Usage examples:
===============

$ ./faust-encode
usage: ./faust-encode -[iorblrth]
i|input PATH
o|output PATH                  (default: encode.output.TIMESTAMP)
r|initial-raw-block-size VALUE (default: 1g)
b|block-size VALUE             (default: 2g)
l|length-threshold VALUE       (default: 64)
d|dynamic-threshold            (default: fasle)
t|threads VALUE                (default: 1)
h|help


Options:
========

input = Input reads. One per line. Containing A C G T. No N characters
are accepted. Currently MAX_READ_LENGTH is set to 100. This can be
modified in common.h.

output = Path to the compressed output.

initial-raw-block-size = The size of the initial block that is encoded in 2bpb.

block-size = The size of each scan block.

length-threshold = Only check candidates if they share a common factor of at least /threshold/.

dynamic-threshold = Dynamically increase the threshold as the scan progresses in the text (to speed up runtime).

threads = Specify the number of threads to search for candidates (on large files this really improves runtime).


Arguments that require a size string:
=====================================

You can specify a human readable string, for example, 1g and it will assume 1GB of space.

G|g M|m K|k and B|b are all acceptable suffixes.

If no suffix is used it is assumed to be bytes.



$ ./faust-decode
usage: ./faust-decode input faust-output



$ ./afin-encode
usage: ./afin-encode faust-input afin-output



$ ./afin-decode
usage: ./afin-encode afin-input output