Package picard.analysis
Class JumpingLibraryMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.JumpingLibraryMetrics
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@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
Fields Modifier and Type Field 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 filelong
JUMP_DUPLICATE_PAIRS
The number of outward-facing pairs that are duplicatesdouble
JUMP_DUPLICATE_PCT
The fraction of outward-facing pairs that are marked as duplicateslong
JUMP_LIBRARY_SIZE
The estimated library size for outward-facing pairsdouble
JUMP_MEAN_INSERT_SIZE
The mean insert size for outward-facing pairslong
JUMP_PAIRS
The number of outward-facing pairs in the SAM filedouble
JUMP_STDEV_INSERT_SIZE
The standard deviation on the insert size for outward-facing pairslong
NONJUMP_DUPLICATE_PAIRS
The number of inward-facing pais that are duplicatesdouble
NONJUMP_DUPLICATE_PCT
The fraction of inward-facing pairs that are marked as duplicateslong
NONJUMP_LIBRARY_SIZE
The estimated library size for inward-facing pairsdouble
NONJUMP_MEAN_INSERT_SIZE
The mean insert size for inward-facing pairslong
NONJUMP_PAIRS
The number of inward-facing pairs in the SAM filedouble
NONJUMP_STDEV_INSERT_SIZE
The standard deviation on the insert size for inward-facing pairsdouble
PCT_CHIMERAS
The number of chimeric pairs expressed as a fraction 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 fraction 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 fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
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Constructor Summary
Constructors Constructor Description JumpingLibraryMetrics()
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Field Detail
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JUMP_PAIRS
public long JUMP_PAIRS
The number of outward-facing pairs in the SAM file
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JUMP_DUPLICATE_PAIRS
public long JUMP_DUPLICATE_PAIRS
The number of outward-facing pairs that are duplicates
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JUMP_DUPLICATE_PCT
public double JUMP_DUPLICATE_PCT
The fraction of outward-facing pairs that are marked as duplicates
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JUMP_LIBRARY_SIZE
public long JUMP_LIBRARY_SIZE
The estimated library size for outward-facing pairs
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JUMP_MEAN_INSERT_SIZE
public double JUMP_MEAN_INSERT_SIZE
The mean insert size for outward-facing pairs
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JUMP_STDEV_INSERT_SIZE
public double JUMP_STDEV_INSERT_SIZE
The standard deviation on the insert size for outward-facing pairs
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NONJUMP_PAIRS
public long NONJUMP_PAIRS
The number of inward-facing pairs in the SAM file
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NONJUMP_DUPLICATE_PAIRS
public long NONJUMP_DUPLICATE_PAIRS
The number of inward-facing pais that are duplicates
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NONJUMP_DUPLICATE_PCT
public double NONJUMP_DUPLICATE_PCT
The fraction of inward-facing pairs that are marked as duplicates
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NONJUMP_LIBRARY_SIZE
public long NONJUMP_LIBRARY_SIZE
The estimated library size for inward-facing pairs
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NONJUMP_MEAN_INSERT_SIZE
public double NONJUMP_MEAN_INSERT_SIZE
The mean insert size for inward-facing pairs
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NONJUMP_STDEV_INSERT_SIZE
public double NONJUMP_STDEV_INSERT_SIZE
The standard deviation on the insert size for inward-facing pairs
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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.
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FRAGMENTS
public long FRAGMENTS
The number of fragments in the SAM file
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PCT_JUMPS
public double PCT_JUMPS
The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
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PCT_NONJUMPS
public double PCT_NONJUMPS
The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
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PCT_CHIMERAS
public double PCT_CHIMERAS
The 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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