// File: /workspace/github_c_makefile_star2_O1/c-zhou[P]yahs/yahs.c
// Function: print_help
static void print_help(FILE *fp_help, int is_long_help)
{
    fprintf(fp_help, "Usage: yahs [options] <contigs.fa> <hic.bed>|<hic.bam>|<hic.pa5>|<hic.bin>\n");
    fprintf(fp_help, "Options:\n");
    fprintf(fp_help, "    -a FILE                AGP file (for rescaffolding) [none]\n");
    fprintf(fp_help, "    -r INT[,INT,...]       list of resolutions in ascending order [automate]\n");
    fprintf(fp_help, "    -R INT                 rounds to run at each resoultion level [1]\n");
    fprintf(fp_help, "    -e STR                 restriction enzyme cutting sites [none]\n");
    fprintf(fp_help, "    -l INT                 minimum length of a contig to scaffold [0]\n");
    fprintf(fp_help, "    -q INT                 minimum mapping quality [10]\n");
    fprintf(fp_help, "\n");
    fprintf(fp_help, "    --no-contig-ec         do not do contig error correction\n");
    fprintf(fp_help, "    --no-scaffold-ec       do not do scaffold error correction\n");
    fprintf(fp_help, "    --no-mem-check         do not do memory check at runtime\n");
    fprintf(fp_help, "    --file-type   STR      input file type BED|BAM|PA5|BIN, file name extension is ignored if set\n");
    fprintf(fp_help, "    --read-length          read length (required for PA5 format input) [150]\n");
    fprintf(fp_help, "    --telo-motif  STR      telomeric sequence motif\n");
    if (is_long_help) {
        fprintf(fp_help, "\n");
        fprintf(fp_help, "    --D-min-cells INT      minimum number of cells to calculate the distance threshold [30]\n");
        fprintf(fp_help, "    --D-mass-frac FLOAT    fraction of HiC signals to calculate the distance threshold [0.99]\n");
        fprintf(fp_help, "\n");
        fprintf(fp_help, "    --seq-ctype   STR      AGP output sequence component type [%s]\n", agp_component_type_val(DEFAULT_AGP_SEQ_COMPONENT_TYPE));
        fprintf(fp_help, "    --gap-ctype   STR      AGP output gap component type [%s]\n", agp_component_type_val(DEFAULT_AGP_GAP_COMPONENT_TYPE));
        fprintf(fp_help, "    --gap-link    STR      AGP output gap linkage evidence [%s]\n", agp_linkage_evidence_val(DEFAULT_AGP_LINKAGE_EVIDENCE));
        fprintf(fp_help, "    --gap-size    INT      AGP output gap size between sequence component [%d]\n", DEFAULT_AGP_GAP_SIZE);
        fprintf(fp_help, "\n");
        fprintf(fp_help, "    --convert-to-binary    make a binary ouput file from the input and exit\n");
        fprintf(fp_help, "    --print-telo-motifs    print telomeric motifs in the database and exit\n");
        fprintf(fp_help, "    --search-telo-ends     search telomeric ends in the sequences and exit\n");
    }
    fprintf(fp_help, "\n");
    fprintf(fp_help, "    -o STR                 prefix of output files [yahs.out]\n");
    fprintf(fp_help, "    -v INT                 verbose level [%d]\n", VERBOSE);
    fprintf(fp_help, "    -?                     print long help with extra option list\n");
    fprintf(fp_help, "    --version              show version number\n");
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %esi, %ebp
