#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 help(void) {
  printf("ma -M <maln input file>\n");
  printf("   -c <consensus code> \n");
  printf("   -f <output format>\n");
  printf("   -R <REGION_START:REGION_END>\n");
  printf("   -I <ID to assign to assembly sequence>\n");
  printf(
      "ma reports information from a maln assembly file as generated by mia\n");
  printf("How the assembly calls each base can be determined by the\n");
  printf(
      "consensus code. 1 = highest, positive aggregate score base (if any)\n");
  printf(
      "                2 = highest aggregate score base if it is %d higher\n",
      (2400));
  printf("                    than second highest\n");
  printf("The output format can be specified through -f as one of the "
         "following.\n");
  printf("More complete descriptions of these output formats is below,\n");
  printf("under FORMATS\n");
  printf("1 => clustalw\n");
  printf("2 => line format; one line each for consensus, reference\n");
  printf("     and coverage\n");
  printf("3 => column format; one line per base, one column for consensus,\n");
  printf("     reference, and coverage; includes header with summary info\n");
  printf("4 => columns description of all assembly data for positions that "
         "differ\n");
  printf("     between consensus and CURRENT reference sequence (see FORMATS, "
         "below)\n");
  printf("41 => same as above, but for ALL positions\n");
  printf("5 => fasta format output of assembled sequence only\n");
  printf("6 => show all fragments in a region specified by -R\n");
  printf(" -C Color format 6 output -> don't pipe this output to file!\n");
  printf("7 => ACE\n\n");
  printf("\nFORMATS (option f):\n");
  printf("1 => clustalw\n");
  printf("2 => line format; first line is \"Consensus, chrM, coverage:\"\n");
  printf("      second line is the entire, assembled, aligned consensus "
         "sequence\n");
  printf("      third line is the entire aligned reference sequence to which "
         "the\n");
  printf("      consensus is aligned\n");
  printf("      fourth line is the sequence coverage at each position in a "
         "space-\n");
  printf("      separated list of integers\n");
  printf("3 => column format; header shows summary statistics; table has one "
         "row\n");
  printf("      per position; columns are described in the output\n");
  printf("4 => alternative column format with one row per base that differes "
         "between\n");
  printf(
      "      the consensus assembly and the reference of this iteration. \n");
  printf("      Note that in the FINAL iteration reference and consensus are "
         "equal! \n");
  printf("      So there won't be any output. Each row has the following\n");
  printf("      columns: (1)position on reference; 0-based coordinates, (2) "
         "reference\n");
  printf("      base, (3)consensus assembly base, (4)coverage, (5)A's, (6)C's, "
         "(7)G's,\n");
  printf(
      "      (8)T's, (9)gaps; columns 5 through 9 should add up to column 4\n");
  printf("      (10) aggregate score for A, (11) aggregate score for C\n");
  printf("      (12) aggregate score for G, (13) aggregate score for T\n");
  printf("41=> same as above, but for every position\n");
  printf("5 => fasta format using ID \"Consensus\" for the assembly\n");
  printf("6 => region; shows the reference sequence, the consensus sequence, "
         "and then\n");
  printf("      all assembled fragments in a region specified by option -R\n");
  printf("61=> same as above, but in multi-fasta format for viewing in "
         "Bioedit, e.g.\n");
  printf("     (also requires a region as specified by the option -R\n");
  printf("7 => ACE format\n");
}


x86 assembly (clang, -O0):
<help>:
push   %rbp
mov    %rsp,%rbp
lea    0xee5(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xef0(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xefb(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf04(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf17(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf34(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf6c(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xf99(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfd0(%rip),%rdi
