#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 printusage_build(char *program) {
  printf("Usage : %s <options> fastafile readlength(range) outdir outprefix\n",
         program);
  printf("\tex (SE, unstranded, readlength 76 bp) : %s Hsa.GRCh37.65.gtf.fa 76 "
         "rsh human.rna.fna.SE.l76\n",
         program);
  printf("\tex (SE, forward-stranded, readlength 50-60 bp) : %s -s ssf "
         "Hsa.GRCh37.65.gtf.fa 50-60 rsh human.rna.fna.SE.l50-60.ssf\n",
         program);
  printf("\tex (PE, unstranded, readlength 101 bp, fraglength range 1-400 bp, "
         "use 4 threads) : %s --PE -p 8 Hsa.GRCh37.65.gtf.fa 101 rsh "
         "human.rna.fna.PE.l101.F1-400\n",
         program);
  printf("\tex (PE, unstranded, readlength 101 bp, fraglength range 1-500 bp, "
         "Refseq format, use 8 threads) : %s --PE -h R -p 8 -F 500 "
         "human.rna.fna 101 rsh human.rna.fna.PE.l101.F1-500\n",
         program);
  printf("\tInput files\n\n");
  printf(
      "\t   fasta file : A transcriptome sequence library file in fasta "
      "format. The header can either be in Refseq format('>xx|xx|xx|name|xx') "
      "in which name or xx does not contain '|' letter, or in Ensembl format "
      "'>name' or '>name xx' in which name does not contain whitespace(space "
      "or tab) and xx is separated by whitespace from the name. Name must be a "
      "unique identifier of a sequence.\n\n");
  printf("\tOptions\n");
  printf("\t  -P, --PE : paired-end data (default : single-end)\n");
  printf("\t  -s, --strand_type <strand_type> : set strand type "
         "('ns','ssf','ssr' for single-end, 'ns','ssfr','ssrf' for "
         "paired-end). (default: ns(unstranded))\n");
  printf("\t  -p, --maxthread <num_thread>: number of threads to use "
         "simultaneously. Using multiple threads comes with a slight increase "
         "in memory usage. We recommend -p 4 for an optimal performance. "
         "(default : 1)\n");
  printf("\t  -F, --maxfraglen <Max_fraglen> : Maximum fragment length. Use a "
         "number that is safely large, unless you want to apply fragment "
         "length filtering. Default 400. Not applicable for SE.\n");
  printf("\t  -f, --minfraglen <Min_fraglen> : Minimum fragment length. Use a "
         "number that is safely small, unless you want to apply fragment "
         "length filtering. Default 1. Not applicable for SE\n");
  printf("\t  -h, --header <E|R> : fasta header option. E : Ensembl "
         "header(default), R : RefSeq header.\n");
  printf("\t  -k, --max_repeat <max_repeat> : the maximum number of alignments "
         "per read allowed. Reads exceeding this number are discarded.\n");
  printf("\t  -T, --print_sfa : print out (mate1) suffix array.\n");
  printf("\t  -v --verbose : make a (very) verbose output log.\n");
  printf("\t  -q --no_verbose : turn-off verbosity.\n\n");
  printf("\tAdvanced Options\n");
  printf("\t  -b, --binsize <binsize> : binsize for indexing transcriptome "
         "(default : 5000). This bin size can be made smaller to improve speed "
         "at the cost of more memory, or vise versa.\n");
  printf("\t  -t, --taglen <taglen> : length of short sequence tags to use for "
         "constructing suffix array on a subset of substrings only. This "
         "affects only speed and memory usage. Currently, three values are "
         "supported (1,2,3). (default 2)\n");
}


x86 assembly (clang, -O0):
<printusage_build>:
push   %rbp
mov    %rsp,%rbp
sub    $0x10,%rsp
mov    %rdi,-0x8(%rbp)
mov    -0x8(%rbp),%rsi
lea    0xed9(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
mov    -0x8(%rbp),%rsi
lea    0xf0a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
mov    -0x8(%rbp),%rsi
lea    0xf56(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
mov    -0x8(%rbp),%rsi
lea    0xfbc(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
mov    -0x8(%rbp),%rsi
