countBam.everted: Counts everted reads from a single BAM file

In drramki-chop/edm: Scalable workflow to identify copy Number variants from exome sequencing data

Description

This is a utility function that is called by the higher level count.everted.reads. It processes each BAM file individually to generate the count data.

Usage

countBam.everted(bam.file, granges, index = bam.file, min.mapq = 1)

Arguments

bam.file	BAM file that needs to be parsed
granges	Genomic Ranges object with the location of the bins for which we want to count the everted reads.
index	Index for the BAM files.
min.mapq	Minimum mapping quality to include reads.

Details

Most users will not use this function, and it will only be called by the higher level count.everted.reads. Nevertheless it may be useful on its own in some cases.

Value

A list with the number of reads in each bin.

Author(s)

Vincent Plagnol

See Also

count.everted.reads

drramki-chop/edm documentation built on June 6, 2020, 8:48 a.m.