#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*/ fprintf(int /*<<< orphan*/, char *, ...);
int /*<<< orphan*/ stderr;
int usage() {
  fprintf(stderr, "\n");
  fprintf(stderr,
          "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
  fprintf(stderr, "Version: %s\n", "0.5.9rc1 (r1561)");
  fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
  fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
  fprintf(stderr,
          "Command: index         index sequences in the FASTA format\n");
  fprintf(stderr, "         aln           gapped/ungapped alignment\n");
  fprintf(stderr, "         samse         generate alignment (single ended)\n");
  fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
  fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
  fprintf(stderr, "\n");
  fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
  fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
  fprintf(stderr,
          "         pac2bwtgen    alternative algorithm for generating BWT\n");
  fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
  fprintf(stderr, "         pac_rev       generate reverse PAC\n");
  fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
  fprintf(stderr, "         pac2cspac     convert PAC to color-space PAC\n");
  fprintf(stderr, "         stdsw         standard SW/NW alignment\n");
  fprintf(stderr, "\n");
  return 1;
}


x86 assembly (clang, -O0):
<usage>:
push   %rbp
mov    %rsp,%rbp
mov    0x2ec5(%rip),%rax
mov    (%rax),%edi
lea    0xf5b(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2eae(%rip),%rax
mov    (%rax),%edi
lea    0xec5(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e97(%rip),%rax
mov    (%rax),%edi
lea    0xeeb(%rip),%rsi
lea    0xef1(%rip),%rdx
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e79(%rip),%rax
mov    (%rax),%edi
lea    0xeeb(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e62(%rip),%rax
mov    (%rax),%edi
lea    0xefa(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e4b(%rip),%rax
mov    (%rax),%edi
lea    0xf06(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e34(%rip),%rax
mov    (%rax),%edi
lea    0xf2b(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e1d(%rip),%rax
mov    (%rax),%edi
lea    0xf46(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2e06(%rip),%rax
mov    (%rax),%edi
lea    0xf69(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2def(%rip),%rax
mov    (%rax),%edi
lea    0xf8c(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2dd8(%rip),%rax
mov    (%rax),%edi
lea    0xe6e(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2dc1(%rip),%rax
mov    (%rax),%edi
lea    0xf8e(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2daa(%rip),%rax
mov    (%rax),%edi
lea    0xfab(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d93(%rip),%rax
mov    (%rax),%edi
lea    0xfc2(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d7c(%rip),%rax
mov    (%rax),%edi
lea    0xfec(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d65(%rip),%rax
mov    (%rax),%edi
lea    0x100b(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d4e(%rip),%rax
mov    (%rax),%edi
lea    0x1021(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d37(%rip),%rax
mov    (%rax),%edi
lea    0x103f(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d20(%rip),%rax
mov    (%rax),%edi
lea    0x105f(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    0x2d09(%rip),%rax
mov    (%rax),%edi