lea    0x1046(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10e8(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10e9(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1259(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1255(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x127d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1305(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x13c3(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x146e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1516(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1566(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x15da(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1602(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1629(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1646(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x164b(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x16ee(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
add    $0x10,%rsp
pop    %rbp
ret

x86 assembly (clang, -O2):
<printusage_build>:
push   %rbx
mov    %rdi,%rbx
lea    0xed5(%rip),%rdi
mov    %rbx,%rsi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xf07(%rip),%rdi
mov    %rbx,%rsi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xf54(%rip),%rdi
mov    %rbx,%rsi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xfbb(%rip),%rdi
mov    %rbx,%rsi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0x1046(%rip),%rdi
mov    %rbx,%rsi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0x10e5(%rip),%rdi
call   1030 <puts@plt>
lea    0x10e7(%rip),%rdi
call   1030 <puts@plt>
lea    0x1258(%rip),%rdi
call   1030 <puts@plt>
lea    0x1255(%rip),%rdi
call   1030 <puts@plt>
lea    0x127e(%rip),%rdi
call   1030 <puts@plt>
lea    0x1307(%rip),%rdi
call   1030 <puts@plt>
lea    0x13c6(%rip),%rdi
call   1030 <puts@plt>
lea    0x1472(%rip),%rdi
call   1030 <puts@plt>
lea    0x151b(%rip),%rdi
call   1030 <puts@plt>
lea    0x156c(%rip),%rdi
call   1030 <puts@plt>
lea    0x15e1(%rip),%rdi
call   1030 <puts@plt>
lea    0x160a(%rip),%rdi
call   1030 <puts@plt>
lea    0x1632(%rip),%rdi
call   1030 <puts@plt>
lea    0x1650(%rip),%rdi
call   1030 <puts@plt>
lea    0x1656(%rip),%rdi
call   1030 <puts@plt>
lea    0x16fa(%rip),%rdi
pop    %rbx
jmp    1030 <puts@plt>

LLVM IR (-O0):
@.str = [67 x i8] c"Usage : %s <options> fastafile readlength(range) outdir outprefix\0A\00"
@.str.1 = [94 x i8] c"\09ex (SE, unstranded, readlength 76 bp) : %s Hsa.GRCh37.65.gtf.fa 76 rsh human.rna.fna.SE.l76\0A\00"
@.str.2 = [120 x i8] c"\09ex (SE, forward-stranded, readlength 50-60 bp) : %s -s ssf Hsa.GRCh37.65.gtf.fa 50-60 rsh human.rna.fna.SE.l50-60.ssf\0A\00"
@.str.3 = [156 x i8] c"\09ex (PE, unstranded, readlength 101 bp, fraglength range 1-400 bp, use 4 threads) : %s --PE -p 8 Hsa.GRCh37.65.gtf.fa 101 rsh human.rna.fna.PE.l101.F1-400\0A\00"
@.str.4 = [176 x i8] c"\09ex (PE, unstranded, readlength 101 bp, fraglength range 1-500 bp, Refseq format, use 8 threads) : %s --PE -h R -p 8 -F 500 human.rna.fna 101 rsh human.rna.fna.PE.l101.F1-500\0A\00"
@.str.5 = [15 x i8] c"\09Input files\0A\0A\00"
@.str.6 = [382 x i8] c"\09 fasta file : A transcriptome sequence library file in fasta format. The header can either be in Refseq format('>xx|xx|xx|name|xx') in which name or xx does not contain '|' letter, or in Ensembl format '>name' or '>name xx' in which name does not contain whitespace(space or tab) and xx is separated by whitespace from the name. Name must be a unique identifier of a sequence.\0A\0A\00"
@.str.7 = [10 x i8] c"\09Options\0A\00"
@.str.8 = [54 x i8] c"\09 -P, --PE : paired-end data (default : single-end)\0A\00"
@.str.9 = [150 x i8] c"\09 -s, --strand_type <strand_type> : set strand type ('ns','ssf','ssr' for single-end, 'ns','ssfr','ssrf' for paired-end). (default: ns(unstranded))\0A\00"
@.str.10 = [204 x i8] c"\09 -p, --maxthread <num_thread>: number of threads to use simultaneously. Using multiple threads comes with a slight increase in memory usage. We recommend -p 4 for an optimal performance. (default : 1)\0A\00"
@.str.11 = [185 x i8] c"\09 -F, --maxfraglen <Max_fraglen> : Maximum fragment length. Use a number that is safely large, unless you want to apply fragment length filtering. Default 400. Not applicable for SE.\0A\00"
@.str.12 = [182 x i8] c"\09 -f, --minfraglen <Min_fraglen> : Minimum fragment length. Use a number that is safely small, unless you want to apply fragment length filtering. Default 1. Not applicable for SE\0A\00"
@.str.13 = [94 x i8] c"\09 -h, --header <E|R> : fasta header option. E : Ensembl header(default), R : RefSeq header.\0A\00"