mov    $0x960,%esi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1002(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x101d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1057(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1087(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1088(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1089(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10b5(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10ba(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x10ee(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1121(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x115c(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x119a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x11b8(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x11df(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1206(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1236(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1233(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0xfd2(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x122d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x125d(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1297(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x12d1(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x12df(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x131a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x132e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1368(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1393(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x13d1(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1407(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1445(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1477(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x14b6(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x14f6(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x152e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x155e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x158e(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x15ac(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x15d7(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1616(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x164a(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x1688(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
lea    0x16b6(%rip),%rdi
mov    $0x0,%al
call   1030 <printf@plt>
pop    %rbp
ret

x86 assembly (clang, -O2):
<help>:
push   %rbx
lea    0xf1d(%rip),%rdi
call   1030 <puts@plt>
lea    0xf29(%rip),%rdi
call   1030 <puts@plt>
lea    0xf35(%rip),%rdi
call   1030 <puts@plt>
lea    0xf3f(%rip),%rdi
call   1030 <puts@plt>
lea    0xf53(%rip),%rdi
call   1030 <puts@plt>
lea    0xf71(%rip),%rdi
call   1030 <puts@plt>
lea    0xfaa(%rip),%rdi
call   1030 <puts@plt>
lea    0xfd8(%rip),%rdi
call   1030 <puts@plt>
lea    0xe78(%rip),%rdi
mov    $0x960,%esi
xor    %eax,%eax
call   1040 <printf@plt>
lea    0xffd(%rip),%rdi
call   1030 <puts@plt>
lea    0x1019(%rip),%rdi
call   1030 <puts@plt>
lea    0x1054(%rip),%rdi
call   1030 <puts@plt>
lea    0x1085(%rip),%rdi
call   1030 <puts@plt>
lea    0x12d5(%rip),%rbx
mov    %rbx,%rdi
call   1030 <puts@plt>
lea    0x1078(%rip),%rdi
call   1030 <puts@plt>
lea    0x10a5(%rip),%rdi
call   1030 <puts@plt>
lea    0x10ab(%rip),%rdi
call   1030 <puts@plt>
lea    0x10e0(%rip),%rdi
call   1030 <puts@plt>
lea    0x1114(%rip),%rdi
call   1030 <puts@plt>
lea    0x1150(%rip),%rdi
call   1030 <puts@plt>
lea    0x118f(%rip),%rdi
call   1030 <puts@plt>
lea    0x11ae(%rip),%rdi
call   1030 <puts@plt>
lea    0x11d6(%rip),%rdi
call   1030 <puts@plt>
lea    0x11fe(%rip),%rdi
call   1030 <puts@plt>
lea    0x122f(%rip),%rdi
call   1030 <puts@plt>
lea    0x122d(%rip),%rdi
call   1030 <puts@plt>
mov    %rbx,%rdi
call   1030 <puts@plt>
lea    0x123c(%rip),%rdi
call   1030 <puts@plt>
lea    0x126d(%rip),%rdi
call   1030 <puts@plt>
lea    0x12a8(%rip),%rdi
call   1030 <puts@plt>
lea    0x12e3(%rip),%rdi
call   1030 <puts@plt>
lea    0x12f2(%rip),%rdi
call   1030 <puts@plt>
lea    0x132e(%rip),%rdi
call   1030 <puts@plt>
lea    0x1343(%rip),%rdi
call   1030 <puts@plt>
lea    0x137e(%rip),%rdi
call   1030 <puts@plt>
lea    0x13aa(%rip),%rdi
call   1030 <puts@plt>
lea    0x13e9(%rip),%rdi
call   1030 <puts@plt>
lea    0x1420(%rip),%rdi
call   1030 <puts@plt>
lea    0x145f(%rip),%rdi
call   1030 <puts@plt>
lea    0x1492(%rip),%rdi
call   1030 <puts@plt>
lea    0x14d2(%rip),%rdi
call   1030 <puts@plt>
lea    0x1513(%rip),%rdi
call   1030 <puts@plt>
lea    0x154c(%rip),%rdi
call   1030 <puts@plt>
lea    0x157d(%rip),%rdi
call   1030 <puts@plt>
lea    0x15ae(%rip),%rdi
call   1030 <puts@plt>
lea    0x15cd(%rip),%rdi
call   1030 <puts@plt>
