// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/ltr/gt_ltrclustering.c
// Function: gt_ltrclustering_runner
static int gt_ltrclustering_runner(int argc, const char **argv,
                                       int parsed_args, void *tool_arguments,
                                       GtError *err)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream      = NULL,
               *last_stream         = NULL,
               *ltr_cluster_stream  = NULL,
               *ltr_classify_stream = NULL,
               *gff3_out_stream     = NULL;
  GtEncseqLoader *el;
  GtEncseq *encseq;
  int had_err = 0, arg = parsed_args;
  const char *indexname = argv[arg];

  gt_error_check(err);
  gt_assert(arguments);
  arg++;

  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, indexname, err);

  if (!encseq)
    had_err = -1;
  if (!had_err) {
    last_stream = gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - arg,
                                                                  argv + arg);
    last_stream = ltr_cluster_stream = gt_ltr_cluster_stream_new(last_stream,
                                                         encseq,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         10,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         arguments->plarge,
                                                         arguments->psmall,
                                                         NULL,
                                                         err);
    last_stream = ltr_classify_stream = gt_ltr_classify_stream_new(last_stream,
                                                                   NULL,
                                                                   NULL,
                                                                   NULL,
                                                                   NULL,
                                                                   err);

    if (!ltr_classify_stream)
      had_err = -1;
    else
      last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
                                                          arguments->outfp);
  }
  if (!had_err)
    had_err = gt_node_stream_pull(last_stream, err);

  gt_node_stream_delete(ltr_classify_stream);
  gt_node_stream_delete(ltr_cluster_stream);
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(gff3_out_stream);
  gt_encseq_loader_delete(el);
  gt_encseq_delete(encseq);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r8, %rbx
movq %rcx, %r13
movq %rsi, %r14
movl %edi, %ebp
movslq %edx, %r12
movq (%rsi,%r12,8), %r15
testq %r8, %r8
je 0x20df00
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x20e037
testq %r13, %r13
je 0x20e032
callq 0xf36ef
movq %rax, 0x10(%rsp)
movq %rax, %rdi
movq %r15, %rsi
movq %rbx, %rdx
callq 0xf374b
movq %rax, %r15
testq %rax, %rax
je 0x20dfba
movl %r12d, %edi
notl %edi
addl %ebp, %edi
leaq (%r14,%r12,8), %rsi
addq $0x8, %rsi
callq 0x14d00b
movq %rax, %rdi
movl $0x80000000, %eax       # imm = 0x80000000
movq %rdi, 0x8(%rsp)
movq %r15, %rsi
movl $0x80000000, %edx       # imm = 0x80000000
movl $0x80000000, %ecx       # imm = 0x80000000
movl $0x80000000, %r8d       # imm = 0x80000000
movl $0x80000000, %r9d       # imm = 0x80000000
pushq %rbx
pushq $0x0
pushq 0x18(%r13)
pushq 0x20(%r13)
pushq %rax
pushq %rax
pushq $0xa
pushq %rax
pushq %rax
pushq %rax
callq 0x211bcf
addq $0x50, %rsp
movq %rax, %rbp
xorl %r14d, %r14d
movq %rax, %rdi
xorl %esi, %esi
xorl %edx, %edx
xorl %ecx, %ecx
xorl %r8d, %r8d
movq %rbx, %r9
callq 0x210ae3
testq %rax, %rax
je 0x20dfcf
movq %rax, %r12
movq (%r13), %rsi
movq %rax, %rdi
callq 0x14e310
movq %rax, %r13
movb $0x1, %al
movq %r12, %r14
jmp 0x20dfd4
xorl %r14d, %r14d
xorl %ebp, %ebp
xorl %r13d, %r13d
xorl %eax, %eax
movq $0x0, 0x8(%rsp)
jmp 0x20dfd4
xorl %r13d, %r13d
xorl %eax, %eax
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
testb %al, %al
je 0x20dfec
movq %r13, %rdi
movq %rbx, %rsi
callq 0x16adca
movl %eax, %r12d
movq %r14, %rdi
callq 0x16ac6e
movq %rbp, %rdi
callq 0x16ac6e
movq 0x8(%rsp), %rdi
callq 0x16ac6e
movq %r13, %rdi
callq 0x16ac6e
movq 0x10(%rsp), %rdi
callq 0xf424d
movq %r15, %rdi
callq 0xee90c
movl %r12d, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x81dbf
callq 0x81d88