returns the bam data.frame with an additional column counts. Only relevant if the fasta file used for mapping input was previously collapsed via fastx_toolkit to return a fasta read name in the format of
An object of class DataFrame (from IRanges). Can be generated from readBam.
Logical. If TRUE, assume the reads in the bam file does not have a count record and sets all counts to 1.
An object of class data.frame having the values from the original bam file with an additional 'count' column.
Diana H.P. Low