#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(void) {
  printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n", 63);
  printf("-nested : runs improvement in a nested fashion\n");
  printf("-postir : incorporates the final improvement phase\n");
  printf("-lazy : uses lazy mode\n");
  printf("-translate : use translated anchors\n");
  printf(
      "-fastreject : use fast rejection (tuned for human/mouse or closer)\n");
  printf("-verbose : give debug output\n");
  printf("-tree \"(...)\" : runs with given phylogenetic tree\n");
  printf("-out \"filename\": outputs to filename\n");
  printf("-nucmatrixfile \"filename\": uses given substitution matrix instead "
         "of $LAGAN_DIR/nucmatrix.txt\n");
  printf("-version : prints version info\n");
}


x86 assembly (clang, -O0):
<usage>:
push   %rbp
mov    %rsp,%rbp
lea    0xee5(%rip),%rdi
mov    $0x3f,%esi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf0e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf30(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf56(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf60(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf77(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfad(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfbd(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfe2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xffa(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x104b(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
pop    %rbp
ret

x86 assembly (clang, -O2):
<usage>:
push   %rax
lea    0xed8(%rip),%rdi
mov    $0x3f,%esi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xf01(%rip),%rdi
call   1030 <puts@plt>
lea    0xf24(%rip),%rdi
call   1030 <puts@plt>
lea    0xf4b(%rip),%rdi
call   1030 <puts@plt>
lea    0xf56(%rip),%rdi
call   1030 <puts@plt>
lea    0xf6e(%rip),%rdi
call   1030 <puts@plt>
lea    0xfa5(%rip),%rdi
call   1030 <puts@plt>
lea    0xfb6(%rip),%rdi
call   1030 <puts@plt>
lea    0xfdc(%rip),%rdi
call   1030 <puts@plt>
lea    0xff5(%rip),%rdi
call   1030 <puts@plt>
lea    0x1047(%rip),%rdi
pop    %rax
jmp    1030 <puts@plt>

LLVM IR (-O0):
@.str = [60 x i8] c"mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\0A\0A\00"
@.str.1 = [48 x i8] c"-nested : runs improvement in a nested fashion\0A\00"
@.str.2 = [52 x i8] c"-postir : incorporates the final improvement phase\0A\00"
@.str.3 = [24 x i8] c"-lazy : uses lazy mode\0A\00"
@.str.4 = [37 x i8] c"-translate : use translated anchors\0A\00"
@.str.5 = [68 x i8] c"-fastreject : use fast rejection (tuned for human/mouse or closer)\0A\00"
@.str.6 = [30 x i8] c"-verbose : give debug output\0A\00"
@.str.7 = [51 x i8] c"-tree \22(...)\22 : runs with given phylogenetic tree\0A\00"
@.str.8 = [38 x i8] c"-out \22filename\22: outputs to filename\0A\00"
@.str.9 = [95 x i8] c"-nucmatrixfile \22filename\22: uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt\0A\00"
@.str.10 = [32 x i8] c"-version : prints version info\0A\00"
define void @usage() {
%1 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([60 x i8], [60 x i8]* @.str, i64 0, i64 0), i32 63)
%2 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([48 x i8], [48 x i8]* @.str.1, i64 0, i64 0))
%3 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([52 x i8], [52 x i8]* @.str.2, i64 0, i64 0))
%4 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([24 x i8], [24 x i8]* @.str.3, i64 0, i64 0))
%5 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([37 x i8], [37 x i8]* @.str.4, i64 0, i64 0))
%6 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.5, i64 0, i64 0))
%7 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([30 x i8], [30 x i8]* @.str.6, i64 0, i64 0))
%8 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([51 x i8], [51 x i8]* @.str.7, i64 0, i64 0))
%9 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.8, i64 0, i64 0))
%10 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([95 x i8], [95 x i8]* @.str.9, i64 0, i64 0))
%11 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([32 x i8], [32 x i8]* @.str.10, i64 0, i64 0))
ret void
}

LLVM IR (-O2):
@.str = [60 x i8] c"mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\0A\0A\00"
@str = [47 x i8] c"-nested : runs improvement in a nested fashion\00"
@str.11 = [51 x i8] c"-postir : incorporates the final improvement phase\00"
@str.12 = [23 x i8] c"-lazy : uses lazy mode\00"
@str.13 = [36 x i8] c"-translate : use translated anchors\00"
@str.14 = [67 x i8] c"-fastreject : use fast rejection (tuned for human/mouse or closer)\00"
@str.15 = [29 x i8] c"-verbose : give debug output\00"
@str.16 = [50 x i8] c"-tree \22(...)\22 : runs with given phylogenetic tree\00"
@str.17 = [37 x i8] c"-out \22filename\22: outputs to filename\00"
@str.18 = [94 x i8] c"-nucmatrixfile \22filename\22: uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt\00"
@str.19 = [31 x i8] c"-version : prints version info\00"
define void @usage() {
%1 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([60 x i8], [60 x i8]* @.str, i64 0, i64 0), i32 63)
%2 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([47 x i8], [47 x i8]* @str, i64 0, i64 0))
%3 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([51 x i8], [51 x i8]* @str.11, i64 0, i64 0))
%4 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([23 x i8], [23 x i8]* @str.12, i64 0, i64 0))
%5 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([36 x i8], [36 x i8]* @str.13, i64 0, i64 0))
%6 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.14, i64 0, i64 0))
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([29 x i8], [29 x i8]* @str.15, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([50 x i8], [50 x i8]* @str.16, i64 0, i64 0))
%9 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([37 x i8], [37 x i8]* @str.17, i64 0, i64 0))
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([94 x i8], [94 x i8]* @str.18, i64 0, i64 0))
%11 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([31 x i8], [31 x i8]* @str.19, i64 0, i64 0))
ret void
}