This is a utility function that is called by the higher level count.everted.reads. It processes each BAM file individually to generate the count data.
countBam.everted(bam.file, granges, index = bam.file, min.mapq = 1)BAM file that needs to be parsed
Genomic Ranges object with the location of the bins for which we want to count the everted reads.
Index for the BAM files.
Minimum mapping quality to include reads.
A list with the number of reads in each bin.
Most users will not use this function, and it will only be called by the higher level count.everted.reads. Nevertheless it may be useful on its own in some cases.
count.everted.reads