#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 bwa_aln(int, char **);
int bwa_bam_to_bam(int, char **, char *);
int bwa_bwt2sa(int, char **);
int bwa_bwtsw2(int, char **);
int bwa_bwtupdate(int, char **);
int bwa_fa2pac(int, char **);
int bwa_index(int, char **);
int bwa_pac2bwt(int, char **);
int bwa_pac2cspac(int, char **);
int bwa_pac_rev(int, char **);
int bwa_sai2sam_pe(int, char **);
int bwa_sai2sam_se(int, char **);
int bwa_stdsw(int, char **);
int bwa_worker(int, char **);
int bwt_bwtgen_main(int, char **);
int /*<<< orphan*/ err_fclose(int /*<<< orphan*/);
int /*<<< orphan*/ err_fflush(int /*<<< orphan*/);
int /*<<< orphan*/ fprintf(int /*<<< orphan*/, char *, char *);
int /*<<< orphan*/ stderr;
int /*<<< orphan*/ stdout;
scalar_t__ strcmp(char *, char *);
int usage();
int main(int argc, char *argv[]) {
  if (argc < 2)
    return usage();
  if (strcmp(argv[1], "fa2pac") == 0)
    return bwa_fa2pac(argc - 1, argv + 1);
  else if (strcmp(argv[1], "pac2bwt") == 0)
    return bwa_pac2bwt(argc - 1, argv + 1);
  else if (strcmp(argv[1], "pac2bwtgen") == 0)
    return bwt_bwtgen_main(argc - 1, argv + 1);
  else if (strcmp(argv[1], "bwtupdate") == 0)
    return bwa_bwtupdate(argc - 1, argv + 1);
  else if (strcmp(argv[1], "pac_rev") == 0)
    return bwa_pac_rev(argc - 1, argv + 1);
  else if (strcmp(argv[1], "bwt2sa") == 0)
    return bwa_bwt2sa(argc - 1, argv + 1);
  else if (strcmp(argv[1], "index") == 0)
    return bwa_index(argc - 1, argv + 1);
  else if (strcmp(argv[1], "aln") == 0)
    return bwa_aln(argc - 1, argv + 1);
  else if (strcmp(argv[1], "bam2bam") == 0)
    return bwa_bam_to_bam(argc - 1, argv + 1, "0.5.10-evan.6.3");
  else if (strcmp(argv[1], "worker") == 0)
    return bwa_worker(argc - 1, argv + 1);
  else if (strcmp(argv[1], "sw") == 0)
    return bwa_stdsw(argc - 1, argv + 1);
  else if (strcmp(argv[1], "samse") == 0)
    return bwa_sai2sam_se(argc - 1, argv + 1);
  else if (strcmp(argv[1], "sampe") == 0)
    return bwa_sai2sam_pe(argc - 1, argv + 1);
  else if (strcmp(argv[1], "pac2cspac") == 0)
    return bwa_pac2cspac(argc - 1, argv + 1);
  else if (strcmp(argv[1], "stdsw") == 0)
    return bwa_stdsw(argc - 1, argv + 1);
  else if (strcmp(argv[1], "bwtsw2") == 0)
    return bwa_bwtsw2(argc - 1, argv + 1);
  else if (strcmp(argv[1], "dbwtsw") == 0)
    return bwa_bwtsw2(argc - 1, argv + 1);
  else if (strcmp(argv[1], "bwasw") == 0)
    return bwa_bwtsw2(argc - 1, argv + 1);
  else {
    fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
    return 1;
  }
  err_fflush(stdout);
  err_fclose(stdout);
  return 0;
}


x86 assembly (clang, -O0):
<main>:
push   %rbp
mov    %rsp,%rbp
sub    $0x10,%rsp
movl   $0x0,-0x4(%rbp)
mov    %edi,-0x8(%rbp)
mov    %rsi,-0x10(%rbp)
cmpl   $0x2,-0x8(%rbp)
jge    124f <main+0x2f>
mov    $0x0,%al
call   10e0 <usage@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xda2(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1288 <main+0x68>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   10d0 <bwa_fa2pac@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xd70(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    12c1 <main+0xa1>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   10c0 <bwa_pac2bwt@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xd3f(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    12fa <main+0xda>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1030 <bwt_bwtgen_main@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xd11(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1333 <main+0x113>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1120 <bwa_bwtupdate@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xce2(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    136c <main+0x14c>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   10b0 <bwa_pac_rev@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xcb1(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    13a5 <main+0x185>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1100 <bwa_bwt2sa@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xc7f(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    13de <main+0x1be>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1140 <bwa_index@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xc4c(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1417 <main+0x1f7>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1070 <bwa_aln@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xc17(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1457 <main+0x237>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
lea    0xbfb(%rip),%rdx
call   1050 <bwa_bam_to_bam@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xbef(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1490 <main+0x270>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1130 <bwa_worker@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xbea(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    14c9 <main+0x2a9>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1040 <bwa_stdsw@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xb84(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1502 <main+0x2e2>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   10f0 <bwa_sai2sam_se@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xb51(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    153b <main+0x31b>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1110 <bwa_sai2sam_pe@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xb1e(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1574 <main+0x354>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1080 <bwa_pac2cspac@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xaef(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    15ad <main+0x38d>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1040 <bwa_stdsw@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xabc(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    15e6 <main+0x3c6>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1060 <bwa_bwtsw2@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xa8a(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    161f <main+0x3ff>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1060 <bwa_bwtsw2@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdi
lea    0xa58(%rip),%rsi
call   1090 <strcmp@plt>
cmp    $0x0,%rax
jne    1658 <main+0x438>
mov    -0x8(%rbp),%edi
sub    $0x1,%edi
mov    -0x10(%rbp),%rsi
add    $0x8,%rsi
call   1060 <bwa_bwtsw2@plt>
mov    %eax,-0x4(%rbp)
jmp    167c <main+0x45c>
mov    0x2981(%rip),%rax
mov    (%rax),%edi
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rdx
lea    0xa1c(%rip),%rsi
call   10a0 <fprintf@plt>
movl   $0x1,-0x4(%rbp)
mov    -0x4(%rbp),%eax
add    $0x10,%rsp
pop    %rbp
ret

x86 assembly (clang, -O2):
<main>:
push   %rbp
push   %rbx
push   %rax
cmp    $0x1,%edi
jg     1235 <main+0x15>
xor    %eax,%eax
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    10e0 <usage@plt>
mov    %rsi,%rbx
mov    %edi,%ebp
mov    0x8(%rsi),%rdi
add    $0x8,%rbx
lea    0xdb7(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1413 <main+0x1f3>
