// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_encseq_check.c
// Function: gt_encseq_check_runner
static int gt_encseq_check_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args, void *tool_arguments,
                                  GtError *err)
{
  GtEncseqCheckArguments *arguments = tool_arguments;
  int had_err = 0;
  GtEncseqLoader *encseq_loader;
  GtEncseq *encseq;
  GtLogger *logger = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  encseq_loader = gt_encseq_loader_new();
  if (arguments->mirror)
    gt_encseq_loader_mirror(encseq_loader);

  if (!(encseq = gt_encseq_loader_load(encseq_loader, argv[parsed_args], err)))
    had_err = -1;
  if (!had_err) {
    int readmode;

    gt_encseq_check_startpositions(encseq,logger);
    for (readmode = 0; readmode < 4; readmode++) {
      if (gt_alphabet_is_dna(gt_encseq_alphabet(encseq)) ||
           ((GtReadmode) readmode) == GT_READMODE_FORWARD ||
           ((GtReadmode) readmode) == GT_READMODE_REVERSE) {
        gt_logger_log(logger,"check consistency for readmode %s",
                      gt_readmode_show((GtReadmode) readmode));
        if (gt_encseq_check_consistency(encseq,
                           gt_encseq_filenames(encseq),
                           (GtReadmode) readmode,
                           arguments->scantrials,
                           arguments->multicharcmptrials,
                           gt_encseq_has_multiseq_support(encseq),
                           !arguments->nocheckunit,
                           logger,
                           err) != 0) {
          had_err = -1;
          break;
        }
      }
    }
    if (!had_err)
      gt_encseq_check_specialranges(encseq);
    if (!had_err && !arguments->mirror)
      gt_encseq_check_markpos(encseq);
    if (!had_err)
      had_err = gt_encseq_check_minmax(encseq, err);
    if (!had_err && arguments->prefixlength > 0) {
      if (gt_verifymappedstr(encseq,
                             arguments->prefixlength,
                             err) != 0) {
        had_err = -1;
      }
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(encseq_loader);
  gt_logger_delete(logger);
  return had_err;
}

