// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_seqorder.c
// Function: gt_seqorder_runner
static int gt_seqorder_runner(GT_UNUSED int argc,
                              const char **argv,
                              int parsed_args,
                              void *tool_arguments,
                              GtError *err)
{
  GtSeqorderArguments *arguments = tool_arguments;
  int had_err = 0;
  GtEncseq *encseq;
  GtEncseqLoader *loader;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  /* load encseq */
  loader = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(loader, argv[parsed_args], err);
  gt_encseq_loader_delete(loader);
  if (encseq == NULL)
  {
    had_err = -1;
  }
  if (had_err == 0 && !gt_encseq_has_description_support(encseq))
  {
    gt_warning("%s has no description support", argv[parsed_args]);
  }
  if (!had_err)
  {
    gt_seqorder_handle_cases(encseq,arguments);
  }
  gt_encseq_delete(encseq);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r8, %rbx
movq %rcx, %r15
movl %edx, %ebp
movq %rsi, %r14
testq %r8, %r8
je 0xc5efc
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xc629f
testq %r15, %r15
je 0xc629a
callq 0xf36ef
movq %rax, %r12
movslq %ebp, %r13
movq (%r14,%r13,8), %rsi
movq %rax, %rdi
movq %rbx, %rdx
callq 0xf374b
movq %rax, %rbx
movq %r12, %rdi
callq 0xf424d
testq %rbx, %rbx
je 0xc6156
movq %rbx, %rdi
callq 0xf0b65
testb %al, %al
jne 0xc5f51
movq (%r14,%r13,8), %rsi
leaq 0x29bdbb(%rip), %rdi    # 0x361d05
xorl %eax, %eax
callq 0x125448
movq %rbx, %rdi
callq 0xec1e8
movq %rax, %r14
cmpb $0x1, (%r15)
jne 0xc5f84
testq %r14, %r14
je 0xc6156
decq %r14
movq %r14, %rdi
movq %rbx, %rsi
callq 0xc62b3
addq $-0x1, %r14
jb 0xc5f6e
jmp 0xc6156
cmpb $0x0, 0x3(%r15)
jne 0xc5fa4
cmpb $0x0, 0x4(%r15)
jne 0xc5fa4
cmpb $0x0, 0x5(%r15)
jne 0xc5fa4
cmpb $0x1, 0x6(%r15)
jne 0xc6177
movq %rbx, %rdi
callq 0xec1e8
movq %rax, %r13
leaq (,%r14,8), %rdi
leaq 0x29bae2(%rip), %rsi    # 0x361aa0
movl $0x129, %edx            # imm = 0x129
callq 0x1092b2
movq %rax, %r12
cmpb $0x0, 0x3(%r15)
je 0xc6014
testq %r12, %r12
je 0xc62a4
movq $0x0, (%r12)
cmpq $0x2, %r14
jb 0xc6126
movl $0x1, %r15d
movq %r15, %rdi
callq 0x10ae3c
movq (%r12,%rax,8), %rcx
movq %rcx, (%r12,%r15,8)
movq %r15, (%r12,%rax,8)
incq %r15
cmpq %r15, %r14
jne 0xc5ff3
jmp 0xc6126
testq %r13, %r13
je 0xc60ae
leaq 0x1(%r13), %rax
andq $-0x2, %rax
leaq -0x1(%r13), %rcx
movq %rcx, %xmm0
pshufd $0x44, %xmm0, %xmm0     # xmm0 = xmm0[0,1,0,1]
movdqa 0x29ba35(%rip), %xmm1   # 0x361a70
xorl %ecx, %ecx
movdqa 0x29ba3b(%rip), %xmm2   # 0x361a80
pxor %xmm2, %xmm0
pcmpeqd %xmm3, %xmm3
movdqa 0x29ba3b(%rip), %xmm4   # 0x361a90
movdqa %xmm1, %xmm5
pxor %xmm2, %xmm5
movdqa %xmm5, %xmm6
pcmpgtd %xmm0, %xmm6
pcmpeqd %xmm0, %xmm5
