com.fulcrumgenomics.umi.CollectDuplexSeqMetrics
DuplexYieldMetric
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package CollectDuplexSeqMetrics
com.fulcrumgenomics.umi.CollectDuplexSeqMetrics
The approximate fraction of the full dataset that was used to generate the remaining values.
The number of read pairs upon which the remaining metrics are based.
The number of _CS_ (Coordinate & Strand) families present in the data.
The number of _SS_ (Single-Strand by UMI) families present in the data.
The number of _DS_ (Double-Strand by UMI) families present in the data.
The number of _DS_ families that had the minimum number of observations on both strands to be called duplexes (default = 1 read on each strand).
The fraction of _DS_ families that are duplexes (ds_duplexes / ds_families).
The fraction of _DS_ families that should be duplexes under an idealized model
where each strand, A and B, have equal probability of being sampled, given
the observed distribution of _DS_ family sizes.
Gets the value of the field by name.
Gets the value of the field by name.
The number of _CS_ (Coordinate & Strand) families present in the data.
The number of _DS_ families that had the minimum number of observations on both strands to be called duplexes (default = 1 read on each strand).
The number of _DS_ (Double-Strand by UMI) families present in the data.
The fraction of _DS_ families that are duplexes (ds_duplexes / ds_families).
The fraction of _DS_ families that should be duplexes under an idealized model
where each strand, A and B, have equal probability of being sampled, given
the observed distribution of _DS_ family sizes.
Override this method to customize how values are formatted.
Override this method to customize how values are formatted.
The approximate fraction of the full dataset that was used to generate the remaining values.
Gets the value of the field by name, returns None if it does not exist.
Gets the value of the field by name, returns None if it does not exist.
Gets an iterator over the fileds of this metric in the order they were defined.
Gets an iterator over the fileds of this metric in the order they were defined. Returns tuples of names and values
Get the names of the arguments in the order they were defined.
Get the names of the arguments in the order they were defined.
The number of read pairs upon which the remaining metrics are based.
(Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.
The number of _SS_ (Single-Strand by UMI) families present in the data.
(Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.
Get the values of the arguments in the order they were defined.
Get the values of the arguments in the order they were defined.
(duplexYieldMetric: MonadOps[(String, String)]).filter(p)
(duplexYieldMetric: MonadOps[(String, String)]).flatMap(f)
(duplexYieldMetric: MonadOps[(String, String)]).map(f)
(duplexYieldMetric: MonadOps[(String, String)]).withFilter(p)
Metrics produced by
CollectDuplexSeqMetricsthat are sampled at various levels of coverage, via random downsampling, during the construction of duplex metrics. The downsampling is done in such a way that thefractions are approximate, and not exact, therefore thefractionfield should only be interpreted as a guide and theread_pairsfield used to quantify how much data was used.See
FamilySizeMetricfor detailed definitions ofCS,SSandDSas used below.The approximate fraction of the full dataset that was used to generate the remaining values.
The number of read pairs upon which the remaining metrics are based.
The number of _CS_ (Coordinate & Strand) families present in the data.
The number of _SS_ (Single-Strand by UMI) families present in the data.
The number of _DS_ (Double-Strand by UMI) families present in the data.
The number of _DS_ families that had the minimum number of observations on both strands to be called duplexes (default = 1 read on each strand).
The fraction of _DS_ families that are duplexes (
ds_duplexes / ds_families).The fraction of _DS_ families that should be duplexes under an idealized model where each strand,
AandB, have equal probability of being sampled, given the observed distribution of _DS_ family sizes.