// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_seqtransform.c
// Function: gt_seqtransform_runner
static int gt_seqtransform_runner(int argc, const char **argv, int parsed_args,
                            void *tool_arguments, GtError *err)
{
  SeqtransformArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  GtUword i;
  GtBioseq *bioseq;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    GtAlphabet *alphabet;
    bool is_protein;
    alphabet = gt_bioseq_get_alphabet(bioseq);
    is_protein = gt_alphabet_is_protein(alphabet);
    for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
      const char *desc, *suffix = NULL;
      char *seq;
      GtUword seqlen;
      desc = gt_bioseq_get_description(bioseq, i);
      seq = gt_bioseq_get_sequence(bioseq, i);
      seqlen = gt_bioseq_get_sequence_length(bioseq, i);
      if (arguments->addstopaminos && is_protein && seqlen &&
          seq[seqlen-1] != GT_STOP_AMINO) {
        suffix = GT_STOP_AMINO_CSTR;
      }
      gt_fasta_show_entry_with_suffix(desc, seq, seqlen, suffix,
                                      arguments->width, arguments->outfp);
      gt_free(seq);
    }
    gt_bioseq_delete(bioseq);
  }

  gt_bioseq_iterator_delete(bsi);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r8, %r12
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %r15
movl %edi, %ebx
testq %r8, %r8
je 0x49306
movq %r12, %rdi
callq 0x89eb7
testb %al, %al
jne 0x49446
testq %r14, %r14
je 0x4941c
subl %ebp, %ebx
movslq %ebp, %rax
leaq (%r15,%rax,8), %rsi
movl %ebx, %edi
callq 0x5d64c
movq %rax, 0x8(%rsp)
pushq $0x6a
popq %rbp
movq %r12, 0x10(%rsp)
movq 0x8(%rsp), %rdi
movq %rsp, %rsi
movq %r12, %rdx
callq 0x5d6eb
movl %eax, %ebx
testl %eax, %eax
jne 0x49401
movq (%rsp), %rdi
testq %rdi, %rdi
je 0x49401
callq 0x5b0cc
movq %rax, %rdi
callq 0x572d7
movl %eax, %r12d
xorl %ebx, %ebx
movq (%rsp), %rdi
callq 0x5ba79
movq (%rsp), %rdi
cmpq %rax, %rbx
jae 0x493f2
movq %rbx, %rsi
callq 0x5b338
movq %rax, %r13
movq (%rsp), %rdi
movq %rbx, %rsi
callq 0x5b1f9
movq %rax, %r15
movq (%rsp), %rdi
movq %rbx, %rsi
callq 0x5b2f1
testq %rax, %rax
setne %cl
movb (%r14), %dl
andb %r12b, %dl
andb %cl, %dl
cmpb $0x1, %dl
jne 0x493c1
cmpb $0x2a, -0x1(%r15,%rax)
je 0x493c1
leaq 0x321211(%rip), %rcx    # 0x36a5d0
jmp 0x493c3
xorl %ecx, %ecx
movq 0x8(%r14), %r8
movq 0x18(%r14), %r9
movq %r13, %rdi
movq %r15, %rsi
movq %rax, %rdx
callq 0x8c0c9
movq %r15, %rdi
leaq 0x2afd33(%rip), %rsi    # 0x2f9116
movl %ebp, %edx
callq 0x936f9
incq %rbx
jmp 0x49365
callq 0x5af87
movq 0x10(%rsp), %r12
jmp 0x4932c
movq 0x8(%rsp), %rdi
callq 0x5d6c5
movl %ebx, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x3eeb45(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x29bbe6(%rip), %rsi    # 0x2e5013
leaq 0x2ff21f(%rip), %rdx    # 0x348653
leaq 0x2afdb6(%rip), %rcx    # 0x2f91f1
leaq 0x2afcd4(%rip), %r8     # 0x2f9116
pushq $0x54
jmp 0x4946e
movq 0x3eeb1b(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x29bbbc(%rip), %rsi    # 0x2e5013
leaq 0x29bd61(%rip), %rdx    # 0x2e51bf
leaq 0x2afd8c(%rip), %rcx    # 0x2f91f1
leaq 0x2afcaa(%rip), %r8     # 0x2f9116
pushq $0x53
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390