#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*/ exit(int /*<<< orphan*/);
int /*<<< orphan*/ printf(char *, ...);
void hmmtop_usage(char *pn) {
  printf("Usage: \"%s options\", where options are the following:\n", pn);
  printf("\n    -if=filename, --input_file=filename\n");
  printf("          path and name of the input sequence file.  If  filename\n");
  printf("          is -- program reads from the standard input.\n");
  printf("\n    -of=filename, --output_file=filename\n");
  printf("          path and name of the output sequence file. If  filename\n");
  printf("          is -- program writes to the standard output.\n");
  printf("\n    -lf=filename, --log_file=filename\n");
  printf("          path and name of the log file.  Use  only for debugging\n");
  printf("          purpose.\n");
  printf("\n    -sf=XXX, --sequence_format=XXX\n");
  printf("          format of sequence(s).  XXX may be FAS for fasta format\n");
  printf("          (default), PIR for NBRF/PIR format or  SWP  for  SWISS-\n");
  printf("          PROT format.\n");
  printf("\n    -pi=xxx, --proces_inputfile=xxx\n");
  printf("          treating sequences in input file as single or homologue\n");
  printf("          sequences. xxx may be spred or mpred.  In case of spred\n");
  printf("          for each sequence in input_file will be made prediction\n");
  printf("          (default). In case of mpred only for the first sequence\n");
  printf("          in the input file will  be made  prediction,  remaining\n");
  printf("          sequences will be treated as helpers.\n");
  printf("\n    -ps=xxx, --pseudo_size=xxx\n");
  printf("          size of the pseudo count vector.  xxx may be from 0 (no\n");
  printf("          pseudo count vector used) to 10000 (default=10000).\n");
  printf("\n    -loc=bpos-epos-spart, --locate=bpos-epos-spart\n");
  printf("          localize a portion of the sequence in a given structur-\n");
  printf("          al part.  bpos and  epos are the begin and end position\n");
  printf("          in the sequence, respectively;  spart is the structural\n");
  printf("          part and may be i,I,H,o and O.  epos  may be the letter\n");
  printf("          'E', which means the C terminal end of the sequence\n");
  printf("\n    -locf=filename, --loc_file=filename\n");
  printf("          name of the  'locate file',  which contains the locates\n");
  printf("          for each protein  if multiple  sequences with  pi=spred\n");
  printf("          are given.  Each line contains one or more locates. The\n");
  printf("          format of the locates are as given in the -loc= switch.\n");
  printf("\n    -noit, --noiteration\n");
  printf("          do not optimize the parameters on the given sequence(s)\n");
  printf("          just calculate the best path if the model is given.  It\n");
  printf("          is useful for rapid but not so accurate prediction.\n");
  printf("\n    -is=xxx, --iteration_start=xxx\n");
  printf("          starting point of the iteration(s).  xxx  may be pseudo\n");
  printf("          or random.  In case of pseudo iteration starts from the\n");
  printf("          pseudo  count  vector  (default).  In  case  of  random\n");
  printf("          iteration starts from random values.\n");
  printf("\n    -in=xxx, --iteration_number=xxx\n");
  printf("          maximum allowed iterations (if is=random).\n");
  printf("\n    -pp, --print_probabilities\n");
  printf("          print the optimized probabilies.\n");
  printf("\n    -pc, --print_pseudocount\n");
  printf("          print the pseudocount vector used.\n");
  printf("\n    -pl, --print_longprediction\n");
  printf("          print prediction in a long format,  ie. localization of\n");
  printf("          each amino acid in the input sequence.\n");
  printf("\n    -h, --help\n");
  printf("          this help message.\n");
  printf("\n    -sh, --short_help\n");
  printf("          print a short help message.\n");
  printf("\n\nReferences:\n");
  printf("          G.E. Tusnady and I. Simon (1998)\n");
  printf("          Principles Governing Amino Acid Composition of Integral\n");
  printf("          Membrane Proteins:  Applications to topology prediction\n");
  printf("          J. Mol. Biol. 283, 489-506\n");
  printf("          http://www.enzim.hu/hmmtop\n\n");
  exit(0);
}


x86 assembly (clang, -O0):
<hmmtop_usage>:
push   %rbp
mov    %rsp,%rbp
sub    $0x10,%rsp
mov    %rdi,-0x8(%rbp)
mov    -0x8(%rbp),%rsi
