If a read is near multiple sites, the nearest is chosen.
Usage
site_reads_into(dest_filename, reads_filename, sites, site_pad, site_upstrand)
Arguments
- site_pad
Reads ending within position-site_pad, position+site_pad will be counted to a site and used for tail estimation.
- site_upstrand
Reads ending at most this far upstrand will also be included in UMI counts.