Allow -f to apply to BAM files in multicov

[arq5x]

Currently -f applies (confusingly) to the -bed file. https://groups.google.com/forum/#!topic/bedtools-discuss/hzRnjQfhyZM

[Distue]

The -f documentation is unfortunately misleading (also contradicting to the description in -r).

I would suggest the developers to deactivate the -f and -r options until fixed, because this is leading to wrong results.

https://groups.google.com/forum/#!topic/bedtools-discuss/hzRnjQfhyZM

[ewallace]

I also had this problem. What about first clarifying the documentation to make it unambiguous that "each A" means the features in the bed/gff/vcf file, and "each B" means reads in the bamfiles, for example: -f | Minimum overlap required as a fraction of each feature in bed/gff/vcf file A. Default is 1E-9 (i.e., 1bp).

Feature request a flag for the inverse, i.e. -fB | Minimum overlap required as a fraction of each read in bamfile B. Default is 1E-9 (i.e., 1bp).