lea    0xec9(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xef2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf0e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf43(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf6d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf8a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfbf(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfe9(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1003(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1038(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x103e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1055(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x108a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10bf(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10c9(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10e1(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1116(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x114b(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1180(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x11b5(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x11ea(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x120d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1220(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1255(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1286(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x12ad(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x12e2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1317(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x134c(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1381(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x13b2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x13ce(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1403(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1438(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x146d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x14a2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x14af(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x14e4(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1519(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x154a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1561(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1596(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x15cb(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1600(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1622(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x163a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1662(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1675(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1693(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x16a4(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x16c4(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x16d8(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x170d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1731(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1734(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1744(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x174e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1767(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1768(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1786(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x17bb(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x17f0(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1808(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
xor    %edi,%edi
call   1040 <exit@plt>

x86 assembly (clang, -O2):
<hmmtop_usage>:
push   %rax
mov    %rdi,%rsi
lea    0xec5(%rip),%rdi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xeee(%rip),%rdi
call   1030 <puts@plt>
lea    0xf0b(%rip),%rdi
call   1030 <puts@plt>
lea    0xf41(%rip),%rdi
call   1030 <puts@plt>
lea    0xf6c(%rip),%rdi
call   1030 <puts@plt>
lea    0xf8a(%rip),%rdi
call   1030 <puts@plt>
lea    0xfc0(%rip),%rdi
call   1030 <puts@plt>
lea    0xfeb(%rip),%rdi
call   1030 <puts@plt>
lea    0x1006(%rip),%rdi
call   1030 <puts@plt>
lea    0x103c(%rip),%rdi
call   1030 <puts@plt>
lea    0x1043(%rip),%rdi
call   1030 <puts@plt>
lea    0x105b(%rip),%rdi
call   1030 <puts@plt>
lea    0x1091(%rip),%rdi
call   1030 <puts@plt>
lea    0x10c7(%rip),%rdi
call   1030 <puts@plt>
lea    0x10d2(%rip),%rdi
call   1030 <puts@plt>
lea    0x10eb(%rip),%rdi
call   1030 <puts@plt>
lea    0x1121(%rip),%rdi
call   1030 <puts@plt>
lea    0x1157(%rip),%rdi
call   1030 <puts@plt>
lea    0x118d(%rip),%rdi
call   1030 <puts@plt>
