Summarize BAM file

Source: R/statsUMI4C.R

Get summary of interesting bam statistics

.getSummaryBam(bam_file, mapped = TRUE, secondary = FALSE)

Arguments

bam_file

Path for the bam file.
mapped

Logical indicating whether to extract mapped reads.
secondary

Logical indicating whether to extract secondary aligned reads.

Value

Returns a numeric containing the number of reads in bam_file that has the specified mapped and secondary status.