mov    (%rbx),%rdi
lea    0xda6(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1426 <main+0x206>
mov    (%rbx),%rdi
lea    0xd96(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1439 <main+0x219>
mov    (%rbx),%rdi
lea    0xd89(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     144c <main+0x22c>
mov    (%rbx),%rdi
lea    0xd7b(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     145f <main+0x23f>
mov    (%rbx),%rdi
lea    0xd6b(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1472 <main+0x252>
mov    (%rbx),%rdi
lea    0xd5a(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1485 <main+0x265>
mov    (%rbx),%rdi
lea    0xd48(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1498 <main+0x278>
mov    (%rbx),%rdi
lea    0xd34(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14ab <main+0x28b>
mov    (%rbx),%rdi
lea    0xd34(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14c5 <main+0x2a5>
mov    (%rbx),%rdi
lea    0xd50(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14d8 <main+0x2b8>
mov    (%rbx),%rdi
lea    0xd0b(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14eb <main+0x2cb>
mov    (%rbx),%rdi
lea    0xcf9(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14fe <main+0x2de>
mov    (%rbx),%rdi
lea    0xce7(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1511 <main+0x2f1>
mov    (%rbx),%rdi
lea    0xcd9(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     14d8 <main+0x2b8>
mov    (%rbx),%rdi
lea    0xcc7(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1524 <main+0x304>
mov    (%rbx),%rdi
lea    0xcb6(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1524 <main+0x304>
mov    (%rbx),%rdi
lea    0xca5(%rip),%rsi
call   1090 <strcmp@plt>
test   %rax,%rax
je     1524 <main+0x304>
mov    0x2bea(%rip),%rax
mov    (%rax),%edi
mov    (%rbx),%rdx
lea    0xc8a(%rip),%rsi
call   10a0 <fprintf@plt>
mov    $0x1,%eax
add    $0x8,%rsp
pop    %rbx
pop    %rbp
ret
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    10d0 <bwa_fa2pac@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    10c0 <bwa_pac2bwt@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1030 <bwt_bwtgen_main@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1120 <bwa_bwtupdate@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    10b0 <bwa_pac_rev@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1100 <bwa_bwt2sa@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1140 <bwa_index@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1070 <bwa_aln@plt>
add    $0xffffffff,%ebp
lea    0xb90(%rip),%rdx
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1050 <bwa_bam_to_bam@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1130 <bwa_worker@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1040 <bwa_stdsw@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    10f0 <bwa_sai2sam_se@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1110 <bwa_sai2sam_pe@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1080 <bwa_pac2cspac@plt>
add    $0xffffffff,%ebp
mov    %ebp,%edi
mov    %rbx,%rsi
add    $0x8,%rsp
pop    %rbx
pop    %rbp
jmp    1060 <bwa_bwtsw2@plt>

LLVM IR (-O0):
@.str = [7 x i8] c"fa2pac\00"
@.str.1 = [8 x i8] c"pac2bwt\00"
@.str.2 = [11 x i8] c"pac2bwtgen\00"
@.str.3 = [10 x i8] c"bwtupdate\00"
@.str.4 = [8 x i8] c"pac_rev\00"
@.str.5 = [7 x i8] c"bwt2sa\00"
@.str.6 = [6 x i8] c"index\00"
@.str.7 = [4 x i8] c"aln\00"
@.str.8 = [8 x i8] c"bam2bam\00"
@.str.9 = [16 x i8] c"0.5.10-evan.6.3\00"
@.str.10 = [7 x i8] c"worker\00"
@.str.11 = [3 x i8] c"sw\00"
@.str.12 = [6 x i8] c"samse\00"