lea    0x11c3(%rip),%rdi
call   1030 <puts@plt>
lea    0x11f9(%rip),%rdi
call   1030 <puts@plt>
lea    0x121d(%rip),%rdi
call   1030 <puts@plt>
lea    0x1231(%rip),%rdi
call   1030 <puts@plt>
lea    0x1267(%rip),%rdi
call   1030 <puts@plt>
lea    0x1299(%rip),%rdi
call   1030 <puts@plt>
lea    0x12c1(%rip),%rdi
call   1030 <puts@plt>
lea    0x12f7(%rip),%rdi
call   1030 <puts@plt>
lea    0x132d(%rip),%rdi
call   1030 <puts@plt>
lea    0x1363(%rip),%rdi
call   1030 <puts@plt>
lea    0x1399(%rip),%rdi
call   1030 <puts@plt>
lea    0x13cb(%rip),%rdi
call   1030 <puts@plt>
lea    0x13e8(%rip),%rdi
call   1030 <puts@plt>
lea    0x141e(%rip),%rdi
call   1030 <puts@plt>
lea    0x1454(%rip),%rdi
call   1030 <puts@plt>
lea    0x148a(%rip),%rdi
call   1030 <puts@plt>
lea    0x14c0(%rip),%rdi
call   1030 <puts@plt>
lea    0x14ce(%rip),%rdi
call   1030 <puts@plt>
lea    0x1504(%rip),%rdi
call   1030 <puts@plt>
lea    0x153a(%rip),%rdi
call   1030 <puts@plt>
lea    0x156c(%rip),%rdi
call   1030 <puts@plt>
lea    0x1584(%rip),%rdi
call   1030 <puts@plt>
lea    0x15ba(%rip),%rdi
call   1030 <puts@plt>
lea    0x15f0(%rip),%rdi
call   1030 <puts@plt>
lea    0x1626(%rip),%rdi
call   1030 <puts@plt>
lea    0x1649(%rip),%rdi
call   1030 <puts@plt>
lea    0x1662(%rip),%rdi
call   1030 <puts@plt>
lea    0x168b(%rip),%rdi
call   1030 <puts@plt>
lea    0x169f(%rip),%rdi
call   1030 <puts@plt>
lea    0x16be(%rip),%rdi
call   1030 <puts@plt>
lea    0x16d0(%rip),%rdi
call   1030 <puts@plt>
lea    0x16f1(%rip),%rdi
call   1030 <puts@plt>
lea    0x1706(%rip),%rdi
call   1030 <puts@plt>
lea    0x173c(%rip),%rdi
call   1030 <puts@plt>
lea    0x1761(%rip),%rdi
call   1030 <puts@plt>
lea    0x1765(%rip),%rdi
call   1030 <puts@plt>
lea    0x1776(%rip),%rdi
call   1030 <puts@plt>
lea    0x1781(%rip),%rdi
call   1030 <puts@plt>
lea    0x179b(%rip),%rdi
call   1030 <puts@plt>
lea    0x179d(%rip),%rdi
call   1030 <puts@plt>
lea    0x17bc(%rip),%rdi
call   1030 <puts@plt>
lea    0x17f2(%rip),%rdi
call   1030 <puts@plt>
lea    0x1828(%rip),%rdi
call   1030 <puts@plt>
lea    0x1841(%rip),%rdi
call   1030 <puts@plt>
xor    %edi,%edi
call   1050 <exit@plt>

LLVM IR (-O0):
@.str = [55 x i8] c"Usage: \22%s options\22, where options are the following:\0A\00"
@.str.1 = [42 x i8] c"\0A -if=filename, --input_file=filename\0A\00"
@.str.2 = [67 x i8] c" path and name of the input sequence file. If filename\0A\00"
@.str.3 = [56 x i8] c" is -- program reads from the standard input.\0A\00"
@.str.4 = [43 x i8] c"\0A -of=filename, --output_file=filename\0A\00"
@.str.5 = [67 x i8] c" path and name of the output sequence file. If filename\0A\00"
@.str.6 = [56 x i8] c" is -- program writes to the standard output.\0A\00"
@.str.7 = [40 x i8] c"\0A -lf=filename, --log_file=filename\0A\00"
@.str.8 = [67 x i8] c" path and name of the log file. Use only for debugging\0A\00"
@.str.9 = [20 x i8] c" purpose.\0A\00"
@.str.10 = [37 x i8] c"\0A -sf=XXX, --sequence_format=XXX\0A\00"
@.str.11 = [67 x i8] c" format of sequence(s). XXX may be FAS for fasta format\0A\00"
@.str.12 = [67 x i8] c" (default), PIR for NBRF/PIR format or SWP for SWISS-\0A\00"
@.str.13 = [24 x i8] c" PROT format.\0A\00"
@.str.14 = [38 x i8] c"\0A -pi=xxx, --proces_inputfile=xxx\0A\00"
@.str.15 = [67 x i8] c" treating sequences in input file as single or homologue\0A\00"
@.str.16 = [67 x i8] c" sequences. xxx may be spred or mpred. In case of spred\0A\00"
@.str.17 = [67 x i8] c" for each sequence in input_file will be made prediction\0A\00"
@.str.18 = [67 x i8] c" (default). In case of mpred only for the first sequence\0A\00"
@.str.19 = [67 x i8] c" in the input file will be made prediction, remaining\0A\00"
@.str.20 = [49 x i8] c" sequences will be treated as helpers.\0A\00"
@.str.21 = [33 x i8] c"\0A -ps=xxx, --pseudo_size=xxx\0A\00"
@.str.22 = [67 x i8] c" size of the pseudo count vector. xxx may be from 0 (no\0A\00"
@.str.23 = [63 x i8] c" pseudo count vector used) to 10000 (default=10000).\0A\00"
@.str.24 = [53 x i8] c"\0A -loc=bpos-epos-spart, --locate=bpos-epos-spart\0A\00"
@.str.25 = [67 x i8] c" localize a portion of the sequence in a given structur-\0A\00"
@.str.26 = [67 x i8] c" al part. bpos and epos are the begin and end position\0A\00"
@.str.27 = [67 x i8] c" in the sequence, respectively; spart is the structural\0A\00"
@.str.28 = [67 x i8] c" part and may be i,I,H,o and O. epos may be the letter\0A\00"
@.str.29 = [63 x i8] c" 'E', which means the C terminal end of the sequence\0A\00"
@.str.30 = [42 x i8] c"\0A -locf=filename, --loc_file=filename\0A\00"
