SYNOPSIS

reapr stats [options] <preprocess-output-directory> <outprefix>

OPTIONS

-f <int>

Insert size [ave from stats.txt]

-i <int>

Minimum insert size [pc1 from stats.txt]

-j <int>

Maximum insert size [pc99 from stats.txt]

-m <int>

Maximum read length (this doesn't need to be exact, it just determines memory allocation, so must be >= max read length) [2000]

-p <string>

Name of .gz perfect mapping file made by perfectmap

-q <int>

Ignore reads with mapping quality less than this [0]

-s <int>

Calculate FCD error every n-th base [ceil((fragment size) / 1000)]

-u <string>

File containing list of chromosomes to look at (one per line)