Read a BAM file

Parse a BAM (Binary Alignment Map) file into a tidy tibble.

Usage

mp_read_bam(path, regions = NULL)

Arguments

path

Character scalar. Path to a .bam file.

regions

Character scalar or NULL. An optional genomic region string such as "chr1:1000-2000" to restrict the query.

Value

A molpath_parsed object whose data slot is a tibble with columns qname, flag, rname, pos, mapq, cigar, seq, and qual.

Details

Attempts Rsamtools::scanBam() first, then falls back to a system call to samtools view. If neither is available an informative error is raised.

Examples

# \donttest{
bam_file <- system.file("extdata", "example.bam", package = "molpathR")
if (nzchar(bam_file)) {
  result <- mp_read_bam(bam_file)
  print(result)
}
# }