@.str.31 = [67 x i8] c" name of the 'locate file', which contains the locates\0A\00"
@.str.32 = [67 x i8] c" for each protein if multiple sequences with pi=spred\0A\00"
@.str.33 = [67 x i8] c" are given. Each line contains one or more locates. The\0A\00"
@.str.34 = [67 x i8] c" format of the locates are as given in the -loc= switch.\0A\00"
@.str.35 = [27 x i8] c"\0A -noit, --noiteration\0A\00"
@.str.36 = [67 x i8] c" do not optimize the parameters on the given sequence(s)\0A\00"
@.str.37 = [67 x i8] c" just calculate the best path if the model is given. It\0A\00"
@.str.38 = [63 x i8] c" is useful for rapid but not so accurate prediction.\0A\00"
@.str.39 = [37 x i8] c"\0A -is=xxx, --iteration_start=xxx\0A\00"
@.str.40 = [67 x i8] c" starting point of the iteration(s). xxx may be pseudo\0A\00"
@.str.41 = [67 x i8] c" or random. In case of pseudo iteration starts from the\0A\00"
@.str.42 = [67 x i8] c" pseudo count vector (default). In case of random\0A\00"
@.str.43 = [48 x i8] c" iteration starts from random values.\0A\00"
@.str.44 = [38 x i8] c"\0A -in=xxx, --iteration_number=xxx\0A\00"
@.str.45 = [54 x i8] c" maximum allowed iterations (if is=random).\0A\00"
@.str.46 = [33 x i8] c"\0A -pp, --print_probabilities\0A\00"
@.str.47 = [44 x i8] c" print the optimized probabilies.\0A\00"
@.str.48 = [31 x i8] c"\0A -pc, --print_pseudocount\0A\00"
@.str.49 = [46 x i8] c" print the pseudocount vector used.\0A\00"
@.str.50 = [34 x i8] c"\0A -pl, --print_longprediction\0A\00"
@.str.51 = [67 x i8] c" print prediction in a long format, ie. localization of\0A\00"
@.str.52 = [50 x i8] c" each amino acid in the input sequence.\0A\00"
@.str.53 = [17 x i8] c"\0A -h, --help\0A\00"
@.str.54 = [30 x i8] c" this help message.\0A\00"
@.str.55 = [24 x i8] c"\0A -sh, --short_help\0A\00"
@.str.56 = [39 x i8] c" print a short help message.\0A\00"
@.str.57 = [15 x i8] c"\0A\0AReferences:\0A\00"
@.str.58 = [44 x i8] c" G.E. Tusnady and I. Simon (1998)\0A\00"
@.str.59 = [67 x i8] c" Principles Governing Amino Acid Composition of Integral\0A\00"
@.str.60 = [67 x i8] c" Membrane Proteins: Applications to topology prediction\0A\00"
@.str.61 = [38 x i8] c" J. Mol. Biol. 283, 489-506\0A\00"
@.str.62 = [39 x i8] c" http://www.enzim.hu/hmmtop\0A\0A\00"
define void @hmmtop_usage(i8* %0) {
%2 = alloca i8*
store i8* %0, i8** %2
%3 = load i8*, i8** %2
%4 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([55 x i8], [55 x i8]* @.str, i64 0, i64 0), i8* %3)
%5 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([42 x i8], [42 x i8]* @.str.1, i64 0, i64 0))
%6 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.2, i64 0, i64 0))
%7 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([56 x i8], [56 x i8]* @.str.3, i64 0, i64 0))
%8 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.4, i64 0, i64 0))
%9 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.5, i64 0, i64 0))
%10 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([56 x i8], [56 x i8]* @.str.6, i64 0, i64 0))
%11 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([40 x i8], [40 x i8]* @.str.7, i64 0, i64 0))
%12 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.8, i64 0, i64 0))
%13 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([20 x i8], [20 x i8]* @.str.9, i64 0, i64 0))
%14 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([37 x i8], [37 x i8]* @.str.10, i64 0, i64 0))
%15 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.11, i64 0, i64 0))
%16 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.12, i64 0, i64 0))
%17 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([24 x i8], [24 x i8]* @.str.13, i64 0, i64 0))
%18 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.14, i64 0, i64 0))
%19 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.15, i64 0, i64 0))
%20 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.16, i64 0, i64 0))
%21 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.17, i64 0, i64 0))
%22 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.18, i64 0, i64 0))
%23 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.19, i64 0, i64 0))
%24 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([49 x i8], [49 x i8]* @.str.20, i64 0, i64 0))
%25 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([33 x i8], [33 x i8]* @.str.21, i64 0, i64 0))
%26 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.22, i64 0, i64 0))
%27 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([63 x i8], [63 x i8]* @.str.23, i64 0, i64 0))
%28 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.24, i64 0, i64 0))
%29 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.25, i64 0, i64 0))
