Load data from a BAM file

Load data from a BAM file. Information about genomic length and tail length is included. One alignment from each multimapping read is kept. Only the 3' end position is kept.

Usage

load_bam_into(
  dest_file,
  bam_file,
  tail_source,
  read_pairs_file = NULL,
  clips_file = NULL,
  limit = NA,
  filter_secondary = TRUE
)

Details

Multimappers are detected using NH attribute, and there should be only one alignment that isn't flagged as a "secondary alignment". This is what STAR does by default.

Tail Tools BAM files don't require this "secondary alignment" filtering step, so it can and should be disabled in this case.