#define NULL ((void *)0)
typedef unsigned long size_t; // Customize by platform.
typedef long intptr_t;
typedef unsigned long uintptr_t;
typedef long scalar_t__; // Either arithmetic or pointer type.
/* By default, we understand bool (as a convenience). */
typedef int bool;
#define false 0
#define true 1

/* Forward declarations */

/* Type definitions */

/* Variables and functions */
int /*<<< orphan*/ printf(char *);
void usage() {
  printf("usage: \nchaos queryfile dbasefile [options]\n\n");
  printf("Options:\n");
  printf("-p     = Peptide sequence [default genomic]\n");
  printf("-v     = Verbose mode [default brief]\n");
  printf("-b     = Both strands [default forward-only]\n");
  printf("-t     = Translated [default off]\n");
  printf("-ext   = do BLAST-like extention with given cutoff [default off]\n");
  printf("-wl #  = Word Length [default 10 for genomic, 4 for peptide]\n");
  printf(
      "-nd #  = Number of Degeneracy [default 1 for genomic, 0 for peptide]\n");
  printf("-co #  = score CutOff [default 25]\n");
  printf("-rsc # = Rescoring cutoff [default 0]\n");
  printf(
      "-lb #  = LookBack distance [default 20 for genomic, 8 for peptide]\n");
  printf(
      "-gl #  = maximum Gap Length [default 5 for genomic, 3 for peptide]\n");
  printf("-gs #  = Gap Start penalty [default 0]\n");
  printf("-gc #  = Gap Continue penalty [default -1]\n");
  printf("-s1 # # = use the given substring of the query [default whole]\n");
  printf("-s2 # # = use the givensubstring of the dbase [default whole]\n");
  printf("-pairs pairfile = read \"-s1 # # -s2 # #\" from pairfile [default "
         "off]\n\t[This is not fully functional!!!]\n");
  printf("-version = prints the version of this CHAOS\n");
}


x86 assembly (clang, -O0):
<usage>:
push   %rbp
mov    %rsp,%rbp
lea    0xee5(%rip),%rdi
call   1030 <printf@plt>
lea    0xf07(%rip),%rdi
call   1030 <printf@plt>
lea    0xf05(%rip),%rdi
call   1030 <printf@plt>
lea    0xf26(%rip),%rdi
call   1030 <printf@plt>
lea    0xf41(%rip),%rdi
call   1030 <printf@plt>
lea    0xf63(%rip),%rdi
call   1030 <printf@plt>
lea    0xf7a(%rip),%rdi
call   1030 <printf@plt>
lea    0xfb0(%rip),%rdi
call   1030 <printf@plt>
lea    0xfe2(%rip),%rdi
call   1030 <printf@plt>
lea    0x101c(%rip),%rdi
call   1030 <printf@plt>
lea    0x1034(%rip),%rdi
call   1030 <printf@plt>
lea    0x104f(%rip),%rdi
call   1030 <printf@plt>
lea    0x1087(%rip),%rdi
call   1030 <printf@plt>
lea    0x10bf(%rip),%rdi
call   1030 <printf@plt>
lea    0x10db(%rip),%rdi
call   1030 <printf@plt>
lea    0x10fb(%rip),%rdi
call   1030 <printf@plt>
lea    0x112f(%rip),%rdi
call   1030 <printf@plt>
lea    0x1162(%rip),%rdi
call   1030 <printf@plt>
lea    0x11bf(%rip),%rdi
call   1030 <printf@plt>
pop    %rbp
ret

x86 assembly (clang, -O2):
<usage>:
push   %rax
lea    0xee8(%rip),%rdi
call   1030 <puts@plt>
lea    0xf09(%rip),%rdi
call   1030 <puts@plt>
lea    0xf06(%rip),%rdi
call   1030 <puts@plt>
lea    0xf26(%rip),%rdi
call   1030 <puts@plt>
lea    0xf40(%rip),%rdi
call   1030 <puts@plt>
lea    0xf61(%rip),%rdi
call   1030 <puts@plt>
lea    0xf77(%rip),%rdi
call   1030 <puts@plt>
lea    0xfac(%rip),%rdi
call   1030 <puts@plt>
lea    0xfdd(%rip),%rdi
call   1030 <puts@plt>
lea    0x1016(%rip),%rdi
call   1030 <puts@plt>
lea    0x102d(%rip),%rdi
call   1030 <puts@plt>
lea    0x1047(%rip),%rdi
call   1030 <puts@plt>
lea    0x107e(%rip),%rdi
call   1030 <puts@plt>
lea    0x10b5(%rip),%rdi
call   1030 <puts@plt>
lea    0x10d0(%rip),%rdi
call   1030 <puts@plt>
lea    0x10ef(%rip),%rdi
call   1030 <puts@plt>
lea    0x1122(%rip),%rdi
call   1030 <puts@plt>
lea    0x1154(%rip),%rdi
call   1030 <puts@plt>
lea    0x11b0(%rip),%rdi
pop    %rax
jmp    1030 <puts@plt>