%30 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.26, i64 0, i64 0))
%31 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.27, i64 0, i64 0))
%32 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.28, i64 0, i64 0))
%33 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([63 x i8], [63 x i8]* @.str.29, i64 0, i64 0))
%34 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([42 x i8], [42 x i8]* @.str.30, i64 0, i64 0))
%35 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.31, i64 0, i64 0))
%36 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.32, i64 0, i64 0))
%37 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.33, i64 0, i64 0))
%38 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.34, i64 0, i64 0))
%39 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([27 x i8], [27 x i8]* @.str.35, i64 0, i64 0))
%40 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.36, i64 0, i64 0))
%41 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.37, i64 0, i64 0))
%42 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([63 x i8], [63 x i8]* @.str.38, i64 0, i64 0))
%43 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([37 x i8], [37 x i8]* @.str.39, i64 0, i64 0))
%44 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.40, i64 0, i64 0))
%45 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.41, i64 0, i64 0))
%46 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.42, i64 0, i64 0))
%47 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([48 x i8], [48 x i8]* @.str.43, i64 0, i64 0))
%48 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.44, i64 0, i64 0))
%49 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.45, i64 0, i64 0))
%50 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([33 x i8], [33 x i8]* @.str.46, i64 0, i64 0))
%51 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.47, i64 0, i64 0))
%52 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([31 x i8], [31 x i8]* @.str.48, i64 0, i64 0))
%53 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.49, i64 0, i64 0))
%54 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([34 x i8], [34 x i8]* @.str.50, i64 0, i64 0))
%55 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.51, i64 0, i64 0))
%56 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([50 x i8], [50 x i8]* @.str.52, i64 0, i64 0))
%57 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([17 x i8], [17 x i8]* @.str.53, i64 0, i64 0))
%58 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([30 x i8], [30 x i8]* @.str.54, i64 0, i64 0))
%59 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([24 x i8], [24 x i8]* @.str.55, i64 0, i64 0))
%60 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([39 x i8], [39 x i8]* @.str.56, i64 0, i64 0))
%61 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([15 x i8], [15 x i8]* @.str.57, i64 0, i64 0))
%62 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.58, i64 0, i64 0))
%63 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.59, i64 0, i64 0))
%64 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str.60, i64 0, i64 0))
%65 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([38 x i8], [38 x i8]* @.str.61, i64 0, i64 0))
%66 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([39 x i8], [39 x i8]* @.str.62, i64 0, i64 0))
%67 = call i32 @exit(i32 0)
unreachable
}

LLVM IR (-O2):
@.str = [55 x i8] c"Usage: \22%s options\22, where options are the following:\0A\00"
@str = [41 x i8] c"\0A -if=filename, --input_file=filename\00"
@str.63 = [66 x i8] c" path and name of the input sequence file. If filename\00"
@str.64 = [55 x i8] c" is -- program reads from the standard input.\00"
@str.65 = [42 x i8] c"\0A -of=filename, --output_file=filename\00"
@str.66 = [66 x i8] c" path and name of the output sequence file. If filename\00"
@str.67 = [55 x i8] c" is -- program writes to the standard output.\00"
@str.68 = [39 x i8] c"\0A -lf=filename, --log_file=filename\00"
@str.69 = [66 x i8] c" path and name of the log file. Use only for debugging\00"
@str.70 = [19 x i8] c" purpose.\00"
@str.71 = [36 x i8] c"\0A -sf=XXX, --sequence_format=XXX\00"
@str.72 = [66 x i8] c" format of sequence(s). XXX may be FAS for fasta format\00"
@str.73 = [66 x i8] c" (default), PIR for NBRF/PIR format or SWP for SWISS-\00"
@str.74 = [23 x i8] c" PROT format.\00"
@str.75 = [37 x i8] c"\0A -pi=xxx, --proces_inputfile=xxx\00"
@str.76 = [66 x i8] c" treating sequences in input file as single or homologue\00"
@str.77 = [66 x i8] c" sequences. xxx may be spred or mpred. In case of spred\00"