// Assembly:
pushq %rbx
subq $0xa0, %rsp
movl %edi, 0x9c(%rsp)
movq %rsi, 0x90(%rsp)
movl %edx, 0x8c(%rsp)
movq %rcx, 0x80(%rsp)
movq %r8, 0x78(%rsp)
movq 0x80(%rsp), %rax
movq %rax, 0x70(%rsp)
movl $0x0, 0x6c(%rsp)
movq $0x0, 0x50(%rsp)
cmpq $0x0, 0x78(%rsp)
je 0x2f6b9
movq 0x78(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x2f681
jmp 0x2f6b9
movq 0x60c918(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4e6981(%rip), %rsi    # 0x516013
leaq 0x4e6b26(%rip), %rdx    # 0x5161bf
leaq 0x4eccff(%rip), %rcx    # 0x51c39f
leaq 0x4ecbd4(%rip), %r8     # 0x51c27b
movl $0x65, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x2f6bb
jmp 0x2f6bd
cmpq $0x0, 0x70(%rsp)
jne 0x2f6fd
movq 0x60c8d4(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4e693d(%rip), %rsi    # 0x516013
leaq 0x54b482(%rip), %rdx    # 0x57ab5f
leaq 0x4eccbb(%rip), %rcx    # 0x51c39f
leaq 0x4ecb90(%rip), %r8     # 0x51c27b
movl $0x66, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x2f6ff
movq 0x70(%rsp), %rax
movb 0x18(%rax), %al
movq 0x60c82a(%rip), %rcx    # 0x63bf38
movq (%rcx), %rdx
leaq 0x4e81d4(%rip), %rsi    # 0x5178ec
andb $0x1, %al
movzbl %al, %edi
callq 0xe7870
movq %rax, 0x50(%rsp)
callq 0xb7a40
movq %rax, 0x60(%rsp)
movq 0x70(%rsp), %rax
testb $0x1, 0x19(%rax)
je 0x2f746
movq 0x60(%rsp), %rdi
callq 0xba710
movq 0x60(%rsp), %rdi
movq 0x90(%rsp), %rax
movslq 0x8c(%rsp), %rcx
movq (%rax,%rcx,8), %rsi
movq 0x78(%rsp), %rdx
callq 0xb7aa0
movq %rax, 0x58(%rsp)
cmpq $0x0, %rax
jne 0x2f77c
movl $0xffffffff, 0x6c(%rsp) # imm = 0xFFFFFFFF
cmpl $0x0, 0x6c(%rsp)
jne 0x2f93a
movq 0x58(%rsp), %rdi
movq 0x50(%rsp), %rsi
callq 0xb21e0
movl $0x0, 0x4c(%rsp)
cmpl $0x4, 0x4c(%rsp)
jge 0x2f8b5
movq 0x58(%rsp), %rdi
callq 0xb0f00
movq %rax, %rdi
callq 0x7f400
testb $0x1, %al
jne 0x2f7d1
cmpl $0x0, 0x4c(%rsp)
je 0x2f7d1
cmpl $0x1, 0x4c(%rsp)
jne 0x2f8a3
movq 0x50(%rsp), %rax
movq %rax, 0x18(%rsp)
movl 0x4c(%rsp), %edi
callq 0x109990
movq 0x18(%rsp), %rdi
movq %rax, %rdx
leaq 0x4ecbc3(%rip), %rsi    # 0x51c3b6
movb $0x0, %al
callq 0xe7cd0
movq 0x58(%rsp), %rax
movq %rax, 0x20(%rsp)
movq 0x58(%rsp), %rdi
callq 0xb1f80
movq %rax, 0x28(%rsp)
movl 0x4c(%rsp), %eax
movl %eax, 0x34(%rsp)
movq 0x70(%rsp), %rax
movq (%rax), %rax
movq %rax, 0x38(%rsp)
movq 0x70(%rsp), %rax
movq 0x8(%rax), %rax
movq %rax, 0x40(%rsp)
movq 0x58(%rsp), %rdi
callq 0xb2480
movq 0x20(%rsp), %rdi
movq 0x28(%rsp), %rsi
movl 0x34(%rsp), %edx
movq 0x38(%rsp), %rcx
movq 0x40(%rsp), %r8
movq 0x70(%rsp), %r9
movb 0x1a(%r9), %r10b
xorb $-0x1, %r10b
movq 0x50(%rsp), %r11
movq 0x78(%rsp), %rbx
movq %rsp, %r9
movq %rbx, 0x10(%r9)
movq %r11, 0x8(%r9)
movzbl %r10b, %r10d
andl $0x1, %r10d
movl %r10d, (%r9)
movzbl %al, %r9d
andl $0x1, %r9d
callq 0xb66c0
cmpl $0x0, %eax
je 0x2f8a1
movl $0xffffffff, 0x6c(%rsp) # imm = 0xFFFFFFFF
jmp 0x2f8b5
jmp 0x2f8a3
jmp 0x2f8a5
movl 0x4c(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x4c(%rsp)
jmp 0x2f79e
cmpl $0x0, 0x6c(%rsp)
jne 0x2f8c6
movq 0x58(%rsp), %rdi
callq 0xb7e80
cmpl $0x0, 0x6c(%rsp)
jne 0x2f8e2
movq 0x70(%rsp), %rax
testb $0x1, 0x19(%rax)
jne 0x2f8e2
movq 0x58(%rsp), %rdi
callq 0xb0b60
cmpl $0x0, 0x6c(%rsp)
jne 0x2f8fc
movq 0x58(%rsp), %rdi
movq 0x78(%rsp), %rsi
callq 0xb64f0
movl %eax, 0x6c(%rsp)
cmpl $0x0, 0x6c(%rsp)
jne 0x2f938
movq 0x70(%rsp), %rax
cmpq $0x0, 0x10(%rax)
jbe 0x2f938
movq 0x58(%rsp), %rdi
movq 0x70(%rsp), %rax
movq 0x10(%rax), %rax
movl %eax, %esi
movq 0x78(%rsp), %rdx
callq 0x2f0b80
cmpl $0x0, %eax
je 0x2f936
movl $0xffffffff, 0x6c(%rsp) # imm = 0xFFFFFFFF
jmp 0x2f938
jmp 0x2f93a
movq 0x58(%rsp), %rdi
callq 0xae070
movq 0x60(%rsp), %rdi
callq 0xb7e50
movq 0x50(%rsp), %rdi
callq 0xe7ed0
movl 0x6c(%rsp), %eax
addq $0xa0, %rsp
popq %rbx
retq
nopw %cs:(%rax,%rax)
nop