@.str.13 = [6 x i8] c"sampe\00"
@.str.14 = [10 x i8] c"pac2cspac\00"
@.str.15 = [6 x i8] c"stdsw\00"
@.str.16 = [7 x i8] c"bwtsw2\00"
@.str.17 = [7 x i8] c"dbwtsw\00"
@.str.18 = [6 x i8] c"bwasw\00"
@stderr = global i32 0
@.str.19 = [34 x i8] c"[main] unrecognized command '%s'\0A\00"
@stdout = global i32 0
define i32 @main(i32 %0, i8** %1) {
%3 = alloca i32
%4 = alloca i32
%5 = alloca i8**
store i32 0, i32* %3
store i32 %0, i32* %4
store i8** %1, i8*** %5
%6 = load i32, i32* %4
%7 = icmp slt i32 %6, 2
br i1 %7, label %8, label %10
8: ; preds = %2
%9 = call i32 (...) @usage()
store i32 %9, i32* %3
br label %232
10: ; preds = %2
%11 = load i8**, i8*** %5
%12 = getelementptr inbounds i8*, i8** %11, i64 1
%13 = load i8*, i8** %12
%14 = call i64 @strcmp(i8* %13, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str, i64 0, i64 0))
%15 = icmp eq i64 %14, 0
br i1 %15, label %16, label %22
16: ; preds = %10
%17 = load i32, i32* %4
%18 = sub nsw i32 %17, 1
%19 = load i8**, i8*** %5
%20 = getelementptr inbounds i8*, i8** %19, i64 1
%21 = call i32 @bwa_fa2pac(i32 %18, i8** %20)
store i32 %21, i32* %3
br label %232
22: ; preds = %10
%23 = load i8**, i8*** %5
%24 = getelementptr inbounds i8*, i8** %23, i64 1
%25 = load i8*, i8** %24
%26 = call i64 @strcmp(i8* %25, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.1, i64 0, i64 0))
%27 = icmp eq i64 %26, 0
br i1 %27, label %28, label %34
28: ; preds = %22
%29 = load i32, i32* %4
%30 = sub nsw i32 %29, 1
%31 = load i8**, i8*** %5
%32 = getelementptr inbounds i8*, i8** %31, i64 1
%33 = call i32 @bwa_pac2bwt(i32 %30, i8** %32)
store i32 %33, i32* %3
br label %232
34: ; preds = %22
%35 = load i8**, i8*** %5
%36 = getelementptr inbounds i8*, i8** %35, i64 1
%37 = load i8*, i8** %36
%38 = call i64 @strcmp(i8* %37, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%39 = icmp eq i64 %38, 0
br i1 %39, label %40, label %46
40: ; preds = %34
%41 = load i32, i32* %4
%42 = sub nsw i32 %41, 1
%43 = load i8**, i8*** %5
%44 = getelementptr inbounds i8*, i8** %43, i64 1
%45 = call i32 @bwt_bwtgen_main(i32 %42, i8** %44)
store i32 %45, i32* %3
br label %232
46: ; preds = %34
%47 = load i8**, i8*** %5
%48 = getelementptr inbounds i8*, i8** %47, i64 1
%49 = load i8*, i8** %48
%50 = call i64 @strcmp(i8* %49, i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.3, i64 0, i64 0))
%51 = icmp eq i64 %50, 0
br i1 %51, label %52, label %58
52: ; preds = %46
%53 = load i32, i32* %4
%54 = sub nsw i32 %53, 1
%55 = load i8**, i8*** %5
%56 = getelementptr inbounds i8*, i8** %55, i64 1
%57 = call i32 @bwa_bwtupdate(i32 %54, i8** %56)
store i32 %57, i32* %3
br label %232
58: ; preds = %46
%59 = load i8**, i8*** %5
%60 = getelementptr inbounds i8*, i8** %59, i64 1
%61 = load i8*, i8** %60
%62 = call i64 @strcmp(i8* %61, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.4, i64 0, i64 0))
%63 = icmp eq i64 %62, 0
br i1 %63, label %64, label %70
64: ; preds = %58
%65 = load i32, i32* %4
%66 = sub nsw i32 %65, 1
%67 = load i8**, i8*** %5
%68 = getelementptr inbounds i8*, i8** %67, i64 1
%69 = call i32 @bwa_pac_rev(i32 %66, i8** %68)
store i32 %69, i32* %3
br label %232
70: ; preds = %58
%71 = load i8**, i8*** %5
%72 = getelementptr inbounds i8*, i8** %71, i64 1
%73 = load i8*, i8** %72
%74 = call i64 @strcmp(i8* %73, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.5, i64 0, i64 0))
%75 = icmp eq i64 %74, 0
br i1 %75, label %76, label %82
76: ; preds = %70
%77 = load i32, i32* %4
%78 = sub nsw i32 %77, 1
%79 = load i8**, i8*** %5
%80 = getelementptr inbounds i8*, i8** %79, i64 1
%81 = call i32 @bwa_bwt2sa(i32 %78, i8** %80)