@.str.14 = [130 x i8] c"\09 -k, --max_repeat <max_repeat> : the maximum number of alignments per read allowed. Reads exceeding this number are discarded.\0A\00"
@.str.15 = [54 x i8] c"\09 -T, --print_sfa : print out (mate1) suffix array.\0A\00"
@.str.16 = [53 x i8] c"\09 -v --verbose : make a (very) verbose output log.\0A\00"
@.str.17 = [43 x i8] c"\09 -q --no_verbose : turn-off verbosity.\0A\0A\00"
@.str.18 = [19 x i8] c"\09Advanced Options\0A\00"
@.str.19 = [177 x i8] c"\09 -b, --binsize <binsize> : binsize for indexing transcriptome (default : 5000). This bin size can be made smaller to improve speed at the cost of more memory, or vise versa.\0A\00"
@.str.20 = [228 x i8] c"\09 -t, --taglen <taglen> : length of short sequence tags to use for constructing suffix array on a subset of substrings only. This affects only speed and memory usage. Currently, three values are supported (1,2,3). (default 2)\0A\00"
define void @printusage_build(i8* %0) {
%2 = alloca i8*
store i8* %0, i8** %2
%3 = load i8*, i8** %2
%4 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([67 x i8], [67 x i8]* @.str, i64 0, i64 0), i8* %3)
%5 = load i8*, i8** %2
%6 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([94 x i8], [94 x i8]* @.str.1, i64 0, i64 0), i8* %5)
%7 = load i8*, i8** %2
%8 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([120 x i8], [120 x i8]* @.str.2, i64 0, i64 0), i8* %7)
%9 = load i8*, i8** %2
%10 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([156 x i8], [156 x i8]* @.str.3, i64 0, i64 0), i8* %9)
%11 = load i8*, i8** %2
%12 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([176 x i8], [176 x i8]* @.str.4, i64 0, i64 0), i8* %11)
%13 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([15 x i8], [15 x i8]* @.str.5, i64 0, i64 0))
%14 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([382 x i8], [382 x i8]* @.str.6, i64 0, i64 0))
%15 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([10 x i8], [10 x i8]* @.str.7, i64 0, i64 0))
%16 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.8, i64 0, i64 0))
%17 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([150 x i8], [150 x i8]* @.str.9, i64 0, i64 0))
%18 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([204 x i8], [204 x i8]* @.str.10, i64 0, i64 0))
%19 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([185 x i8], [185 x i8]* @.str.11, i64 0, i64 0))
%20 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([182 x i8], [182 x i8]* @.str.12, i64 0, i64 0))
%21 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([94 x i8], [94 x i8]* @.str.13, i64 0, i64 0))
%22 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([130 x i8], [130 x i8]* @.str.14, i64 0, i64 0))
%23 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.15, i64 0, i64 0))
%24 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.16, i64 0, i64 0))
%25 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.17, i64 0, i64 0))
%26 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.18, i64 0, i64 0))
%27 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([177 x i8], [177 x i8]* @.str.19, i64 0, i64 0))
%28 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([228 x i8], [228 x i8]* @.str.20, i64 0, i64 0))
ret void
}

LLVM IR (-O2):
@.str = [67 x i8] c"Usage : %s <options> fastafile readlength(range) outdir outprefix\0A\00"
@.str.1 = [94 x i8] c"\09ex (SE, unstranded, readlength 76 bp) : %s Hsa.GRCh37.65.gtf.fa 76 rsh human.rna.fna.SE.l76\0A\00"
@.str.2 = [120 x i8] c"\09ex (SE, forward-stranded, readlength 50-60 bp) : %s -s ssf Hsa.GRCh37.65.gtf.fa 50-60 rsh human.rna.fna.SE.l50-60.ssf\0A\00"
@.str.3 = [156 x i8] c"\09ex (PE, unstranded, readlength 101 bp, fraglength range 1-400 bp, use 4 threads) : %s --PE -p 8 Hsa.GRCh37.65.gtf.fa 101 rsh human.rna.fna.PE.l101.F1-400\0A\00"
@.str.4 = [176 x i8] c"\09ex (PE, unstranded, readlength 101 bp, fraglength range 1-500 bp, Refseq format, use 8 threads) : %s --PE -h R -p 8 -F 500 human.rna.fna 101 rsh human.rna.fna.PE.l101.F1-500\0A\00"
@str = [14 x i8] c"\09Input files\0A\00"
@str.21 = [381 x i8] c"\09 fasta file : A transcriptome sequence library file in fasta format. The header can either be in Refseq format('>xx|xx|xx|name|xx') in which name or xx does not contain '|' letter, or in Ensembl format '>name' or '>name xx' in which name does not contain whitespace(space or tab) and xx is separated by whitespace from the name. Name must be a unique identifier of a sequence.\0A\00"
