* fix phred calculation

* fix phred avg output

* calc_phred_average.cpp: newline eof

* calc_phred_average.cpp: use uint32_t

* calc_phred_average: use int instead of uint32_t because of negative number

* goldrush_path.cpp: fix phred sum silver path log to use delog

* goldrush_path.cpp: change types

* goldrush_path.cpp: calc median phred based on dataset

* fix automatically calculate median

* adjust test case

* adjust test case

* update help and default values in goldrush_path

* goldrush: update make file defaults

* Update README.md

* Update README.md

Co-authored-by: Lauren Coombe <[email protected]>

* Update bin/goldrush

Co-authored-by: Lauren Coombe <[email protected]>

* Update goldrush_path/goldrush_path.cpp

Co-authored-by: Lauren Coombe <[email protected]>

* refactor and use std max

* change phred sum func code location

* azure-pipelines.yml: set min pyopenssl version

* goldrush_path.cpp: refactor constexpr out to main

---------

Co-authored-by: jowong04 <[email protected]>
Co-authored-by: jowong04 <[email protected]>
Co-authored-by: Lauren Coombe <[email protected]>
Co-authored-by: jowong04 <[email protected]>

* refactor silver path log info struct

* print out gr version for each rule

* refactor valid reads out

---------

Co-authored-by: jowong04 <[email protected]>

* Ensures miBf is deterministic

* remove extra space

* add dev only function description

* ensure all insert functions are equivalent

* remove unused variable