store i32 %81, i32* %3
br label %232
82: ; preds = %70
%83 = load i8**, i8*** %5
%84 = getelementptr inbounds i8*, i8** %83, i64 1
%85 = load i8*, i8** %84
%86 = call i64 @strcmp(i8* %85, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.6, i64 0, i64 0))
%87 = icmp eq i64 %86, 0
br i1 %87, label %88, label %94
88: ; preds = %82
%89 = load i32, i32* %4
%90 = sub nsw i32 %89, 1
%91 = load i8**, i8*** %5
%92 = getelementptr inbounds i8*, i8** %91, i64 1
%93 = call i32 @bwa_index(i32 %90, i8** %92)
store i32 %93, i32* %3
br label %232
94: ; preds = %82
%95 = load i8**, i8*** %5
%96 = getelementptr inbounds i8*, i8** %95, i64 1
%97 = load i8*, i8** %96
%98 = call i64 @strcmp(i8* %97, i8* getelementptr inbounds ([4 x i8], [4 x i8]* @.str.7, i64 0, i64 0))
%99 = icmp eq i64 %98, 0
br i1 %99, label %100, label %106
100: ; preds = %94
%101 = load i32, i32* %4
%102 = sub nsw i32 %101, 1
%103 = load i8**, i8*** %5
%104 = getelementptr inbounds i8*, i8** %103, i64 1
%105 = call i32 @bwa_aln(i32 %102, i8** %104)
store i32 %105, i32* %3
br label %232
106: ; preds = %94
%107 = load i8**, i8*** %5
%108 = getelementptr inbounds i8*, i8** %107, i64 1
%109 = load i8*, i8** %108
%110 = call i64 @strcmp(i8* %109, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.8, i64 0, i64 0))
%111 = icmp eq i64 %110, 0
br i1 %111, label %112, label %118
112: ; preds = %106
%113 = load i32, i32* %4
%114 = sub nsw i32 %113, 1
%115 = load i8**, i8*** %5
%116 = getelementptr inbounds i8*, i8** %115, i64 1
%117 = call i32 @bwa_bam_to_bam(i32 %114, i8** %116, i8* getelementptr inbounds ([16 x i8], [16 x i8]* @.str.9, i64 0, i64 0))
store i32 %117, i32* %3
br label %232
118: ; preds = %106
%119 = load i8**, i8*** %5
%120 = getelementptr inbounds i8*, i8** %119, i64 1
%121 = load i8*, i8** %120
%122 = call i64 @strcmp(i8* %121, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.10, i64 0, i64 0))
%123 = icmp eq i64 %122, 0
br i1 %123, label %124, label %130
124: ; preds = %118
%125 = load i32, i32* %4
%126 = sub nsw i32 %125, 1
%127 = load i8**, i8*** %5
%128 = getelementptr inbounds i8*, i8** %127, i64 1
%129 = call i32 @bwa_worker(i32 %126, i8** %128)
store i32 %129, i32* %3
br label %232
130: ; preds = %118
%131 = load i8**, i8*** %5
%132 = getelementptr inbounds i8*, i8** %131, i64 1
%133 = load i8*, i8** %132
%134 = call i64 @strcmp(i8* %133, i8* getelementptr inbounds ([3 x i8], [3 x i8]* @.str.11, i64 0, i64 0))
%135 = icmp eq i64 %134, 0
br i1 %135, label %136, label %142
136: ; preds = %130
%137 = load i32, i32* %4
%138 = sub nsw i32 %137, 1
%139 = load i8**, i8*** %5
%140 = getelementptr inbounds i8*, i8** %139, i64 1
%141 = call i32 @bwa_stdsw(i32 %138, i8** %140)
store i32 %141, i32* %3
br label %232
142: ; preds = %130
%143 = load i8**, i8*** %5
%144 = getelementptr inbounds i8*, i8** %143, i64 1
%145 = load i8*, i8** %144
%146 = call i64 @strcmp(i8* %145, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.12, i64 0, i64 0))
%147 = icmp eq i64 %146, 0
br i1 %147, label %148, label %154
148: ; preds = %142
%149 = load i32, i32* %4
%150 = sub nsw i32 %149, 1
%151 = load i8**, i8*** %5
%152 = getelementptr inbounds i8*, i8** %151, i64 1
%153 = call i32 @bwa_sai2sam_se(i32 %150, i8** %152)
store i32 %153, i32* %3
br label %232
154: ; preds = %142
%155 = load i8**, i8*** %5
%156 = getelementptr inbounds i8*, i8** %155, i64 1
%157 = load i8*, i8** %156
%158 = call i64 @strcmp(i8* %157, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.13, i64 0, i64 0))
%159 = icmp eq i64 %158, 0
br i1 %159, label %160, label %166
160: ; preds = %154
