reverse-complement Lisp SBCL #2 program

;;; The Computer Language Benchmarks Game
;;; https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
;;; contributed by Antonio Saade

(declaim (optimize (speed 3) (safety 0) (debug 0))
         (inline compl))

(defconstant +lut+
  (let ((lut (make-array 256 :element-type 'base-char)))
    (loop
      for a across "ACGTMRWSYKVHDBNUacgtmrwsykvhdbnu"
      for b across "TGCAKYWSRMBDHVNATGCAKYWSRMBDHVNA"
      do (setf (aref lut (char-code a)) b))
    lut))

(defun compl (a)
  (declare (type base-char a))
  (aref +lut+ (char-code a)))

(defun write-seq-by-n (s n out)
  (declare (type simple-string s)
           (type fixnum n))
  (loop
    with length = (length s)
    for start from 0 by n below length
    do (write-line s out :start start :end (min length (+ start n)))))

(defun process-fasta (s out)
  (declare (type simple-string s))
  (do ((start 0 (1+ start))
       (end (- (length s) 1) (1- end))
       (b #\0))
      ((< end start))
    (setf b (schar s start))
    (setf (schar s start) (compl (schar s end)))
    (setf (schar s end) (compl b)))
  (write-seq-by-n s 60 out))

(defun main ()
  (with-open-file (in #p"/dev/stdin" :direction :input)
    (with-open-file (out #p"/dev/stdout"
                         :direction :output
                         :if-exists :supersede)
      (loop
        with fasta = (make-string-output-stream :element-type 'base-char)
        for line simple-string = (read-line in nil)
        while line
        do (if (char= (char line 0) #\>)
               (progn
                 (process-fasta (get-output-stream-string fasta) out)
                 (write-line line out))
               (write-string line fasta))
        finally (process-fasta (get-output-stream-string fasta) out)))))
    

NOTES:
64-bit Ubuntu quad core
SBCL 2.0.4


Fri, 22 May 2020 00:24:43 GMT

MAKE:
cp: 'revcomp.sbcl-2.sbcl' and './revcomp.sbcl-2.sbcl' are the same file
SBCL built with: /usr/local/bin/sbcl --userinit /dev/null --batch --eval '(load "revcomp.sbcl-2.sbcl_compile")'
### START revcomp.sbcl-2.sbcl_compile
(handler-bind ((sb-ext:defconstant-uneql      (lambda (c) (abort c))))      (require :sb-concurrency)      (load (compile-file "revcomp.sbcl-2.sbcl" ))) (save-lisp-and-die "sbcl.core" :purify t)
### END revcomp.sbcl-2.sbcl_compile

; compiling file "/home/dunham/8000-benchmarksgame/bench/revcomp/revcomp.sbcl-2.sbcl" (written 20 MAY 2019 10:50:35 AM):
; compiling (DECLAIM (OPTIMIZE # ...) ...)
; compiling (DEFCONSTANT +LUT+ ...)
; compiling (DEFUN COMPL ...)
; compiling (DEFUN WRITE-SEQ-BY-N ...)
; compiling (DEFUN PROCESS-FASTA ...)
; compiling (DEFUN MAIN ...)
; file: /home/dunham/8000-benchmarksgame/bench/revcomp/revcomp.sbcl-2.sbcl
; in: DEFUN MAIN
;     (GET-OUTPUT-STREAM-STRING FASTA)
; ==>
;   FASTA
; 
; note: deleting unreachable code
; 
; compilation unit finished
;   printed 1 note


; wrote /home/dunham/benchmarksgame_quadcore/revcomp/tmp/revcomp.sbcl-2.fasl
; compilation finished in 0:00:00.834
### START revcomp.sbcl-2.sbcl_run
(main) (quit)
### END revcomp.sbcl-2.sbcl_run


5.44s to complete and log all make actions

COMMAND LINE:
/usr/local/bin/sbcl --dynamic-space-size 3072 --noinform --core sbcl.core --userinit /dev/null --load revcomp.sbcl-2.sbcl_run 0 < revcomp-input100000000.txt

PROGRAM FAILED