Package picard.analysis
Class JumpingLibraryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.JumpingLibraryMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
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".
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
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
The number of fragments in the SAM filelong
The number of outward-facing pairs that are duplicatesdouble
The fraction of outward-facing pairs that are marked as duplicateslong
The estimated library size for outward-facing pairsdouble
The mean insert size for outward-facing pairslong
The number of outward-facing pairs in the SAM filedouble
The standard deviation on the insert size for outward-facing pairslong
The number of inward-facing pais that are duplicatesdouble
The fraction of inward-facing pairs that are marked as duplicateslong
The estimated library size for inward-facing pairsdouble
The mean insert size for inward-facing pairslong
The number of inward-facing pairs in the SAM filedouble
The standard deviation on the insert size for inward-facing pairsdouble
The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.double
The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.double
The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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JUMP_PAIRS
public long JUMP_PAIRSThe number of outward-facing pairs in the SAM file -
JUMP_DUPLICATE_PAIRS
public long JUMP_DUPLICATE_PAIRSThe number of outward-facing pairs that are duplicates -
JUMP_DUPLICATE_PCT
public double JUMP_DUPLICATE_PCTThe fraction of outward-facing pairs that are marked as duplicates -
JUMP_LIBRARY_SIZE
public long JUMP_LIBRARY_SIZEThe estimated library size for outward-facing pairs -
JUMP_MEAN_INSERT_SIZE
public double JUMP_MEAN_INSERT_SIZEThe mean insert size for outward-facing pairs -
JUMP_STDEV_INSERT_SIZE
public double JUMP_STDEV_INSERT_SIZEThe standard deviation on the insert size for outward-facing pairs -
NONJUMP_PAIRS
public long NONJUMP_PAIRSThe number of inward-facing pairs in the SAM file -
NONJUMP_DUPLICATE_PAIRS
public long NONJUMP_DUPLICATE_PAIRSThe number of inward-facing pais that are duplicates -
NONJUMP_DUPLICATE_PCT
public double NONJUMP_DUPLICATE_PCTThe fraction of inward-facing pairs that are marked as duplicates -
NONJUMP_LIBRARY_SIZE
public long NONJUMP_LIBRARY_SIZEThe estimated library size for inward-facing pairs -
NONJUMP_MEAN_INSERT_SIZE
public double NONJUMP_MEAN_INSERT_SIZEThe mean insert size for inward-facing pairs -
NONJUMP_STDEV_INSERT_SIZE
public double NONJUMP_STDEV_INSERT_SIZEThe standard deviation on the insert size for inward-facing pairs -
CHIMERIC_PAIRS
public long CHIMERIC_PAIRSThe 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 FRAGMENTSThe number of fragments in the SAM file -
PCT_JUMPS
public double PCT_JUMPSThe number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. -
PCT_NONJUMPS
public double PCT_NONJUMPSThe number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. -
PCT_CHIMERAS
public double PCT_CHIMERASThe number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
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Constructor Details
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JumpingLibraryMetrics
public JumpingLibraryMetrics()
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