lea    0x15f9(%rip),%rdi
call   1030 <puts@plt>
lea    0x1639(%rip),%rdi
call   1030 <puts@plt>
lea    0x166e(%rip),%rdi
call   1030 <puts@plt>
lea    0x16ad(%rip),%rdi
call   1030 <puts@plt>
lea    0x16dc(%rip),%rdi
pop    %rbx
jmp    1030 <puts@plt>

LLVM IR (-O0):
@.str = [25 x i8] c"ma -M <maln input file>\0A\00"
@.str.1 = [25 x i8] c" -c <consensus code> \0A\00"
@.str.2 = [23 x i8] c" -f <output format>\0A\00"
@.str.3 = [33 x i8] c" -R <REGION_START:REGION_END>\0A\00"
@.str.4 = [43 x i8] c" -I <ID to assign to assembly sequence>\0A\00"
@.str.5 = [70 x i8] c"ma reports information from a maln assembly file as generated by mia\0A\00"
@.str.6 = [59 x i8] c"How the assembly calls each base can be determined by the\0A\00"
@.str.7 = [69 x i8] c"consensus code. 1 = highest, positive aggregate score base (if any)\0A\00"
@.str.8 = [69 x i8] c" 2 = highest aggregate score base if it is %d higher\0A\00"
@.str.9 = [41 x i8] c" than second highest\0A\00"
@.str.10 = [72 x i8] c"The output format can be specified through -f as one of the following.\0A\00"
@.str.11 = [62 x i8] c"More complete descriptions of these output formats is below,\0A\00"
@.str.12 = [15 x i8] c"under FORMATS\0A\00"
@.str.13 = [15 x i8] c"1 => clustalw\0A\00"
@.str.14 = [58 x i8] c"2 => line format; one line each for consensus, reference\0A\00"
@.str.15 = [19 x i8] c" and coverage\0A\00"
@.str.16 = [66 x i8] c"3 => column format; one line per base, one column for consensus,\0A\00"
@.str.17 = [65 x i8] c" reference, and coverage; includes header with summary info\0A\00"
@.str.18 = [73 x i8] c"4 => columns description of all assembly data for positions that differ\0A\00"
@.str.19 = [76 x i8] c" between consensus and CURRENT reference sequence (see FORMATS, below)\0A\00"
@.str.20 = [44 x i8] c"41 => same as above, but for ALL positions\0A\00"
@.str.21 = [53 x i8] c"5 => fasta format output of assembled sequence only\0A\00"
@.str.22 = [53 x i8] c"6 => show all fragments in a region specified by -R\0A\00"
@.str.23 = [62 x i8] c" -C Color format 6 output -> don't pipe this output to file!\0A\00"
@.str.24 = [11 x i8] c"7 => ACE\0A\0A\00"
@.str.25 = [22 x i8] c"\0AFORMATS (option f):\0A\00"
@.str.26 = [62 x i8] c"2 => line format; first line is \22Consensus, chrM, coverage:\22\0A\00"
@.str.27 = [72 x i8] c" second line is the entire, assembled, aligned consensus sequence\0A\00"
@.str.28 = [72 x i8] c" third line is the entire aligned reference sequence to which the\0A\00"
@.str.29 = [28 x i8] c" consensus is aligned\0A\00"
@.str.30 = [73 x i8] c" fourth line is the sequence coverage at each position in a space-\0A\00"
@.str.31 = [34 x i8] c" separated list of integers\0A\00"
@.str.32 = [72 x i8] c"3 => column format; header shows summary statistics; table has one row\0A\00"
@.str.33 = [57 x i8] c" per position; columns are described in the output\0A\00"
@.str.34 = [76 x i8] c"4 => alternative column format with one row per base that differes between\0A\00"
@.str.35 = [68 x i8] c" the consensus assembly and the reference of this iteration. \0A\00"
@.str.36 = [76 x i8] c" Note that in the FINAL iteration reference and consensus are equal! \0A\00"
@.str.37 = [64 x i8] c" So there won't be any output. Each row has the following\0A\00"
@.str.38 = [77 x i8] c" columns: (1)position on reference; 0-based coordinates, (2) reference\0A\00"
@.str.39 = [78 x i8] c" base, (3)consensus assembly base, (4)coverage, (5)A's, (6)C's, (7)G's,\0A\00"
@.str.40 = [70 x i8] c" (8)T's, (9)gaps; columns 5 through 9 should add up to column 4\0A\00"
@.str.41 = [62 x i8] c" (10) aggregate score for A, (11) aggregate score for C\0A\00"
@.str.42 = [62 x i8] c" (12) aggregate score for G, (13) aggregate score for T\0A\00"
@.str.43 = [44 x i8] c"41=> same as above, but for every position\0A\00"
@.str.44 = [57 x i8] c"5 => fasta format using ID \22Consensus\22 for the assembly\0A\00"
@.str.45 = [77 x i8] c"6 => region; shows the reference sequence, the consensus sequence, and then\0A\00"
@.str.46 = [66 x i8] c" all assembled fragments in a region specified by option -R\0A\00"
@.str.47 = [76 x i8] c"61=> same as above, but in multi-fasta format for viewing in Bioedit, e.g.\0A\00"
@.str.48 = [60 x i8] c" (also requires a region as specified by the option -R\0A\00"
@.str.49 = [17 x i8] c"7 => ACE format\0A\00"
define void @help() {
%1 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([25 x i8], [25 x i8]* @.str, i64 0, i64 0))
%2 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([25 x i8], [25 x i8]* @.str.1, i64 0, i64 0))
