A function to import paired end bam files as GRanges. Can be quite lengthy for .bam files with 5+ millions fragments.

A function to import paired end bam files as GRanges. Can be quite lengthy for .bam files with 5+ millions fragments.

importPEBamFiles(files, where = NULL, max_insert_size = 1000,
  shift_ATAC_fragments = FALSE, verbose = TRUE)

Arguments

files	A character vector. Each element of the vector is the path of an individual .bam file.
where	GRanges. Only import the fragments mapping to the input GRanges (can fasten the import process a lot). (mapping to the same coordinates) be removed?
max_insert_size	Integer Filter out fragments larger than this size.
shift_ATAC_fragments	If the fragments come from ATAC-seq, one might want to shift the extremities by +5 / -4 bp.
verbose	Boolean

Value

A GRanges object containing fragments from the input .bam file.