%161 = load i32, i32* %4
%162 = sub nsw i32 %161, 1
%163 = load i8**, i8*** %5
%164 = getelementptr inbounds i8*, i8** %163, i64 1
%165 = call i32 @bwa_sai2sam_pe(i32 %162, i8** %164)
store i32 %165, i32* %3
br label %232
166: ; preds = %154
%167 = load i8**, i8*** %5
%168 = getelementptr inbounds i8*, i8** %167, i64 1
%169 = load i8*, i8** %168
%170 = call i64 @strcmp(i8* %169, i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.14, i64 0, i64 0))
%171 = icmp eq i64 %170, 0
br i1 %171, label %172, label %178
172: ; preds = %166
%173 = load i32, i32* %4
%174 = sub nsw i32 %173, 1
%175 = load i8**, i8*** %5
%176 = getelementptr inbounds i8*, i8** %175, i64 1
%177 = call i32 @bwa_pac2cspac(i32 %174, i8** %176)
store i32 %177, i32* %3
br label %232
178: ; preds = %166
%179 = load i8**, i8*** %5
%180 = getelementptr inbounds i8*, i8** %179, i64 1
%181 = load i8*, i8** %180
%182 = call i64 @strcmp(i8* %181, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.15, i64 0, i64 0))
%183 = icmp eq i64 %182, 0
br i1 %183, label %184, label %190
184: ; preds = %178
%185 = load i32, i32* %4
%186 = sub nsw i32 %185, 1
%187 = load i8**, i8*** %5
%188 = getelementptr inbounds i8*, i8** %187, i64 1
%189 = call i32 @bwa_stdsw(i32 %186, i8** %188)
store i32 %189, i32* %3
br label %232
190: ; preds = %178
%191 = load i8**, i8*** %5
%192 = getelementptr inbounds i8*, i8** %191, i64 1
%193 = load i8*, i8** %192
%194 = call i64 @strcmp(i8* %193, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.16, i64 0, i64 0))
%195 = icmp eq i64 %194, 0
br i1 %195, label %196, label %202
196: ; preds = %190
%197 = load i32, i32* %4
%198 = sub nsw i32 %197, 1
%199 = load i8**, i8*** %5
%200 = getelementptr inbounds i8*, i8** %199, i64 1
%201 = call i32 @bwa_bwtsw2(i32 %198, i8** %200)
store i32 %201, i32* %3
br label %232
202: ; preds = %190
%203 = load i8**, i8*** %5
%204 = getelementptr inbounds i8*, i8** %203, i64 1
%205 = load i8*, i8** %204
%206 = call i64 @strcmp(i8* %205, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.17, i64 0, i64 0))
%207 = icmp eq i64 %206, 0
br i1 %207, label %208, label %214
208: ; preds = %202
%209 = load i32, i32* %4
%210 = sub nsw i32 %209, 1
%211 = load i8**, i8*** %5
%212 = getelementptr inbounds i8*, i8** %211, i64 1
%213 = call i32 @bwa_bwtsw2(i32 %210, i8** %212)
store i32 %213, i32* %3
br label %232
214: ; preds = %202
%215 = load i8**, i8*** %5
%216 = getelementptr inbounds i8*, i8** %215, i64 1
%217 = load i8*, i8** %216
%218 = call i64 @strcmp(i8* %217, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.18, i64 0, i64 0))
%219 = icmp eq i64 %218, 0
br i1 %219, label %220, label %226
220: ; preds = %214
%221 = load i32, i32* %4
%222 = sub nsw i32 %221, 1
%223 = load i8**, i8*** %5
%224 = getelementptr inbounds i8*, i8** %223, i64 1
%225 = call i32 @bwa_bwtsw2(i32 %222, i8** %224)
store i32 %225, i32* %3
br label %232
226: ; preds = %214
%227 = load i32, i32* @stderr
%228 = load i8**, i8*** %5
%229 = getelementptr inbounds i8*, i8** %228, i64 1
%230 = load i8*, i8** %229
%231 = call i32 @fprintf(i32 %227, i8* getelementptr inbounds ([34 x i8], [34 x i8]* @.str.19, i64 0, i64 0), i8* %230)
store i32 1, i32* %3
br label %232
232: ; preds = %226, %220, %208, %196, %184, %172, %160, %148, %136, %124, %112, %100, %88, %76, %64, %52, %40, %28, %16, %8
%233 = load i32, i32* %3
ret i32 %233
}

LLVM IR (-O2):
@.str = [7 x i8] c"fa2pac\00"
@.str.1 = [8 x i8] c"pac2bwt\00"
@.str.2 = [11 x i8] c"pac2bwtgen\00"
@.str.3 = [10 x i8] c"bwtupdate\00"
@.str.4 = [8 x i8] c"pac_rev\00"
@.str.5 = [7 x i8] c"bwt2sa\00"
