This function reads a single sorted, dedupliated paired end bam file and returns either a GRanges object or a GenomicAlignmentPairs object. The former requires much less memory but a the cost of retaining the outer boundaries of each read. If read 1 has start S1 and end E1 and read 2 has start S2 and end S2, the Granges object spans S1-E2.
Usage
bb_read_bam(
sortedBam,
genome = c("hg38", "danRer11"),
return_type = c("GenomicAlignmentPairs", "GRanges")
)
Arguments
- sortedBam
File path to the bam file to load.
- genome
One of "hg38" or "danRer11". This is used to clean up the granges object if necessary.
- return_type
Type of object to return. GRanges is smaller. GenomicAlignmentPairs retains read pair data.
Value
An object according to return_type.