importBAM: Parallel import of BAM files

In tanaylab/reputils: Utility functions for working with transposable elements

Description

Imports reads stored in BAM files

Usage

importBAM(bams, paired = NA, multi = TRUE, what = NA, tag = NA,
  mate = NA, anchor = NULL, meta = NA, granges = FALSE,
  barcode = NA, data.table = TRUE, sorted = TRUE,
  use_gcluster = FALSE)

Arguments

path	Character. Path to file.
main_assembly	Logical. If TRUE (the default), only returns TE intervals on the main chromosomes.

Value

Returns a GRanges object with TE intervals

tanaylab/reputils documentation built on Nov. 5, 2019, 9:58 a.m.