lea    0xd9f(%rip),%rsi
mov    $0x0,%al
call   1030 <fprintf@plt>
mov    $0x1,%eax
pop    %rbp
ret

x86 assembly (clang, -O2):
<usage>:
push   %r14
push   %rbx
push   %rax
mov    0x2ec5(%rip),%rbx
mov    (%rbx),%edi
lea    0xf5b(%rip),%r14
mov    %r14,%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xec9(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xef6(%rip),%rsi
lea    0xefc(%rip),%rdx
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xefd(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xf13(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xf26(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xf52(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xf74(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xf9e(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xfc8(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
mov    %r14,%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0xfdc(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x1000(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x101e(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x104f(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x1075(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x1092(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x10b7(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
lea    0x10de(%rip),%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    (%rbx),%edi
mov    %r14,%rsi
xor    %eax,%eax
call   1030 <fprintf@plt>
mov    $0x1,%eax
add    $0x8,%rsp
pop    %rbx
pop    %r14
ret

LLVM IR (-O0):
@stderr = global i32 0
@.str = [2 x i8] c"\0A\00"
@.str.1 = [61 x i8] c"Program: bwa (alignment via Burrows-Wheeler transformation)\0A\00"
@.str.2 = [13 x i8] c"Version: %s\0A\00"
@.str.3 = [17 x i8] c"0.5.9rc1 (r1561)\00"
@.str.4 = [38 x i8] c"Contact: Heng Li <lh3@sanger.ac.uk>\0A\0A\00"
@.str.5 = [35 x i8] c"Usage: bwa <command> [options]\0A\0A\00"
@.str.6 = [60 x i8] c"Command: index index sequences in the FASTA format\0A\00"
@.str.7 = [50 x i8] c" aln gapped/ungapped alignment\0A\00"
@.str.8 = [58 x i8] c" samse generate alignment (single ended)\0A\00"
@.str.9 = [58 x i8] c" sampe generate alignment (paired ended)\0A\00"
@.str.10 = [48 x i8] c" bwasw BWA-SW for long queries\0A\00"
@.str.11 = [52 x i8] c" fa2pac convert FASTA to PAC format\0A\00"
@.str.12 = [46 x i8] c" pac2bwt generate BWT from PAC\0A\00"
@.str.13 = [65 x i8] c" pac2bwtgen alternative algorithm for generating BWT\0A\00"
@.str.14 = [54 x i8] c" bwtupdate update .bwt to the new format\0A\00"
@.str.15 = [45 x i8] c" pac_rev generate reverse PAC\0A\00"
@.str.16 = [53 x i8] c" bwt2sa generate SA from BWT and Occ\0A\00"
@.str.17 = [55 x i8] c" pac2cspac convert PAC to color-space PAC\0A\00"
@.str.18 = [49 x i8] c" stdsw standard SW/NW alignment\0A\00"
define i32 @usage() {
%1 = load i32, i32* @stderr
%2 = call i32 (i32, i8*, ...) @fprintf(i32 %1, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
%3 = load i32, i32* @stderr
%4 = call i32 (i32, i8*, ...) @fprintf(i32 %3, i8* getelementptr inbounds ([61 x i8], [61 x i8]* @.str.1, i64 0, i64 0))
%5 = load i32, i32* @stderr
%6 = call i32 (i32, i8*, ...) @fprintf(i32 %5, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.2, i64 0, i64 0), i8* getelementptr inbounds ([17 x i8], [17 x i8]* @.str.3, i64 0, i64 0))
%7 = load i32, i32* @stderr
%8 = call i32 (i32, i8*, ...) @fprintf(i32 %7, i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.4, i64 0, i64 0))
