com.fulcrumgenomics.umi.CollectDuplexSeqMetrics
The family size, i.e. the number of read pairs grouped together into a family.
The count of families with size == family_size
when grouping just by coordinates and strand information.
The fraction of all _CS_ families where size == family_size
.
The fraction of all _CS_ families where size >= family_size
.
The count of families with size == family_size
when also grouping by UMI to create single-strand families.
The fraction of all _SS_ families where size == family_size
.
The fraction of all _SS_ families where size >= family_size
.
The count of families with size == family_size
when also grouping by UMI and merging single-strand
families from opposite strands of the same source molecule.
The fraction of all _DS_ families where size == family_size
.
The fraction of all _DS_ families where size >= family_size
.
Gets the value of the field by name.
Gets the value of the field by name.
The count of families with size == family_size
when grouping just by coordinates and strand information.
The fraction of all _CS_ families where size == family_size
.
The fraction of all _CS_ families where size >= family_size
.
The count of families with size == family_size
when also grouping by UMI and merging single-strand
families from opposite strands of the same source molecule.
The fraction of all _DS_ families where size == family_size
.
The fraction of all _DS_ families where size >= family_size
.
The family size, i.e.
The family size, i.e. the number of read pairs grouped together into a family.
Override this method to customize how values are formatted.
Override this method to customize how values are formatted.
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.
(Changed in version 2.9.0) The behavior of scanRight
has changed. The previous behavior can be reproduced with scanRight.reverse.
The count of families with size == family_size
when also grouping by UMI to create single-strand families.
The fraction of all _SS_ families where size == family_size
.
The fraction of all _SS_ families where size >= family_size
.
(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.
(familySizeMetric: MonadOps[(String, String)]).filter(p)
(familySizeMetric: MonadOps[(String, String)]).flatMap(f)
(familySizeMetric: MonadOps[(String, String)]).map(f)
(familySizeMetric: MonadOps[(String, String)]).withFilter(p)
Metrics produced by
CollectDuplexSeqMetrics
to quantify the distribution of different kinds of read family sizes. Three kinds of families are described:1. _CS_ or _Coordinate & Strand_: families of reads that are grouped together by their unclipped 5' genomic positions and strands just as they are in traditional PCR duplicate marking 2. _SS_ or _Single Strand_: single-strand families that are each subsets of a CS family create by also using the UMIs to partition the larger family, but not linking up families that are created from opposing strands of the same source molecule. 3. _DS_ or _Double Strand_: families that are created by combining single-strand families that are from opposite strands of the same source molecule. This does **not** imply that all DS families are composed of reads from both strands; where only one strand of a source molecule is observed a DS family is still counted.
The family size, i.e. the number of read pairs grouped together into a family.
The count of families with
size == family_size
when grouping just by coordinates and strand information.The fraction of all _CS_ families where
size == family_size
.The fraction of all _CS_ families where
size >= family_size
.The count of families with
size == family_size
when also grouping by UMI to create single-strand families.The fraction of all _SS_ families where
size == family_size
.The fraction of all _SS_ families where
size >= family_size
.The count of families with
size == family_size
when also grouping by UMI and merging single-strand families from opposite strands of the same source molecule.The fraction of all _DS_ families where
size == family_size
.The fraction of all _DS_ families where
size >= family_size
.