@.str.6 = [6 x i8] c"index\00"
@.str.7 = [4 x i8] c"aln\00"
@.str.8 = [8 x i8] c"bam2bam\00"
@.str.9 = [16 x i8] c"0.5.10-evan.6.3\00"
@.str.10 = [7 x i8] c"worker\00"
@.str.11 = [3 x i8] c"sw\00"
@.str.12 = [6 x i8] c"samse\00"
@.str.13 = [6 x i8] c"sampe\00"
@.str.14 = [10 x i8] c"pac2cspac\00"
@.str.15 = [6 x i8] c"stdsw\00"
@.str.16 = [7 x i8] c"bwtsw2\00"
@.str.17 = [7 x i8] c"dbwtsw\00"
@.str.18 = [6 x i8] c"bwasw\00"
@stderr = global i32 0
@.str.19 = [34 x i8] c"[main] unrecognized command '%s'\0A\00"
@stdout = global i32 0
define i32 @main(i32 %0, i8** %1) {
%3 = icmp slt i32 %0, 2
br i1 %3, label %4, label %6
4: ; preds = %2
%5 = tail call i32 (...) @usage()
br label %137
6: ; preds = %2
%7 = getelementptr inbounds i8*, i8** %1, i64 1
%8 = load i8*, i8** %7
%9 = tail call i64 @strcmp(i8* %8, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str, i64 0, i64 0))
%10 = icmp eq i64 %9, 0
br i1 %10, label %11, label %14
11: ; preds = %6
%12 = add nsw i32 %0, -1
%13 = tail call i32 @bwa_fa2pac(i32 %12, i8** %7)
br label %137
14: ; preds = %6
%15 = load i8*, i8** %7
%16 = tail call i64 @strcmp(i8* %15, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.1, i64 0, i64 0))
%17 = icmp eq i64 %16, 0
br i1 %17, label %18, label %21
18: ; preds = %14
%19 = add nsw i32 %0, -1
%20 = tail call i32 @bwa_pac2bwt(i32 %19, i8** %7)
br label %137
21: ; preds = %14
%22 = load i8*, i8** %7
%23 = tail call i64 @strcmp(i8* %22, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%24 = icmp eq i64 %23, 0
br i1 %24, label %25, label %28
25: ; preds = %21
%26 = add nsw i32 %0, -1
%27 = tail call i32 @bwt_bwtgen_main(i32 %26, i8** %7)
br label %137
28: ; preds = %21
%29 = load i8*, i8** %7
%30 = tail call i64 @strcmp(i8* %29, i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.3, i64 0, i64 0))
%31 = icmp eq i64 %30, 0
br i1 %31, label %32, label %35
32: ; preds = %28
%33 = add nsw i32 %0, -1
%34 = tail call i32 @bwa_bwtupdate(i32 %33, i8** %7)
br label %137
35: ; preds = %28
%36 = load i8*, i8** %7
%37 = tail call i64 @strcmp(i8* %36, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.4, i64 0, i64 0))
%38 = icmp eq i64 %37, 0
br i1 %38, label %39, label %42
39: ; preds = %35
%40 = add nsw i32 %0, -1
%41 = tail call i32 @bwa_pac_rev(i32 %40, i8** %7)
br label %137
42: ; preds = %35
%43 = load i8*, i8** %7
%44 = tail call i64 @strcmp(i8* %43, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.5, i64 0, i64 0))
%45 = icmp eq i64 %44, 0
br i1 %45, label %46, label %49
46: ; preds = %42
%47 = add nsw i32 %0, -1
%48 = tail call i32 @bwa_bwt2sa(i32 %47, i8** %7)
br label %137
49: ; preds = %42
%50 = load i8*, i8** %7
%51 = tail call i64 @strcmp(i8* %50, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.6, i64 0, i64 0))
%52 = icmp eq i64 %51, 0
br i1 %52, label %53, label %56
53: ; preds = %49
%54 = add nsw i32 %0, -1
%55 = tail call i32 @bwa_index(i32 %54, i8** %7)
br label %137
56: ; preds = %49
%57 = load i8*, i8** %7
%58 = tail call i64 @strcmp(i8* %57, i8* getelementptr inbounds ([4 x i8], [4 x i8]* @.str.7, i64 0, i64 0))
%59 = icmp eq i64 %58, 0
br i1 %59, label %60, label %63
60: ; preds = %56
%61 = add nsw i32 %0, -1
%62 = tail call i32 @bwa_aln(i32 %61, i8** %7)
br label %137
63: ; preds = %56
%64 = load i8*, i8** %7
%65 = tail call i64 @strcmp(i8* %64, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.8, i64 0, i64 0))
%66 = icmp eq i64 %65, 0
br i1 %66, label %67, label %70
67: ; preds = %63
%68 = add nsw i32 %0, -1
%69 = tail call i32 @bwa_bam_to_bam(i32 %68, i8** %7, i8* getelementptr inbounds ([16 x i8], [16 x i8]* @.str.9, i64 0, i64 0))