%9 = load i32, i32* @stderr
%10 = call i32 (i32, i8*, ...) @fprintf(i32 %9, i8* getelementptr inbounds ([35 x i8], [35 x i8]* @.str.5, i64 0, i64 0))
%11 = load i32, i32* @stderr
%12 = call i32 (i32, i8*, ...) @fprintf(i32 %11, i8* getelementptr inbounds ([60 x i8], [60 x i8]* @.str.6, i64 0, i64 0))
%13 = load i32, i32* @stderr
%14 = call i32 (i32, i8*, ...) @fprintf(i32 %13, i8* getelementptr inbounds ([50 x i8], [50 x i8]* @.str.7, i64 0, i64 0))
%15 = load i32, i32* @stderr
%16 = call i32 (i32, i8*, ...) @fprintf(i32 %15, i8* getelementptr inbounds ([58 x i8], [58 x i8]* @.str.8, i64 0, i64 0))
%17 = load i32, i32* @stderr
%18 = call i32 (i32, i8*, ...) @fprintf(i32 %17, i8* getelementptr inbounds ([58 x i8], [58 x i8]* @.str.9, i64 0, i64 0))
%19 = load i32, i32* @stderr
%20 = call i32 (i32, i8*, ...) @fprintf(i32 %19, i8* getelementptr inbounds ([48 x i8], [48 x i8]* @.str.10, i64 0, i64 0))
%21 = load i32, i32* @stderr
%22 = call i32 (i32, i8*, ...) @fprintf(i32 %21, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
%23 = load i32, i32* @stderr
%24 = call i32 (i32, i8*, ...) @fprintf(i32 %23, i8* getelementptr inbounds ([52 x i8], [52 x i8]* @.str.11, i64 0, i64 0))
%25 = load i32, i32* @stderr
%26 = call i32 (i32, i8*, ...) @fprintf(i32 %25, i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.12, i64 0, i64 0))
%27 = load i32, i32* @stderr
%28 = call i32 (i32, i8*, ...) @fprintf(i32 %27, i8* getelementptr inbounds ([65 x i8], [65 x i8]* @.str.13, i64 0, i64 0))
%29 = load i32, i32* @stderr
%30 = call i32 (i32, i8*, ...) @fprintf(i32 %29, i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.14, i64 0, i64 0))
%31 = load i32, i32* @stderr
%32 = call i32 (i32, i8*, ...) @fprintf(i32 %31, i8* getelementptr inbounds ([45 x i8], [45 x i8]* @.str.15, i64 0, i64 0))
%33 = load i32, i32* @stderr
%34 = call i32 (i32, i8*, ...) @fprintf(i32 %33, i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.16, i64 0, i64 0))
%35 = load i32, i32* @stderr
%36 = call i32 (i32, i8*, ...) @fprintf(i32 %35, i8* getelementptr inbounds ([55 x i8], [55 x i8]* @.str.17, i64 0, i64 0))
%37 = load i32, i32* @stderr
%38 = call i32 (i32, i8*, ...) @fprintf(i32 %37, i8* getelementptr inbounds ([49 x i8], [49 x i8]* @.str.18, i64 0, i64 0))
%39 = load i32, i32* @stderr
%40 = call i32 (i32, i8*, ...) @fprintf(i32 %39, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
ret i32 1
}

LLVM IR (-O2):
@stderr = global i32 0
@.str = [2 x i8] c"\0A\00"
@.str.1 = [61 x i8] c"Program: bwa (alignment via Burrows-Wheeler transformation)\0A\00"
@.str.2 = [13 x i8] c"Version: %s\0A\00"
@.str.3 = [17 x i8] c"0.5.9rc1 (r1561)\00"
@.str.4 = [38 x i8] c"Contact: Heng Li <lh3@sanger.ac.uk>\0A\0A\00"
@.str.5 = [35 x i8] c"Usage: bwa <command> [options]\0A\0A\00"
@.str.6 = [60 x i8] c"Command: index index sequences in the FASTA format\0A\00"
@.str.7 = [50 x i8] c" aln gapped/ungapped alignment\0A\00"
@.str.8 = [58 x i8] c" samse generate alignment (single ended)\0A\00"
@.str.9 = [58 x i8] c" sampe generate alignment (paired ended)\0A\00"
@.str.10 = [48 x i8] c" bwasw BWA-SW for long queries\0A\00"
@.str.11 = [52 x i8] c" fa2pac convert FASTA to PAC format\0A\00"
@.str.12 = [46 x i8] c" pac2bwt generate BWT from PAC\0A\00"
@.str.13 = [65 x i8] c" pac2bwtgen alternative algorithm for generating BWT\0A\00"
@.str.14 = [54 x i8] c" bwtupdate update .bwt to the new format\0A\00"