LLVM IR (-O0):
@.str = [46 x i8] c"usage: \0Achaos queryfile dbasefile [options]\0A\0A\00"
@.str.1 = [10 x i8] c"Options:\0A\00"
@.str.2 = [45 x i8] c"-p = Peptide sequence [default genomic]\0A\00"
@.str.3 = [39 x i8] c"-v = Verbose mode [default brief]\0A\00"
@.str.4 = [46 x i8] c"-b = Both strands [default forward-only]\0A\00"
@.str.5 = [35 x i8] c"-t = Translated [default off]\0A\00"
@.str.6 = [66 x i8] c"-ext = do BLAST-like extention with given cutoff [default off]\0A\00"
@.str.7 = [62 x i8] c"-wl # = Word Length [default 10 for genomic, 4 for peptide]\0A\00"
@.str.8 = [70 x i8] c"-nd # = Number of Degeneracy [default 1 for genomic, 0 for peptide]\0A\00"
@.str.9 = [36 x i8] c"-co # = score CutOff [default 25]\0A\00"
@.str.10 = [39 x i8] c"-rsc # = Rescoring cutoff [default 0]\0A\00"
@.str.11 = [68 x i8] c"-lb # = LookBack distance [default 20 for genomic, 8 for peptide]\0A\00"
@.str.12 = [68 x i8] c"-gl # = maximum Gap Length [default 5 for genomic, 3 for peptide]\0A\00"
@.str.13 = [40 x i8] c"-gs # = Gap Start penalty [default 0]\0A\00"
@.str.14 = [44 x i8] c"-gc # = Gap Continue penalty [default -1]\0A\00"
@.str.15 = [64 x i8] c"-s1 # # = use the given substring of the query [default whole]\0A\00"
@.str.16 = [63 x i8] c"-s2 # # = use the givensubstring of the dbase [default whole]\0A\00"
@.str.17 = [105 x i8] c"-pairs pairfile = read \22-s1 # # -s2 # #\22 from pairfile [default off]\0A\09[This is not fully functional!!!]\0A\00"
@.str.18 = [45 x i8] c"-version = prints the version of this CHAOS\0A\00"
define void @usage() {
%1 = call i32 @printf(i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str, i64 0, i64 0))
%2 = call i32 @printf(i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.1, i64 0, i64 0))
%3 = call i32 @printf(i8* getelementptr inbounds ([45 x i8], [45 x i8]* @.str.2, i64 0, i64 0))
%4 = call i32 @printf(i8* getelementptr inbounds ([39 x i8], [39 x i8]* @.str.3, i64 0, i64 0))
%5 = call i32 @printf(i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.4, i64 0, i64 0))
%6 = call i32 @printf(i8* getelementptr inbounds ([35 x i8], [35 x i8]* @.str.5, i64 0, i64 0))
%7 = call i32 @printf(i8* getelementptr inbounds ([66 x i8], [66 x i8]* @.str.6, i64 0, i64 0))
%8 = call i32 @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.7, i64 0, i64 0))
%9 = call i32 @printf(i8* getelementptr inbounds ([70 x i8], [70 x i8]* @.str.8, i64 0, i64 0))
%10 = call i32 @printf(i8* getelementptr inbounds ([36 x i8], [36 x i8]* @.str.9, i64 0, i64 0))
%11 = call i32 @printf(i8* getelementptr inbounds ([39 x i8], [39 x i8]* @.str.10, i64 0, i64 0))
%12 = call i32 @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.11, i64 0, i64 0))
%13 = call i32 @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.12, i64 0, i64 0))
%14 = call i32 @printf(i8* getelementptr inbounds ([40 x i8], [40 x i8]* @.str.13, i64 0, i64 0))
%15 = call i32 @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.14, i64 0, i64 0))
%16 = call i32 @printf(i8* getelementptr inbounds ([64 x i8], [64 x i8]* @.str.15, i64 0, i64 0))
%17 = call i32 @printf(i8* getelementptr inbounds ([63 x i8], [63 x i8]* @.str.16, i64 0, i64 0))
%18 = call i32 @printf(i8* getelementptr inbounds ([105 x i8], [105 x i8]* @.str.17, i64 0, i64 0))
%19 = call i32 @printf(i8* getelementptr inbounds ([45 x i8], [45 x i8]* @.str.18, i64 0, i64 0))
ret void
}

