#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 *, char *, char *, char *, char *);
void help(char *argv[]) {
  printf(
      "Renames nodes using a mapping\n"
      "\n"
      "Synopsis\n"
      "--------\n"
      "\n"
      "%s [-hl] <newick trees filename|-> <map filename>\n"
      "\n"
      "Input\n"
      "-----\n"
      "\n"
      "First argument is the name of a file that contains Newick trees, or '-' "
      "(in\n"
      "which case trees are read from standard input).\n"
      "\n"
      "Second argument is the name of the map file, which has one (old-name,\n"
      "new-name) pair per line, e.g:\n"
      "\n"
      "cmp1	Compsognathus\n"
      "trc	Triceratops\n"
      "vlcr	Velociraptor\n"
      "\n"
      "Old and new names should be separated by whitespace.\n"
      "\n"
      "Output\n"
      "------\n"
      "\n"
      "Prints the tree, after replacing all old names by the specified new "
      "name.\n"
      "\n"
      "Options\n"
      "-------\n"
      "\n"
      "    -h: print this message and exit\n"
      "    -l: only replace leaf labels. This is useful if all labels are "
      "numeric,\n"
      "        but inner labels represent bootstraps, and you don't want to\n"
      "        accidentally modify bootstrap values.\n"
      "\n"
      "Examples\n"
      "--------\n"
      "\n"
      "# Some tree-building programs don't allow labels longer than 10 "
      "characters\n"
      "# or so. One way around this limitation is to relabel the sequences "
      "using\n"
      "# numbers.  Tree data/HRV_numeric has numeric labels, because its "
      "outgroup,\n"
      "# \"Foot_and_Mouth\" is longer than 10 characters. The number->label "
      "mapping\n"
      "# was stored in file data/HRV.map. Now we can rename the whole tree:\n"
      "\n"
      "$ %s data/HRV_numeric data/HRV.map\n"
      "\n"
      "# We can construct a tree of families from a genus tree and a "
      "genus->family\n"
      "# map. File data/falconiformes is a tree of diurnal raptor genera, and\n"
      "# data/falc_map maps the genera to families. To produce a family tree, "
      "we do: \n"
      "\n"
      "$ %s data/falconiformes data/falc_map\n"
      "\n"
      "# In fact, we could directly condense the tree, so that only one leaf "
      "per\n"
      "# family is left:\n"
      "\n"
      "$ %s data/falconiformes data/falc_map | nw_condense -\n",
      argv[0], argv[0], argv[0], argv[0]);
}


x86 assembly (clang, -O0):
<help>:
push   %rbp
mov    %rsp,%rbp
sub    $0x10,%rsp
mov    %rdi,-0x8(%rbp)
mov    -0x8(%rbp),%rax
mov    (%rax),%rsi
mov    -0x8(%rbp),%rax
mov    (%rax),%rdx
mov    -0x8(%rbp),%rax
mov    (%rax),%rcx
mov    -0x8(%rbp),%rax
mov    (%rax),%r8
lea    0xec1(%rip),%rdi
call   1030 <printf@plt>
add    $0x10,%rsp
pop    %rbp
ret

x86 assembly (clang, -O2):
<help>:
mov    (%rdi),%rcx
lea    0xee6(%rip),%rdi
mov    %rcx,%rsi
mov    %rcx,%rdx
mov    %rcx,%r8
jmp    1030 <printf@plt>

