// File: /workspace/github_c_makefile_star2_O0/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:
subq $0xc8, %rsp
movl %edi, 0xc4(%rsp)
movq %rsi, 0xb8(%rsp)
movl %edx, 0xb4(%rsp)
movq %rcx, 0xa8(%rsp)
movq %r8, 0xa0(%rsp)
movq 0xa8(%rsp), %rax
movq %rax, 0x98(%rsp)
movq $0x0, 0x90(%rsp)
movq $0x0, 0x88(%rsp)
movq $0x0, 0x80(%rsp)
movq $0x0, 0x78(%rsp)
movq $0x0, 0x70(%rsp)
movl $0x0, 0x5c(%rsp)
movl 0xb4(%rsp), %eax
movl %eax, 0x58(%rsp)
movq 0xb8(%rsp), %rax
movslq 0x58(%rsp), %rcx
movq (%rax,%rcx,8), %rax
movq %rax, 0x50(%rsp)
cmpq $0x0, 0xa0(%rsp)
je 0x2fa542
movq 0xa0(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x2fa50a
jmp 0x2fa542
movq 0x341a8f(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x21baf8(%rip), %rsi    # 0x516013
leaq 0x21bc9d(%rip), %rdx    # 0x5161bf
leaq 0x296fdb(%rip), %rcx    # 0x591504
leaq 0x296e50(%rip), %r8     # 0x591380
movl $0x71, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x2fa544
jmp 0x2fa546
cmpq $0x0, 0x98(%rsp)
jne 0x2fa589
movq 0x341a48(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x21bab1(%rip), %rsi    # 0x516013
leaq 0x2805f6(%rip), %rdx    # 0x57ab5f
leaq 0x296f94(%rip), %rcx    # 0x591504
leaq 0x296e09(%rip), %r8     # 0x591380
movl $0x72, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x2fa58b
movl 0x58(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x58(%rsp)
callq 0xb7a40
movq %rax, 0x68(%rsp)
movq 0x68(%rsp), %rdi
movq 0x50(%rsp), %rsi
movq 0xa0(%rsp), %rdx
callq 0xb7aa0
movq %rax, 0x60(%rsp)
cmpq $0x0, 0x60(%rsp)
jne 0x2fa5cc
movl $0xffffffff, 0x5c(%rsp) # imm = 0xFFFFFFFF
cmpl $0x0, 0x5c(%rsp)
jne 0x2fa70e
movl 0xc4(%rsp), %edi
subl 0x58(%rsp), %edi
movq 0xb8(%rsp), %rsi
movslq 0x58(%rsp), %rax
shlq $0x3, %rax
addq %rax, %rsi
callq 0x1746b0
movq %rax, 0x90(%rsp)
movq %rax, 0x88(%rsp)
movq 0x88(%rsp), %rdi
movq 0x60(%rsp), %rsi
movq 0x98(%rsp), %rax
movq 0x20(%rax), %r11
movq 0x98(%rsp), %rax
movq 0x18(%rax), %r10
movq 0xa0(%rsp), %rax
movl $0x80000000, %r9d       # imm = 0x80000000
xorl %ecx, %ecx
movl %r9d, %edx
movl %r9d, %ecx
movl %r9d, %r8d
movl $0x80000000, (%rsp)     # imm = 0x80000000
movl $0x80000000, 0x8(%rsp)  # imm = 0x80000000
movl $0x80000000, 0x10(%rsp) # imm = 0x80000000
movl $0xa, 0x18(%rsp)
movl $0x80000000, 0x20(%rsp) # imm = 0x80000000
movl $0x80000000, 0x28(%rsp) # imm = 0x80000000
movq %r11, 0x30(%rsp)
movq %r10, 0x38(%rsp)
movq $0x0, 0x40(%rsp)
movq %rax, 0x48(%rsp)
callq 0x2ff630
movq %rax, 0x80(%rsp)
movq %rax, 0x88(%rsp)
movq 0x88(%rsp), %rdi
movq 0xa0(%rsp), %r9
xorl %eax, %eax
movl %eax, %r8d
movq %r8, %rsi
movq %r8, %rdx
movq %r8, %rcx
callq 0x2fdfa0
movq %rax, 0x78(%rsp)
movq %rax, 0x88(%rsp)
cmpq $0x0, 0x78(%rsp)
jne 0x2fa6e7
movl $0xffffffff, 0x5c(%rsp) # imm = 0xFFFFFFFF
jmp 0x2fa70c
movq 0x88(%rsp), %rdi
movq 0x98(%rsp), %rax
movq (%rax), %rsi
callq 0x176d50
movq %rax, 0x70(%rsp)
movq %rax, 0x88(%rsp)
jmp 0x2fa70e
cmpl $0x0, 0x5c(%rsp)
jne 0x2fa72e
movq 0x88(%rsp), %rdi
movq 0xa0(%rsp), %rsi
callq 0x1b1f90
movl %eax, 0x5c(%rsp)
movq 0x78(%rsp), %rdi
callq 0x1b1cb0
movq 0x80(%rsp), %rdi
callq 0x1b1cb0
movq 0x90(%rsp), %rdi
callq 0x1b1cb0
movq 0x70(%rsp), %rdi
callq 0x1b1cb0
movq 0x68(%rsp), %rdi
callq 0xb7e50
movq 0x60(%rsp), %rdi
callq 0xae070
movl 0x5c(%rsp), %eax
addq $0xc8, %rsp
retq
nopl (%rax)