movq %rdi, %rbx
leaq 0x3d23(%rip), %rdi      # 0x241b0
movl $0x4b, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3d56(%rip), %rdi      # 0x241fc
movl $0x9, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3d47(%rip), %rdi      # 0x24206
movl $0x3f, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3d6e(%rip), %rdi      # 0x24246
movl $0x4d, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3da3(%rip), %rdi      # 0x24294
movl $0x46, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3dd1(%rip), %rdi      # 0x242db
movl $0x43, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3dfc(%rip), %rdi      # 0x2431f
movl $0x46, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3e2a(%rip), %rdi      # 0x24366
movl $0x38, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
movl $0xa, %edi
movq %rbx, %rsi
callq 0x2260
leaq 0x3e3d(%rip), %rdi      # 0x2439f
movl $0x3d, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3e62(%rip), %rdi      # 0x243dd
movl $0x3f, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3e89(%rip), %rdi      # 0x2441d
movl $0x3d, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3eae(%rip), %rdi      # 0x2445b
movl $0x62, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3ef8(%rip), %rdi      # 0x244be
movl $0x4d, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3f2d(%rip), %rdi      # 0x2450c
movl $0x34, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
testl %ebp, %ebp
je 0x2090f
movl $0xa, %edi
movq %rbx, %rsi
callq 0x2260
leaq 0x3f34(%rip), %rdi      # 0x24541
movl $0x5c, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3f78(%rip), %rdi      # 0x2459e
movl $0x5e, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
movl $0xa, %edi
movq %rbx, %rsi
callq 0x2260
leaq 0xac94(%rip), %rax      # 0x2b2e0
movl (%rax), %eax
leaq 0x1bbf(%rip), %r14      # 0x22214
leal -0x2b609(%rax), %ecx
cmpl $0x13, %ecx
ja 0x20679
leaq 0x2db1(%rip), %rdx      # 0x23418
movslq (%rdx,%rcx,4), %rcx
addq %rdx, %rcx
jmpq *%rcx
leaq 0x33e7(%rip), %rdx      # 0x23a5e
jmp 0x206d5
movq %r14, %rdx
cmpl $0x2b606, %eax          # imm = 0x2B606
je 0x206d5
leaq 0x1fa4(%rip), %rdi      # 0x2262e
leaq 0x1fc7(%rip), %rsi      # 0x22658
movl %eax, %edx
jmp 0x20990
leaq 0x1b7b(%rip), %rdx      # 0x2221a
jmp 0x206d5
leaq 0x1922(%rip), %rdx      # 0x21fca
jmp 0x206d5
leaq 0x1b65(%rip), %rdx      # 0x22216
jmp 0x206d5
leaq 0x33ac(%rip), %rdx      # 0x23a66
jmp 0x206d5
leaq 0x1b55(%rip), %rdx      # 0x22218
jmp 0x206d5
leaq 0xa59(%rip), %rdx       # 0x21125
jmp 0x206d5
leaq 0x2ba3(%rip), %rdx      # 0x23278
leaq 0x3f21(%rip), %rsi      # 0x245fd
movq %rbx, %rdi
xorl %eax, %eax
callq 0x22c0
leaq 0xabf7(%rip), %rax      # 0x2b2e4
movl (%rax), %edx
leal -0x2b609(%rdx), %eax
cmpl $0x13, %eax
ja 0x20713
leaq 0x2d67(%rip), %rcx      # 0x23468
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
jmpq *%rax
leaq 0x334d(%rip), %r14      # 0x23a5e
jmp 0x2076b
cmpl $0x2b606, %edx          # imm = 0x2B606
je 0x2076b
leaq 0x1f0c(%rip), %rdi      # 0x2262e
leaq 0x1f2f(%rip), %rsi      # 0x22658
jmp 0x20990
leaq 0x1ae5(%rip), %r14      # 0x2221a
jmp 0x2076b