%3 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([23 x i8], [23 x i8]* @.str.2, i64 0, i64 0))
%4 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([33 x i8], [33 x i8]* @.str.3, i64 0, i64 0))
%5 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.4, i64 0, i64 0))
%6 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([70 x i8], [70 x i8]* @.str.5, i64 0, i64 0))
%7 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([59 x i8], [59 x i8]* @.str.6, i64 0, i64 0))
%8 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([69 x i8], [69 x i8]* @.str.7, i64 0, i64 0))
%9 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([69 x i8], [69 x i8]* @.str.8, i64 0, i64 0), i32 2400)
%10 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([41 x i8], [41 x i8]* @.str.9, i64 0, i64 0))
%11 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.10, i64 0, i64 0))
%12 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.11, i64 0, i64 0))
%13 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([15 x i8], [15 x i8]* @.str.12, i64 0, i64 0))
%14 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([15 x i8], [15 x i8]* @.str.13, i64 0, i64 0))
%15 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([58 x i8], [58 x i8]* @.str.14, i64 0, i64 0))
%16 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.15, i64 0, i64 0))
%17 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([66 x i8], [66 x i8]* @.str.16, i64 0, i64 0))
%18 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([65 x i8], [65 x i8]* @.str.17, i64 0, i64 0))
%19 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([73 x i8], [73 x i8]* @.str.18, i64 0, i64 0))
%20 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([76 x i8], [76 x i8]* @.str.19, i64 0, i64 0))
%21 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.20, i64 0, i64 0))
%22 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.21, i64 0, i64 0))
%23 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([53 x i8], [53 x i8]* @.str.22, i64 0, i64 0))
%24 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.23, i64 0, i64 0))
%25 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.24, i64 0, i64 0))
%26 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([22 x i8], [22 x i8]* @.str.25, i64 0, i64 0))
%27 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([15 x i8], [15 x i8]* @.str.13, i64 0, i64 0))
%28 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.26, i64 0, i64 0))
%29 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.27, i64 0, i64 0))
%30 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.28, i64 0, i64 0))
%31 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([28 x i8], [28 x i8]* @.str.29, i64 0, i64 0))
%32 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([73 x i8], [73 x i8]* @.str.30, i64 0, i64 0))
%33 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([34 x i8], [34 x i8]* @.str.31, i64 0, i64 0))
%34 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.32, i64 0, i64 0))
%35 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([57 x i8], [57 x i8]* @.str.33, i64 0, i64 0))
%36 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([76 x i8], [76 x i8]* @.str.34, i64 0, i64 0))
%37 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.35, i64 0, i64 0))
%38 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([76 x i8], [76 x i8]* @.str.36, i64 0, i64 0))
%39 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([64 x i8], [64 x i8]* @.str.37, i64 0, i64 0))
%40 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([77 x i8], [77 x i8]* @.str.38, i64 0, i64 0))
%41 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([78 x i8], [78 x i8]* @.str.39, i64 0, i64 0))
%42 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([70 x i8], [70 x i8]* @.str.40, i64 0, i64 0))
%43 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.41, i64 0, i64 0))
%44 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([62 x i8], [62 x i8]* @.str.42, i64 0, i64 0))
%45 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.43, i64 0, i64 0))
%46 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([57 x i8], [57 x i8]* @.str.44, i64 0, i64 0))
%47 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([77 x i8], [77 x i8]* @.str.45, i64 0, i64 0))
%48 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([66 x i8], [66 x i8]* @.str.46, i64 0, i64 0))
%49 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([76 x i8], [76 x i8]* @.str.47, i64 0, i64 0))
%50 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([60 x i8], [60 x i8]* @.str.48, i64 0, i64 0))
