picard.analysis

Class CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.CollectWgsMetrics.WgsMetrics

picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics

Enclosing class:

CollectWgsMetricsFromQuerySorted

public static class CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
extends CollectWgsMetrics.WgsMetrics

Metrics for evaluating the performance of whole genome sequencing experiments.

Field Summary

Fields

Modifier and Type	Field and Description
double	MEAN_INSERT_SIZE The mean insert size, after filters are applied.
long	TOTAL_BASES The total number of bases, before any filters are applied.
long	TOTAL_DUPE_PAIRS The number of duplicate read pairs, before all filters are applied.
long	TOTAL_ORIENTED_PAIRS The number of read pairs with standard orientations from which to calculate mean insert size, after filters are applied.
long	TOTAL_READ_PAIRS The number of read pairs, before all filters are applied.
long	TOTAL_USABLE_BASES The number of usable bases, after all filters are applied.

Fields inherited from class picard.analysis.CollectWgsMetrics.WgsMetrics

GENOME_TERRITORY, MAD_COVERAGE, MEAN_COVERAGE, MEDIAN_COVERAGE, PCT_100X, PCT_10X, PCT_15X, PCT_1X, PCT_20X, PCT_25X, PCT_30X, PCT_40X, PCT_50X, PCT_5X, PCT_60X, PCT_70X, PCT_80X, PCT_90X, PCT_EXC_BASEQ, PCT_EXC_CAPPED, PCT_EXC_DUPE, PCT_EXC_MAPQ, PCT_EXC_OVERLAP, PCT_EXC_TOTAL, PCT_EXC_UNPAIRED, SD_COVERAGE

Constructor Summary

Constructors

Constructor and Description
QuerySortedSeqMetrics()

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

TOTAL_BASES

public long TOTAL_BASES

The total number of bases, before any filters are applied.

TOTAL_USABLE_BASES

public long TOTAL_USABLE_BASES

The number of usable bases, after all filters are applied.

TOTAL_READ_PAIRS

public long TOTAL_READ_PAIRS

The number of read pairs, before all filters are applied.

TOTAL_DUPE_PAIRS

public long TOTAL_DUPE_PAIRS

The number of duplicate read pairs, before all filters are applied.

TOTAL_ORIENTED_PAIRS

public long TOTAL_ORIENTED_PAIRS

The number of read pairs with standard orientations from which to calculate mean insert size, after filters are applied.

MEAN_INSERT_SIZE

public double MEAN_INSERT_SIZE

The mean insert size, after filters are applied.

Constructor Detail

QuerySortedSeqMetrics

public QuerySortedSeqMetrics()