@str.22 = [9 x i8] c"\09Options\00"
@str.23 = [53 x i8] c"\09 -P, --PE : paired-end data (default : single-end)\00"
@str.24 = [149 x i8] c"\09 -s, --strand_type <strand_type> : set strand type ('ns','ssf','ssr' for single-end, 'ns','ssfr','ssrf' for paired-end). (default: ns(unstranded))\00"
@str.25 = [203 x i8] c"\09 -p, --maxthread <num_thread>: number of threads to use simultaneously. Using multiple threads comes with a slight increase in memory usage. We recommend -p 4 for an optimal performance. (default : 1)\00"
@str.26 = [184 x i8] c"\09 -F, --maxfraglen <Max_fraglen> : Maximum fragment length. Use a number that is safely large, unless you want to apply fragment length filtering. Default 400. Not applicable for SE.\00"
@str.27 = [181 x i8] c"\09 -f, --minfraglen <Min_fraglen> : Minimum fragment length. Use a number that is safely small, unless you want to apply fragment length filtering. Default 1. Not applicable for SE\00"
@str.28 = [93 x i8] c"\09 -h, --header <E|R> : fasta header option. E : Ensembl header(default), R : RefSeq header.\00"
@str.29 = [129 x i8] c"\09 -k, --max_repeat <max_repeat> : the maximum number of alignments per read allowed. Reads exceeding this number are discarded.\00"
@str.30 = [53 x i8] c"\09 -T, --print_sfa : print out (mate1) suffix array.\00"
@str.31 = [52 x i8] c"\09 -v --verbose : make a (very) verbose output log.\00"
@str.32 = [42 x i8] c"\09 -q --no_verbose : turn-off verbosity.\0A\00"
@str.33 = [18 x i8] c"\09Advanced Options\00"
@str.34 = [176 x i8] c"\09 -b, --binsize <binsize> : binsize for indexing transcriptome (default : 5000). This bin size can be made smaller to improve speed at the cost of more memory, or vise versa.\00"
@str.35 = [227 x i8] c"\09 -t, --taglen <taglen> : length of short sequence tags to use for constructing suffix array on a subset of substrings only. This affects only speed and memory usage. Currently, three values are supported (1,2,3). (default 2)\00"
define void @printusage_build(i8* %0) {
%2 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @.str, i64 0, i64 0), i8* %0)
%3 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([94 x i8], [94 x i8]* @.str.1, i64 0, i64 0), i8* %0)
%4 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([120 x i8], [120 x i8]* @.str.2, i64 0, i64 0), i8* %0)
%5 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([156 x i8], [156 x i8]* @.str.3, i64 0, i64 0), i8* %0)
%6 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([176 x i8], [176 x i8]* @.str.4, i64 0, i64 0), i8* %0)
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([14 x i8], [14 x i8]* @str, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([381 x i8], [381 x i8]* @str.21, i64 0, i64 0))
%9 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([9 x i8], [9 x i8]* @str.22, i64 0, i64 0))
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([53 x i8], [53 x i8]* @str.23, i64 0, i64 0))
%11 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([149 x i8], [149 x i8]* @str.24, i64 0, i64 0))
%12 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([203 x i8], [203 x i8]* @str.25, i64 0, i64 0))
%13 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([184 x i8], [184 x i8]* @str.26, i64 0, i64 0))
%14 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([181 x i8], [181 x i8]* @str.27, i64 0, i64 0))
%15 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([93 x i8], [93 x i8]* @str.28, i64 0, i64 0))
%16 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([129 x i8], [129 x i8]* @str.29, i64 0, i64 0))
%17 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([53 x i8], [53 x i8]* @str.30, i64 0, i64 0))
%18 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([52 x i8], [52 x i8]* @str.31, i64 0, i64 0))
%19 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([42 x i8], [42 x i8]* @str.32, i64 0, i64 0))
%20 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([18 x i8], [18 x i8]* @str.33, i64 0, i64 0))
%21 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([176 x i8], [176 x i8]* @str.34, i64 0, i64 0))
%22 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([227 x i8], [227 x i8]* @str.35, i64 0, i64 0))
ret void
}