@str.78 = [66 x i8] c" for each sequence in input_file will be made prediction\00"
@str.79 = [66 x i8] c" (default). In case of mpred only for the first sequence\00"
@str.80 = [66 x i8] c" in the input file will be made prediction, remaining\00"
@str.81 = [48 x i8] c" sequences will be treated as helpers.\00"
@str.82 = [32 x i8] c"\0A -ps=xxx, --pseudo_size=xxx\00"
@str.83 = [66 x i8] c" size of the pseudo count vector. xxx may be from 0 (no\00"
@str.84 = [62 x i8] c" pseudo count vector used) to 10000 (default=10000).\00"
@str.85 = [52 x i8] c"\0A -loc=bpos-epos-spart, --locate=bpos-epos-spart\00"
@str.86 = [66 x i8] c" localize a portion of the sequence in a given structur-\00"
@str.87 = [66 x i8] c" al part. bpos and epos are the begin and end position\00"
@str.88 = [66 x i8] c" in the sequence, respectively; spart is the structural\00"
@str.89 = [66 x i8] c" part and may be i,I,H,o and O. epos may be the letter\00"
@str.90 = [62 x i8] c" 'E', which means the C terminal end of the sequence\00"
@str.91 = [41 x i8] c"\0A -locf=filename, --loc_file=filename\00"
@str.92 = [66 x i8] c" name of the 'locate file', which contains the locates\00"
@str.93 = [66 x i8] c" for each protein if multiple sequences with pi=spred\00"
@str.94 = [66 x i8] c" are given. Each line contains one or more locates. The\00"
@str.95 = [66 x i8] c" format of the locates are as given in the -loc= switch.\00"
@str.96 = [26 x i8] c"\0A -noit, --noiteration\00"
@str.97 = [66 x i8] c" do not optimize the parameters on the given sequence(s)\00"
@str.98 = [66 x i8] c" just calculate the best path if the model is given. It\00"
@str.99 = [62 x i8] c" is useful for rapid but not so accurate prediction.\00"
@str.100 = [36 x i8] c"\0A -is=xxx, --iteration_start=xxx\00"
@str.101 = [66 x i8] c" starting point of the iteration(s). xxx may be pseudo\00"
@str.102 = [66 x i8] c" or random. In case of pseudo iteration starts from the\00"
@str.103 = [66 x i8] c" pseudo count vector (default). In case of random\00"
@str.104 = [47 x i8] c" iteration starts from random values.\00"
@str.105 = [37 x i8] c"\0A -in=xxx, --iteration_number=xxx\00"
@str.106 = [53 x i8] c" maximum allowed iterations (if is=random).\00"
@str.107 = [32 x i8] c"\0A -pp, --print_probabilities\00"
@str.108 = [43 x i8] c" print the optimized probabilies.\00"
@str.109 = [30 x i8] c"\0A -pc, --print_pseudocount\00"
@str.110 = [45 x i8] c" print the pseudocount vector used.\00"
@str.111 = [33 x i8] c"\0A -pl, --print_longprediction\00"
@str.112 = [66 x i8] c" print prediction in a long format, ie. localization of\00"
@str.113 = [49 x i8] c" each amino acid in the input sequence.\00"
@str.114 = [16 x i8] c"\0A -h, --help\00"
@str.115 = [29 x i8] c" this help message.\00"
@str.116 = [23 x i8] c"\0A -sh, --short_help\00"
@str.117 = [38 x i8] c" print a short help message.\00"
@str.118 = [14 x i8] c"\0A\0AReferences:\00"
@str.119 = [43 x i8] c" G.E. Tusnady and I. Simon (1998)\00"
@str.120 = [66 x i8] c" Principles Governing Amino Acid Composition of Integral\00"
@str.121 = [66 x i8] c" Membrane Proteins: Applications to topology prediction\00"
@str.122 = [37 x i8] c" J. Mol. Biol. 283, 489-506\00"
@str.123 = [38 x i8] c" http://www.enzim.hu/hmmtop\0A\00"
define void @hmmtop_usage(i8* %0) {
%2 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([55 x i8], [55 x i8]* @.str, i64 0, i64 0), i8* %0)
%3 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([41 x i8], [41 x i8]* @str, i64 0, i64 0))
%4 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.63, i64 0, i64 0))
%5 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([55 x i8], [55 x i8]* @str.64, i64 0, i64 0))
%6 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([42 x i8], [42 x i8]* @str.65, i64 0, i64 0))
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.66, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([55 x i8], [55 x i8]* @str.67, i64 0, i64 0))
%9 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([39 x i8], [39 x i8]* @str.68, i64 0, i64 0))
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.69, i64 0, i64 0))
%11 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([19 x i8], [19 x i8]* @str.70, i64 0, i64 0))
%12 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([36 x i8], [36 x i8]* @str.71, i64 0, i64 0))
%13 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.72, i64 0, i64 0))
%14 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.73, i64 0, i64 0))
%15 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([23 x i8], [23 x i8]* @str.74, i64 0, i64 0))