LLVM IR (-O2):
@str = [45 x i8] c"usage: \0Achaos queryfile dbasefile [options]\0A\00"
@str.19 = [9 x i8] c"Options:\00"
@str.20 = [44 x i8] c"-p = Peptide sequence [default genomic]\00"
@str.21 = [38 x i8] c"-v = Verbose mode [default brief]\00"
@str.22 = [45 x i8] c"-b = Both strands [default forward-only]\00"
@str.23 = [34 x i8] c"-t = Translated [default off]\00"
@str.24 = [65 x i8] c"-ext = do BLAST-like extention with given cutoff [default off]\00"
@str.25 = [61 x i8] c"-wl # = Word Length [default 10 for genomic, 4 for peptide]\00"
@str.26 = [69 x i8] c"-nd # = Number of Degeneracy [default 1 for genomic, 0 for peptide]\00"
@str.27 = [35 x i8] c"-co # = score CutOff [default 25]\00"
@str.28 = [38 x i8] c"-rsc # = Rescoring cutoff [default 0]\00"
@str.29 = [67 x i8] c"-lb # = LookBack distance [default 20 for genomic, 8 for peptide]\00"
@str.30 = [67 x i8] c"-gl # = maximum Gap Length [default 5 for genomic, 3 for peptide]\00"
@str.31 = [39 x i8] c"-gs # = Gap Start penalty [default 0]\00"
@str.32 = [43 x i8] c"-gc # = Gap Continue penalty [default -1]\00"
@str.33 = [63 x i8] c"-s1 # # = use the given substring of the query [default whole]\00"
@str.34 = [62 x i8] c"-s2 # # = use the givensubstring of the dbase [default whole]\00"
@str.35 = [104 x i8] c"-pairs pairfile = read \22-s1 # # -s2 # #\22 from pairfile [default off]\0A\09[This is not fully functional!!!]\00"
@str.36 = [44 x i8] c"-version = prints the version of this CHAOS\00"
define void @usage() {
%1 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([45 x i8], [45 x i8]* @str, i64 0, i64 0))
%2 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([9 x i8], [9 x i8]* @str.19, i64 0, i64 0))
%3 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([44 x i8], [44 x i8]* @str.20, i64 0, i64 0))
%4 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([38 x i8], [38 x i8]* @str.21, i64 0, i64 0))
%5 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([45 x i8], [45 x i8]* @str.22, i64 0, i64 0))
%6 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([34 x i8], [34 x i8]* @str.23, i64 0, i64 0))
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([65 x i8], [65 x i8]* @str.24, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.25, i64 0, i64 0))
%9 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([69 x i8], [69 x i8]* @str.26, i64 0, i64 0))
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([35 x i8], [35 x i8]* @str.27, i64 0, i64 0))
%11 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([38 x i8], [38 x i8]* @str.28, i64 0, i64 0))
%12 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.29, i64 0, i64 0))
%13 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.30, i64 0, i64 0))
%14 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([39 x i8], [39 x i8]* @str.31, i64 0, i64 0))
%15 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([43 x i8], [43 x i8]* @str.32, i64 0, i64 0))
%16 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([63 x i8], [63 x i8]* @str.33, i64 0, i64 0))
%17 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([62 x i8], [62 x i8]* @str.34, i64 0, i64 0))
%18 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([104 x i8], [104 x i8]* @str.35, i64 0, i64 0))
%19 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([44 x i8], [44 x i8]* @str.36, i64 0, i64 0))
ret void
}