@.str.15 = [45 x i8] c" pac_rev generate reverse PAC\0A\00"
@.str.16 = [53 x i8] c" bwt2sa generate SA from BWT and Occ\0A\00"
@.str.17 = [55 x i8] c" pac2cspac convert PAC to color-space PAC\0A\00"
@.str.18 = [49 x i8] c" stdsw standard SW/NW alignment\0A\00"
define i32 @usage() {
%1 = load i32, i32* @stderr
%2 = tail call i32 (i32, i8*, ...) @fprintf(i32 %1, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
%3 = load i32, i32* @stderr
%4 = tail call i32 (i32, i8*, ...) @fprintf(i32 %3, i8* getelementptr inbounds ([61 x i8], [61 x i8]* @.str.1, i64 0, i64 0))
%5 = load i32, i32* @stderr
%6 = tail call i32 (i32, i8*, ...) @fprintf(i32 %5, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.2, i64 0, i64 0), i8* getelementptr inbounds ([17 x i8], [17 x i8]* @.str.3, i64 0, i64 0))
%7 = load i32, i32* @stderr
%8 = tail call i32 (i32, i8*, ...) @fprintf(i32 %7, i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.4, i64 0, i64 0))
%9 = load i32, i32* @stderr
%10 = tail call i32 (i32, i8*, ...) @fprintf(i32 %9, i8* getelementptr inbounds ([35 x i8], [35 x i8]* @.str.5, i64 0, i64 0))
%11 = load i32, i32* @stderr
%12 = tail call i32 (i32, i8*, ...) @fprintf(i32 %11, i8* getelementptr inbounds ([60 x i8], [60 x i8]* @.str.6, i64 0, i64 0))
%13 = load i32, i32* @stderr
%14 = tail call i32 (i32, i8*, ...) @fprintf(i32 %13, i8* getelementptr inbounds ([50 x i8], [50 x i8]* @.str.7, i64 0, i64 0))
%15 = load i32, i32* @stderr
%16 = tail call i32 (i32, i8*, ...) @fprintf(i32 %15, i8* getelementptr inbounds ([58 x i8], [58 x i8]* @.str.8, i64 0, i64 0))
%17 = load i32, i32* @stderr
%18 = tail call i32 (i32, i8*, ...) @fprintf(i32 %17, i8* getelementptr inbounds ([58 x i8], [58 x i8]* @.str.9, i64 0, i64 0))
%19 = load i32, i32* @stderr
%20 = tail call i32 (i32, i8*, ...) @fprintf(i32 %19, i8* getelementptr inbounds ([48 x i8], [48 x i8]* @.str.10, i64 0, i64 0))
%21 = load i32, i32* @stderr
%22 = tail call i32 (i32, i8*, ...) @fprintf(i32 %21, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
%23 = load i32, i32* @stderr
%24 = tail call i32 (i32, i8*, ...) @fprintf(i32 %23, i8* getelementptr inbounds ([52 x i8], [52 x i8]* @.str.11, i64 0, i64 0))
%25 = load i32, i32* @stderr
%26 = tail call i32 (i32, i8*, ...) @fprintf(i32 %25, i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.12, i64 0, i64 0))
%27 = load i32, i32* @stderr
%28 = tail call i32 (i32, i8*, ...) @fprintf(i32 %27, i8* getelementptr inbounds ([65 x i8], [65 x i8]* @.str.13, i64 0, i64 0))
%29 = load i32, i32* @stderr
%30 = tail call i32 (i32, i8*, ...) @fprintf(i32 %29, i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.14, i64 0, i64 0))
%31 = load i32, i32* @stderr
%32 = tail call i32 (i32, i8*, ...) @fprintf(i32 %31, i8* getelementptr inbounds ([45 x i8], [45 x i8]* @.str.15, i64 0, i64 0))
%33 = load i32, i32* @stderr
%34 = tail call i32 (i32, i8*, ...) @fprintf(i32 %33, i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.16, i64 0, i64 0))
%35 = load i32, i32* @stderr
%36 = tail call i32 (i32, i8*, ...) @fprintf(i32 %35, i8* getelementptr inbounds ([55 x i8], [55 x i8]* @.str.17, i64 0, i64 0))
%37 = load i32, i32* @stderr
%38 = tail call i32 (i32, i8*, ...) @fprintf(i32 %37, i8* getelementptr inbounds ([49 x i8], [49 x i8]* @.str.18, i64 0, i64 0))
%39 = load i32, i32* @stderr
%40 = tail call i32 (i32, i8*, ...) @fprintf(i32 %39, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str, i64 0, i64 0))
ret i32 1
}