%51 = call i32 (i8*, ...) @printf(i8* getelementptr inbounds ([17 x i8], [17 x i8]* @.str.49, i64 0, i64 0))
ret void
}

LLVM IR (-O2):
@.str.8 = [69 x i8] c" 2 = highest aggregate score base if it is %d higher\0A\00"
@str = [24 x i8] c"ma -M <maln input file>\00"
@str.50 = [24 x i8] c" -c <consensus code> \00"
@str.51 = [22 x i8] c" -f <output format>\00"
@str.52 = [32 x i8] c" -R <REGION_START:REGION_END>\00"
@str.53 = [42 x i8] c" -I <ID to assign to assembly sequence>\00"
@str.54 = [69 x i8] c"ma reports information from a maln assembly file as generated by mia\00"
@str.55 = [58 x i8] c"How the assembly calls each base can be determined by the\00"
@str.56 = [68 x i8] c"consensus code. 1 = highest, positive aggregate score base (if any)\00"
@str.57 = [40 x i8] c" than second highest\00"
@str.58 = [71 x i8] c"The output format can be specified through -f as one of the following.\00"
@str.59 = [61 x i8] c"More complete descriptions of these output formats is below,\00"
@str.60 = [14 x i8] c"under FORMATS\00"
@str.62 = [57 x i8] c"2 => line format; one line each for consensus, reference\00"
@str.63 = [18 x i8] c" and coverage\00"
@str.64 = [65 x i8] c"3 => column format; one line per base, one column for consensus,\00"
@str.65 = [64 x i8] c" reference, and coverage; includes header with summary info\00"
@str.66 = [72 x i8] c"4 => columns description of all assembly data for positions that differ\00"
@str.67 = [75 x i8] c" between consensus and CURRENT reference sequence (see FORMATS, below)\00"
@str.68 = [43 x i8] c"41 => same as above, but for ALL positions\00"
@str.69 = [52 x i8] c"5 => fasta format output of assembled sequence only\00"
@str.70 = [52 x i8] c"6 => show all fragments in a region specified by -R\00"
@str.71 = [61 x i8] c" -C Color format 6 output -> don't pipe this output to file!\00"
@str.72 = [10 x i8] c"7 => ACE\0A\00"
@str.73 = [21 x i8] c"\0AFORMATS (option f):\00"
@str.74 = [14 x i8] c"1 => clustalw\00"
@str.75 = [61 x i8] c"2 => line format; first line is \22Consensus, chrM, coverage:\22\00"
@str.76 = [71 x i8] c" second line is the entire, assembled, aligned consensus sequence\00"
@str.77 = [71 x i8] c" third line is the entire aligned reference sequence to which the\00"
@str.78 = [27 x i8] c" consensus is aligned\00"
@str.79 = [72 x i8] c" fourth line is the sequence coverage at each position in a space-\00"
@str.80 = [33 x i8] c" separated list of integers\00"
@str.81 = [71 x i8] c"3 => column format; header shows summary statistics; table has one row\00"
@str.82 = [56 x i8] c" per position; columns are described in the output\00"
@str.83 = [75 x i8] c"4 => alternative column format with one row per base that differes between\00"
@str.84 = [67 x i8] c" the consensus assembly and the reference of this iteration. \00"
@str.85 = [75 x i8] c" Note that in the FINAL iteration reference and consensus are equal! \00"
@str.86 = [63 x i8] c" So there won't be any output. Each row has the following\00"
@str.87 = [76 x i8] c" columns: (1)position on reference; 0-based coordinates, (2) reference\00"
@str.88 = [77 x i8] c" base, (3)consensus assembly base, (4)coverage, (5)A's, (6)C's, (7)G's,\00"
@str.89 = [69 x i8] c" (8)T's, (9)gaps; columns 5 through 9 should add up to column 4\00"
@str.90 = [61 x i8] c" (10) aggregate score for A, (11) aggregate score for C\00"
@str.91 = [61 x i8] c" (12) aggregate score for G, (13) aggregate score for T\00"
@str.92 = [43 x i8] c"41=> same as above, but for every position\00"
@str.93 = [56 x i8] c"5 => fasta format using ID \22Consensus\22 for the assembly\00"
@str.94 = [76 x i8] c"6 => region; shows the reference sequence, the consensus sequence, and then\00"
@str.95 = [65 x i8] c" all assembled fragments in a region specified by option -R\00"
@str.96 = [75 x i8] c"61=> same as above, but in multi-fasta format for viewing in Bioedit, e.g.\00"
@str.97 = [59 x i8] c" (also requires a region as specified by the option -R\00"
@str.98 = [16 x i8] c"7 => ACE format\00"
define void @help() {
%1 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([24 x i8], [24 x i8]* @str, i64 0, i64 0))
%2 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([24 x i8], [24 x i8]* @str.50, i64 0, i64 0))
%3 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([22 x i8], [22 x i8]* @str.51, i64 0, i64 0))
%4 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([32 x i8], [32 x i8]* @str.52, i64 0, i64 0))
%5 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([42 x i8], [42 x i8]* @str.53, i64 0, i64 0))
