// File: /workspace/github_c_makefile_star2_O3/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 0xc4f75
movq %r12, %rdi
callq 0xfcc32
testb %al, %al
jne 0xc50c7
testq %r14, %r14
je 0xc50c2
subl %ebp, %ebx
movslq %ebp, %rax
leaq (%r15,%rax,8), %rsi
movl %ebx, %edi
callq 0xd63a0
movq %rsp, %r15
movq %rax, 0x8(%rsp)
movq %rax, %rdi
movq %r15, %rsi
movq %r12, %rdx
callq 0xd6416
movl %eax, %ebx
testl %eax, %eax
sete %al
movq (%r15), %rdi
testq %rdi, %rdi
setne %cl
andb %al, %cl
cmpb $0x1, %cl
jne 0xc50a7
leaq 0x294178(%rip), %r13    # 0x35913e
movq %r12, 0x10(%rsp)
callq 0xd4a72
movq %rax, %rdi
callq 0xd15f5
movl %eax, %ebp
movq (%rsp), %rdi
callq 0xd4fc8
testq %rax, %rax
je 0xc5079
xorl %r12d, %r12d
movq (%rsp), %rdi
movq %r12, %rsi
callq 0xd4bb7
movq %rax, %r15
movq (%rsp), %rdi
movq %r12, %rsi
callq 0xd4b0d
movq %rax, %rbx
movq (%rsp), %rdi
movq %r12, %rsi
callq 0xd4ba3
testq %rax, %rax
setne %cl
movb (%r14), %dl
andb %bpl, %dl
andb %cl, %dl
cmpb $0x1, %dl
jne 0xc503c
cmpb $0x2a, -0x1(%rbx,%rax)
je 0xc503c
leaq 0x305190(%rip), %rcx    # 0x3ca1ca
jmp 0xc503e
xorl %ecx, %ecx
movq 0x8(%r14), %r8
movq 0x18(%r14), %r9
movq %r15, %rdi
movq %rbx, %rsi
movq %rax, %rdx
callq 0xfe00d
movq %rbx, %rdi
movq %r13, %rsi
movl $0x6a, %edx
callq 0x1045eb
incq %r12
movq (%rsp), %rdi
callq 0xd4fc8
cmpq %rax, %r12
jb 0xc4fef
movq (%rsp), %rdi
callq 0xd491d
movq 0x8(%rsp), %rdi
movq %rsp, %rsi
movq 0x10(%rsp), %rdx
callq 0xd6416
movl %eax, %ebx
testl %eax, %eax
jne 0xc50a7
movq (%rsp), %rdi
testq %rdi, %rdi
jne 0xc4fcb
movq 0x8(%rsp), %rdi
callq 0xd63ee
movl %ebx, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1f463
callq 0x1f42c