br label %137
70: ; preds = %63
%71 = load i8*, i8** %7
%72 = tail call i64 @strcmp(i8* %71, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.10, i64 0, i64 0))
%73 = icmp eq i64 %72, 0
br i1 %73, label %74, label %77
74: ; preds = %70
%75 = add nsw i32 %0, -1
%76 = tail call i32 @bwa_worker(i32 %75, i8** %7)
br label %137
77: ; preds = %70
%78 = load i8*, i8** %7
%79 = tail call i64 @strcmp(i8* %78, i8* getelementptr inbounds ([3 x i8], [3 x i8]* @.str.11, i64 0, i64 0))
%80 = icmp eq i64 %79, 0
br i1 %80, label %81, label %84
81: ; preds = %77
%82 = add nsw i32 %0, -1
%83 = tail call i32 @bwa_stdsw(i32 %82, i8** %7)
br label %137
84: ; preds = %77
%85 = load i8*, i8** %7
%86 = tail call i64 @strcmp(i8* %85, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.12, i64 0, i64 0))
%87 = icmp eq i64 %86, 0
br i1 %87, label %88, label %91
88: ; preds = %84
%89 = add nsw i32 %0, -1
%90 = tail call i32 @bwa_sai2sam_se(i32 %89, i8** %7)
br label %137
91: ; preds = %84
%92 = load i8*, i8** %7
%93 = tail call i64 @strcmp(i8* %92, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.13, i64 0, i64 0))
%94 = icmp eq i64 %93, 0
br i1 %94, label %95, label %98
95: ; preds = %91
%96 = add nsw i32 %0, -1
%97 = tail call i32 @bwa_sai2sam_pe(i32 %96, i8** %7)
br label %137
98: ; preds = %91
%99 = load i8*, i8** %7
%100 = tail call i64 @strcmp(i8* %99, i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.14, i64 0, i64 0))
%101 = icmp eq i64 %100, 0
br i1 %101, label %102, label %105
102: ; preds = %98
%103 = add nsw i32 %0, -1
%104 = tail call i32 @bwa_pac2cspac(i32 %103, i8** %7)
br label %137
105: ; preds = %98
%106 = load i8*, i8** %7
%107 = tail call i64 @strcmp(i8* %106, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.15, i64 0, i64 0))
%108 = icmp eq i64 %107, 0
br i1 %108, label %109, label %112
109: ; preds = %105
%110 = add nsw i32 %0, -1
%111 = tail call i32 @bwa_stdsw(i32 %110, i8** %7)
br label %137
112: ; preds = %105
%113 = load i8*, i8** %7
%114 = tail call i64 @strcmp(i8* %113, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.16, i64 0, i64 0))
%115 = icmp eq i64 %114, 0
br i1 %115, label %116, label %119
116: ; preds = %112
%117 = add nsw i32 %0, -1
%118 = tail call i32 @bwa_bwtsw2(i32 %117, i8** %7)
br label %137
119: ; preds = %112
%120 = load i8*, i8** %7
%121 = tail call i64 @strcmp(i8* %120, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.17, i64 0, i64 0))
%122 = icmp eq i64 %121, 0
br i1 %122, label %123, label %126
123: ; preds = %119
%124 = add nsw i32 %0, -1
%125 = tail call i32 @bwa_bwtsw2(i32 %124, i8** %7)
br label %137
126: ; preds = %119
%127 = load i8*, i8** %7
%128 = tail call i64 @strcmp(i8* %127, i8* getelementptr inbounds ([6 x i8], [6 x i8]* @.str.18, i64 0, i64 0))
%129 = icmp eq i64 %128, 0
br i1 %129, label %130, label %133
130: ; preds = %126
%131 = add nsw i32 %0, -1
%132 = tail call i32 @bwa_bwtsw2(i32 %131, i8** %7)
br label %137
133: ; preds = %126
%134 = load i32, i32* @stderr
%135 = load i8*, i8** %7
%136 = tail call i32 @fprintf(i32 %134, i8* getelementptr inbounds ([34 x i8], [34 x i8]* @.str.19, i64 0, i64 0), i8* %135)
br label %137
137: ; preds = %133, %130, %123, %116, %109, %102, %95, %88, %81, %74, %67, %60, %53, %46, %39, %32, %25, %18, %11, %4
%138 = phi i32 [ %5, %4 ], [ %13, %11 ], [ %20, %18 ], [ %27, %25 ], [ %34, %32 ], [ %41, %39 ], [ %48, %46 ], [ %55, %53 ], [ %62, %60 ], [ %69, %67 ], [ %76, %74 ], [ %83, %81 ], [ %90, %88 ], [ %97, %95 ], [ %104, %102 ], [ %111, %109 ], [ %118, %116 ], [ %125, %123 ], [ %132, %130 ], [ 1, %133 ]
ret i32 %138
}