LLVM IR (-O0):
@.str = [1622 x i8] c"Renames nodes using a mapping\0A\0ASynopsis\0A--------\0A\0A%s [-hl] <newick trees filename|-> <map filename>\0A\0AInput\0A-----\0A\0AFirst argument is the name of a file that contains Newick trees, or '-' (in\0Awhich case trees are read from standard input).\0A\0ASecond argument is the name of the map file, which has one (old-name,\0Anew-name) pair per line, e.g:\0A\0Acmp1\09Compsognathus\0Atrc\09Triceratops\0Avlcr\09Velociraptor\0A\0AOld and new names should be separated by whitespace.\0A\0AOutput\0A------\0A\0APrints the tree, after replacing all old names by the specified new name.\0A\0AOptions\0A-------\0A\0A -h: print this message and exit\0A -l: only replace leaf labels. This is useful if all labels are numeric,\0A but inner labels represent bootstraps, and you don't want to\0A accidentally modify bootstrap values.\0A\0AExamples\0A--------\0A\0A# Some tree-building programs don't allow labels longer than 10 characters\0A# or so. One way around this limitation is to relabel the sequences using\0A# numbers. Tree data/HRV_numeric has numeric labels, because its outgroup,\0A# \22Foot_and_Mouth\22 is longer than 10 characters. The number->label mapping\0A# was stored in file data/HRV.map. Now we can rename the whole tree:\0A\0A$ %s data/HRV_numeric data/HRV.map\0A\0A# We can construct a tree of families from a genus tree and a genus->family\0A# map. File data/falconiformes is a tree of diurnal raptor genera, and\0A# data/falc_map maps the genera to families. To produce a family tree, we do: \0A\0A$ %s data/falconiformes data/falc_map\0A\0A# In fact, we could directly condense the tree, so that only one leaf per\0A# family is left:\0A\0A$ %s data/falconiformes data/falc_map | nw_condense -\0A\00"
define void @help(i8** %0) {
%2 = alloca i8**
store i8** %0, i8*** %2
%3 = load i8**, i8*** %2
%4 = getelementptr inbounds i8*, i8** %3, i64 0
%5 = load i8*, i8** %4
%6 = load i8**, i8*** %2
%7 = getelementptr inbounds i8*, i8** %6, i64 0
%8 = load i8*, i8** %7
%9 = load i8**, i8*** %2
%10 = getelementptr inbounds i8*, i8** %9, i64 0
%11 = load i8*, i8** %10
%12 = load i8**, i8*** %2
%13 = getelementptr inbounds i8*, i8** %12, i64 0
%14 = load i8*, i8** %13
%15 = call i32 @printf(i8* getelementptr inbounds ([1622 x i8], [1622 x i8]* @.str, i64 0, i64 0), i8* %5, i8* %8, i8* %11, i8* %14)
ret void
}

LLVM IR (-O2):
@.str = [1622 x i8] c"Renames nodes using a mapping\0A\0ASynopsis\0A--------\0A\0A%s [-hl] <newick trees filename|-> <map filename>\0A\0AInput\0A-----\0A\0AFirst argument is the name of a file that contains Newick trees, or '-' (in\0Awhich case trees are read from standard input).\0A\0ASecond argument is the name of the map file, which has one (old-name,\0Anew-name) pair per line, e.g:\0A\0Acmp1\09Compsognathus\0Atrc\09Triceratops\0Avlcr\09Velociraptor\0A\0AOld and new names should be separated by whitespace.\0A\0AOutput\0A------\0A\0APrints the tree, after replacing all old names by the specified new name.\0A\0AOptions\0A-------\0A\0A -h: print this message and exit\0A -l: only replace leaf labels. This is useful if all labels are numeric,\0A but inner labels represent bootstraps, and you don't want to\0A accidentally modify bootstrap values.\0A\0AExamples\0A--------\0A\0A# Some tree-building programs don't allow labels longer than 10 characters\0A# or so. One way around this limitation is to relabel the sequences using\0A# numbers. Tree data/HRV_numeric has numeric labels, because its outgroup,\0A# \22Foot_and_Mouth\22 is longer than 10 characters. The number->label mapping\0A# was stored in file data/HRV.map. Now we can rename the whole tree:\0A\0A$ %s data/HRV_numeric data/HRV.map\0A\0A# We can construct a tree of families from a genus tree and a genus->family\0A# map. File data/falconiformes is a tree of diurnal raptor genera, and\0A# data/falc_map maps the genera to families. To produce a family tree, we do: \0A\0A$ %s data/falconiformes data/falc_map\0A\0A# In fact, we could directly condense the tree, so that only one leaf per\0A# family is left:\0A\0A$ %s data/falconiformes data/falc_map | nw_condense -\0A\00"
define void @help(i8** nocapture %0) {
%2 = load i8*, i8** %0
%3 = tail call i32 @printf(i8* getelementptr inbounds ([1622 x i8], [1622 x i8]* @.str, i64 0, i64 0), i8* %2, i8* %2, i8* %2, i8* %2)
ret void
}