%6 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([69 x i8], [69 x i8]* @str.54, i64 0, i64 0))
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([58 x i8], [58 x i8]* @str.55, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([68 x i8], [68 x i8]* @str.56, i64 0, i64 0))
%9 = tail call i32 (i8*, ...) @printf(i8* dereferenceable(1) getelementptr inbounds ([69 x i8], [69 x i8]* @.str.8, i64 0, i64 0), i32 2400)
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([40 x i8], [40 x i8]* @str.57, i64 0, i64 0))
%11 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.58, i64 0, i64 0))
%12 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.59, i64 0, i64 0))
%13 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([14 x i8], [14 x i8]* @str.60, i64 0, i64 0))
%14 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([14 x i8], [14 x i8]* @str.74, i64 0, i64 0))
%15 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([57 x i8], [57 x i8]* @str.62, i64 0, i64 0))
%16 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([18 x i8], [18 x i8]* @str.63, i64 0, i64 0))
%17 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([65 x i8], [65 x i8]* @str.64, i64 0, i64 0))
%18 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([64 x i8], [64 x i8]* @str.65, i64 0, i64 0))
%19 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([72 x i8], [72 x i8]* @str.66, i64 0, i64 0))
%20 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([75 x i8], [75 x i8]* @str.67, i64 0, i64 0))
%21 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([43 x i8], [43 x i8]* @str.68, i64 0, i64 0))
%22 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([52 x i8], [52 x i8]* @str.69, i64 0, i64 0))
%23 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([52 x i8], [52 x i8]* @str.70, i64 0, i64 0))
%24 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.71, i64 0, i64 0))
%25 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([10 x i8], [10 x i8]* @str.72, i64 0, i64 0))
%26 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([21 x i8], [21 x i8]* @str.73, i64 0, i64 0))
%27 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([14 x i8], [14 x i8]* @str.74, i64 0, i64 0))
%28 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.75, i64 0, i64 0))
%29 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.76, i64 0, i64 0))
%30 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.77, i64 0, i64 0))
%31 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([27 x i8], [27 x i8]* @str.78, i64 0, i64 0))
%32 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([72 x i8], [72 x i8]* @str.79, i64 0, i64 0))
%33 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([33 x i8], [33 x i8]* @str.80, i64 0, i64 0))
%34 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.81, i64 0, i64 0))
%35 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([56 x i8], [56 x i8]* @str.82, i64 0, i64 0))
%36 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([75 x i8], [75 x i8]* @str.83, i64 0, i64 0))
%37 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.84, i64 0, i64 0))
%38 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([75 x i8], [75 x i8]* @str.85, i64 0, i64 0))
%39 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([63 x i8], [63 x i8]* @str.86, i64 0, i64 0))
%40 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([76 x i8], [76 x i8]* @str.87, i64 0, i64 0))
%41 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([77 x i8], [77 x i8]* @str.88, i64 0, i64 0))
%42 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([69 x i8], [69 x i8]* @str.89, i64 0, i64 0))
%43 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.90, i64 0, i64 0))
%44 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([61 x i8], [61 x i8]* @str.91, i64 0, i64 0))
%45 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([43 x i8], [43 x i8]* @str.92, i64 0, i64 0))
%46 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([56 x i8], [56 x i8]* @str.93, i64 0, i64 0))
%47 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([76 x i8], [76 x i8]* @str.94, i64 0, i64 0))
%48 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([65 x i8], [65 x i8]* @str.95, i64 0, i64 0))
%49 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([75 x i8], [75 x i8]* @str.96, i64 0, i64 0))
%50 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([59 x i8], [59 x i8]* @str.97, i64 0, i64 0))
%51 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([16 x i8], [16 x i8]* @str.98, i64 0, i64 0))
ret void
}