%16 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([37 x i8], [37 x i8]* @str.75, i64 0, i64 0))
%17 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.76, i64 0, i64 0))
%18 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.77, i64 0, i64 0))
%19 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.78, i64 0, i64 0))
%20 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.79, i64 0, i64 0))
%21 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.80, i64 0, i64 0))
%22 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([48 x i8], [48 x i8]* @str.81, i64 0, i64 0))
%23 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([32 x i8], [32 x i8]* @str.82, i64 0, i64 0))
%24 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.83, i64 0, i64 0))
%25 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([62 x i8], [62 x i8]* @str.84, i64 0, i64 0))
%26 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([52 x i8], [52 x i8]* @str.85, i64 0, i64 0))
%27 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.86, i64 0, i64 0))
%28 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.87, i64 0, i64 0))
%29 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.88, i64 0, i64 0))
%30 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.89, i64 0, i64 0))
%31 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([62 x i8], [62 x i8]* @str.90, i64 0, i64 0))
%32 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([41 x i8], [41 x i8]* @str.91, i64 0, i64 0))
%33 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.92, i64 0, i64 0))
%34 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.93, i64 0, i64 0))
%35 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.94, i64 0, i64 0))
%36 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.95, i64 0, i64 0))
%37 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([26 x i8], [26 x i8]* @str.96, i64 0, i64 0))
%38 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.97, i64 0, i64 0))
%39 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.98, i64 0, i64 0))
%40 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([62 x i8], [62 x i8]* @str.99, i64 0, i64 0))
%41 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([36 x i8], [36 x i8]* @str.100, i64 0, i64 0))
%42 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.101, i64 0, i64 0))
%43 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.102, i64 0, i64 0))
%44 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.103, i64 0, i64 0))
%45 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([47 x i8], [47 x i8]* @str.104, i64 0, i64 0))
%46 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([37 x i8], [37 x i8]* @str.105, i64 0, i64 0))
%47 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([53 x i8], [53 x i8]* @str.106, i64 0, i64 0))
%48 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([32 x i8], [32 x i8]* @str.107, i64 0, i64 0))
%49 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([43 x i8], [43 x i8]* @str.108, i64 0, i64 0))
%50 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([30 x i8], [30 x i8]* @str.109, i64 0, i64 0))
%51 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([45 x i8], [45 x i8]* @str.110, i64 0, i64 0))
%52 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([33 x i8], [33 x i8]* @str.111, i64 0, i64 0))
%53 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.112, i64 0, i64 0))
%54 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([49 x i8], [49 x i8]* @str.113, i64 0, i64 0))
%55 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([16 x i8], [16 x i8]* @str.114, i64 0, i64 0))
%56 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([29 x i8], [29 x i8]* @str.115, i64 0, i64 0))
%57 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([23 x i8], [23 x i8]* @str.116, i64 0, i64 0))
%58 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([38 x i8], [38 x i8]* @str.117, i64 0, i64 0))
%59 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([14 x i8], [14 x i8]* @str.118, i64 0, i64 0))
%60 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([43 x i8], [43 x i8]* @str.119, i64 0, i64 0))
%61 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.120, i64 0, i64 0))
%62 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([66 x i8], [66 x i8]* @str.121, i64 0, i64 0))
%63 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([37 x i8], [37 x i8]* @str.122, i64 0, i64 0))
%64 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([38 x i8], [38 x i8]* @str.123, i64 0, i64 0))
%65 = tail call i32 @exit(i32 0)
unreachable
}