countBam.everted: Counts everted reads from a single BAM file
Description
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.
Usage
countBam.everted(bam.file, granges, index = bam.file, min.mapq = 1)
Arguments
bam.file
BAM file that needs to be parsed
granges
Genomic Ranges object with the location of the bins for which we want
to count the everted reads.
index
Index for the BAM files.
min.mapq
Minimum mapping quality to include reads.
Value
A list with the number of reads in each bin.
Details
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.