pshufd $0xf5, %xmm5, %xmm7     # xmm7 = xmm5[1,1,3,3]
pand %xmm6, %xmm7
pshufd $0xf5, %xmm6, %xmm5     # xmm5 = xmm6[1,1,3,3]
por %xmm7, %xmm5
movd %xmm5, %edx
notl %edx
testb $0x1, %dl
je 0xc608a
movq %rcx, (%r12,%rcx,8)
pxor %xmm3, %xmm5
pextrw $0x4, %xmm5, %edx
testb $0x1, %dl
je 0xc60a1
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r12,%rcx,8)
addq $0x2, %rcx
paddq %xmm4, %xmm1
cmpq %rcx, %rax
jne 0xc6055
cmpb $0x1, 0x6(%r15)
jne 0xc60c9
movq %rbx, %rdi
callq 0xef200
movq %rax, %rbp
leaq 0x2c9(%rip), %r8        # 0xc6390
jmp 0xc60ee
cmpb $0x0, 0x4(%r15)
je 0xc60d9
leaq 0x2dd(%rip), %r8        # 0xc63b4
jmp 0xc60eb
cmpb $0x0, 0x5(%r15)
je 0xc62a9
leaq 0x33e(%rip), %r8        # 0xc6429
movq %rbx, %rbp
testq %rbp, %rbp
je 0xc6106
movl $0x8, %edx
movq %r12, %rdi
movq %r13, %rsi
movq %rbp, %rcx
callq 0x1118d4
testq %rbp, %rbp
je 0xc6126
cmpb $0x0, 0x6(%r15)
je 0xc6126
leaq 0x29b987(%rip), %rsi    # 0x361aa0
movq %rbp, %rdi
movl $0x154, %edx            # imm = 0x154
callq 0x109670
testq %r14, %r14
je 0xc6142
xorl %r15d, %r15d
movq (%r12,%r15,8), %rdi
movq %rbx, %rsi
callq 0xc62b3
incq %r15
cmpq %r15, %r14
jne 0xc612e
leaq 0x29b957(%rip), %rsi    # 0x361aa0
movq %r12, %rdi
movl $0x15b, %edx            # imm = 0x15B
callq 0x109670
xorl %ebp, %ebp
cmpq $0x1, %rbx
sbbl %ebp, %ebp
movq %rbx, %rdi
callq 0xee90c
movl %ebp, %eax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
cmpb $0x0, 0x1(%r15)
jne 0xc6189
cmpb $0x0, 0x2(%r15)
je 0xc62ae
leaq -0x1(%r14), %r13
movq %rbx, %rdi
movq %r13, %rsi
callq 0xefce0
movq %r14, %rdi
movq %rax, %rsi
xorl %edx, %edx
xorl %ecx, %ecx
callq 0x205c84
movq %rax, %r12
leaq 0x20(%rsp), %rbp
movq $0x1, (%rbp)
movq $0x3, 0x8(%rbp)
movq $0x3e8, 0x10(%rbp)      # imm = 0x3E8
movq $0xfa0, 0x18(%rbp)      # imm = 0xFA0
xorl %eax, %eax
movq %rax, 0x20(%rbp)
movq %rax, 0x28(%rbp)
movabsq $0x10000000000, %rax    # imm = 0x10000000000
movq %rax, 0x30(%rbp)
movq %r12, %rdi
movq %rbx, %rsi
callq 0x206175
movq %rbx, %rdi
callq 0xec1e8
xorl %ecx, %ecx
movq %rcx, 0x18(%rsp)
pxor %xmm0, %xmm0
movdqu %xmm0, 0x8(%rsp)
movq %rbp, (%rsp)
movq %r12, %rdi
movq %rax, %rsi
movq %rbx, %rdx
xorl %ecx, %ecx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x1ee49b
cmpb $0x0, 0x1(%r15)
je 0xc625f
testq %r14, %r14
je 0xc628b
xorl %r15d, %r15d
movq %r12, %rdi
movq %r15, %rsi
callq 0x205eeb
movq %rbx, %rdi
movq %rax, %rsi
callq 0xefc48
movq %rax, %rdi
movq %rbx, %rsi
callq 0xc62b3
incq %r15
cmpq %r15, %r14
jne 0xc6234
jmp 0xc628b
testq %r14, %r14
je 0xc628b
movq %r12, %rdi
movq %r13, %rsi
callq 0x205eeb
movq %rbx, %rdi
movq %rax, %rsi
callq 0xefc48
movq %rax, %rdi
movq %rbx, %rsi
callq 0xc62b3
addq $-0x1, %r13
jb 0xc6264
movq %r12, %rdi
xorl %esi, %esi
callq 0x205e63
jmp 0xc6156
callq 0x1f580
callq 0x1f49c
callq 0x1f547
callq 0x1f50e
callq 0x1f4d5