leaq 0x188c(%rip), %r14      # 0x21fca
jmp 0x2076b
leaq 0x1acf(%rip), %r14      # 0x22216
jmp 0x2076b
leaq 0x3316(%rip), %r14      # 0x23a66
jmp 0x2076b
leaq 0x1abf(%rip), %r14      # 0x22218
jmp 0x2076b
leaq 0x9c3(%rip), %r14       # 0x21125
jmp 0x2076b
leaq 0x2b0d(%rip), %r14      # 0x23278
leaq 0x3ecf(%rip), %rsi      # 0x24641
movq %rbx, %rdi
movq %r14, %rdx
xorl %eax, %eax
callq 0x22c0
leaq 0xab66(%rip), %rax      # 0x2b2ec
movl (%rax), %edx
cmpl $0xb888f82, %edx        # imm = 0xB888F82
jg 0x207c8
cmpl $0xe2eecd08, %edx       # imm = 0xE2EECD08
jg 0x207fc
cmpl $0x995556b4, %edx       # imm = 0x995556B4
je 0x20846
cmpl $0xb57b3070, %edx       # imm = 0xB57B3070
je 0x2086a
cmpl $0xd37e4828, %edx       # imm = 0xD37E4828
jne 0x20982
leaq 0x1c2c(%rip), %rdx      # 0x223ef
jmp 0x2088c
cmpl $0x13baa0b0, %edx       # imm = 0x13BAA0B0
jg 0x20821
cmpl $0xb888f83, %edx        # imm = 0xB888F83
je 0x2084f
cmpl $0xb889c8a, %edx        # imm = 0xB889C8A
je 0x20873
cmpl $0xdc4ffd9, %edx        # imm = 0xDC4FFD9
jne 0x20982
leaq 0x1c05(%rip), %rdx      # 0x223fc
jmp 0x2088c
cmpl $0xe2eecd09, %edx       # imm = 0xE2EECD09
je 0x20858
cmpl $0xf627ffb1, %edx       # imm = 0xF627FFB1
je 0x2087c
cmpl $0x5978d4, %edx         # imm = 0x5978D4
jne 0x20982
leaq 0x185b(%rip), %rdx      # 0x2207a
jmp 0x2088c
cmpl $0x272d87fd, %edx       # imm = 0x272D87FD
je 0x20861
cmpl $0x1c93c7f4, %edx       # imm = 0x1C93C7F4
je 0x20885
cmpl $0x13baa0b1, %edx       # imm = 0x13BAA0B1
jne 0x20982
leaq 0x1b78(%rip), %rdx      # 0x223bc
jmp 0x2088c
leaq 0x1bde(%rip), %rdx      # 0x2242b
jmp 0x2088c
leaq 0x1bb3(%rip), %rdx      # 0x22409
jmp 0x2088c
leaq 0x1b75(%rip), %rdx      # 0x223d4
jmp 0x2088c
leaq 0x1b79(%rip), %rdx      # 0x223e1
jmp 0x2088c
leaq 0x1ba0(%rip), %rdx      # 0x22411
jmp 0x2088c
leaq 0x1b93(%rip), %rdx      # 0x2240d
jmp 0x2088c
leaq 0x1b45(%rip), %rdx      # 0x223c8
jmp 0x2088c
leaq 0x1b98(%rip), %rdx      # 0x22424
leaq 0x3ded(%rip), %rsi      # 0x24680
movq %rbx, %rdi
xorl %eax, %eax
callq 0x22c0
leaq 0xaa4c(%rip), %rax      # 0x2b2f0
movl (%rax), %edx
leaq 0x3e14(%rip), %rsi      # 0x246c1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x22c0
movl $0xa, %edi
movq %rbx, %rsi
callq 0x2260
leaq 0x3e46(%rip), %rdi      # 0x24711
movl $0x4c, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3e7a(%rip), %rdi      # 0x2475e
movl $0x4b, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3ead(%rip), %rdi      # 0x247aa
movl $0x4b, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
movl $0xa, %edi
movq %rbx, %rsi
callq 0x2260
leaq 0x3ed3(%rip), %rdi      # 0x247f6
movl $0x3d, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
movl 0xace5(%rip), %edx      # 0x2b620
leaq 0x3ef2(%rip), %rsi      # 0x24834
movq %rbx, %rdi
xorl %eax, %eax
callq 0x22c0
leaq 0x3f10(%rip), %rdi      # 0x24863
movl $0x42, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x24d0
leaq 0x3f3a(%rip), %rdi      # 0x248a6
movl $0x2f, %esi
movl $0x1, %edx
movq %rbx, %rcx
popq %rbx
popq %r14
popq %rbp
jmp 0x24d0
leaq 0x1c2e(%rip), %rdi      # 0x225b7
leaq 0x1c53(%rip), %rsi      # 0x225e3
xorl %eax, %eax
callq 0x20ce6