getSRPartitionScores: Get a score for each shortread in a bam file on specific...

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

Get a score for each shortread in a bam file on specific positions. Scores based on a consensus matrix of longreads.

Usage

getSRPartitionScores(bamfile, mats, ...)

Arguments

bamfile	BAM file path.
mats	Consensus matrix from longread clustering at positions in ppos.

Details

Returns a srpartition object: A list with slots:

bamfile

<character>; Path to the bam file used to construct the pileup

ppos

<numeric>; Positions used for scoring

srpartition

A data.frame with colums:

read

<character>; The read name

pos

<integer>; Genomic position of base

Haplotype

<character>; Haplotype

prob

<integer>; probability for a base at a position

consmat

Consensus matrix

Value

A srpatition object. See Details.

Examples

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DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.