_SIZE The mean insert size for outward-facing pairs
long	JUMP_PAIRS The number of outward-facing pairs in the SAM file
double	JUMP_STDEV_INSERT_SIZE The standard deviation on the insert size for outward-facing pairs
long	NONJUMP_DUPLICATE_PAIRS The number of inward-facing pais that are duplicates
double	NONJUMP_DUPLICATE_PCT The percentage of inward-facing pairs that are marked as duplicates
long	NONJUMP_LIBRARY_SIZE The estimated library size for inward-facing pairs
double	NONJUMP_MEAN_INSERT_SIZE The mean insert size for inward-facing pairs
long	NONJUMP_PAIRS The number of inward-facing pairs in the SAM file
double	NONJUMP_STDEV_INSERT_SIZE The standard deviation on the insert size for inward-facing pairs
double	PCT_CHIMERAS The number of chimeric pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
double	PCT_JUMPS The number of outward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
double	PCT_NONJUMPS The number of inward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.

Constructor Summary

Constructors

Constructor and Description
JumpingLibraryMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

JUMP_PAIRS

public long JUMP_PAIRS

The number of outward-facing pairs in the SAM file

JUMP_DUPLICATE_PAIRS

public long JUMP_DUPLICATE_PAIRS

The number of outward-facing pairs that are duplicates

JUMP_DUPLICATE_PCT

public double JUMP_DUPLICATE_PCT

The percentage of outward-facing pairs that are marked as duplicates

JUMP_LIBRARY_SIZE

public long JUMP_LIBRARY_SIZE

The estimated library size for outward-facing pairs

JUMP_MEAN_INSERT_SIZE

public double JUMP_MEAN_INSERT_SIZE

The mean insert size for outward-facing pairs

JUMP_STDEV_INSERT_SIZE

public double JUMP_STDEV_INSERT_SIZE

The standard deviation on the insert size for outward-facing pairs

NONJUMP_PAIRS

public long NONJUMP_PAIRS

The number of inward-facing pairs in the SAM file

NONJUMP_DUPLICATE_PAIRS

public long NONJUMP_DUPLICATE_PAIRS

The number of inward-facing pais that are duplicates

NONJUMP_DUPLICATE_PCT

public double NONJUMP_DUPLICATE_PCT

The percentage of inward-facing pairs that are marked as duplicates

NONJUMP_LIBRARY_SIZE

public long NONJUMP_LIBRARY_SIZE

The estimated library size for inward-facing pairs

NONJUMP_MEAN_INSERT_SIZE

public double NONJUMP_MEAN_INSERT_SIZE

The mean insert size for inward-facing pairs

NONJUMP_STDEV_INSERT_SIZE

public double NONJUMP_STDEV_INSERT_SIZE

The standard deviation on the insert size for inward-facing pairs

CHIMERIC_PAIRS

public long CHIMERIC_PAIRS

The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.

FRAGMENTS

public long FRAGMENTS

The number of fragments in the SAM file

PCT_JUMPS

public double PCT_JUMPS

The number of outward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.

PCT_NONJUMPS

public double PCT_NONJUMPS

The number of inward-facing pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.

PCT_CHIMERAS

public double PCT_CHIMERAS

The number of chimeric pairs expressed as a percentage of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.

Constructor Detail

JumpingLibraryMetrics

public JumpingLibraryMetrics()