// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_compreads_refcompress.c
// Function: gt_compreads_refcompress_runner
static int gt_compreads_refcompress_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments, GtError *err)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  int had_err = 0;
  GtTimer *timer = NULL;
  GtEncseq *encseq = NULL;
  GtRcrEncoder *rcre = NULL;
  GtEncseqLoader *el = NULL;
  GtSplitter *splitter = NULL;
  GtStr *buffer;
  GtUword i;
  gt_error_check(err);
  gt_assert(arguments);
  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }
  if (!had_err) {
    if (timer != NULL)
      gt_timer_show_progress(timer, "encoding", stdout);

    if (gt_str_length(arguments->name) == 0) {
      splitter = gt_splitter_new();
      buffer = gt_str_clone(arguments->align);
      gt_splitter_split(splitter, gt_str_get(buffer), gt_str_length(buffer),
                        '.');
      for (i = 0; i < gt_splitter_size(splitter) - 1; i++) {
        gt_str_append_cstr(arguments->name,
                           gt_splitter_get_token(splitter, i));
        if (i < gt_splitter_size(splitter) - 2)
          gt_str_append_char(arguments->name, '.');
      }
      gt_splitter_delete(splitter);
      gt_str_delete(buffer);
    }
    el = gt_encseq_loader_new();
    gt_encseq_loader_enable_autosupport(el);
    gt_encseq_loader_require_description_support(el);
    encseq = gt_encseq_loader_load(el, gt_str_get(arguments->ref), err);
    gt_encseq_loader_delete(el);
    if (!encseq) {
      gt_error_set(err, "could not load GtEncseq %s",
                   gt_str_get(arguments->ref));
      had_err = -1;
    }

    if (!had_err) {
      if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq))) {
        gt_error_set(err, "alphabet in %s has to be DNA",
                     gt_str_get(arguments->ref));
        had_err = -1;
      }
      if (!had_err) {

        rcre = gt_rcr_encoder_new(encseq, gt_str_get(arguments->align),
                                  arguments->vquals, arguments->mquals,
                                  arguments->quals, arguments->ureads,
                                  arguments->descs, timer, err);
        if (!rcre)
          had_err = -1;
        else {
          if (arguments->verbose)
            gt_rcr_encoder_enable_verbosity(rcre);
          had_err = gt_rcr_encoder_encode(rcre, gt_str_get(arguments->name),
                                          timer, err);
        }
        gt_rcr_encoder_delete(rcre);
      }
    }
    gt_encseq_delete(encseq);
  }
  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  return had_err;
}

// Assembly:
subq $0xd8, %rsp
movl %edi, 0xd4(%rsp)
movq %rsi, 0xc8(%rsp)
movl %edx, 0xc4(%rsp)
movq %rcx, 0xb8(%rsp)
movq %r8, 0xb0(%rsp)
movq 0xb8(%rsp), %rax
movq %rax, 0xa8(%rsp)
movl $0x0, 0xa4(%rsp)
movq $0x0, 0x98(%rsp)
movq $0x0, 0x90(%rsp)
movq $0x0, 0x88(%rsp)
movq $0x0, 0x80(%rsp)
movq $0x0, 0x78(%rsp)
cmpq $0x0, 0xb0(%rsp)
je 0x214a7
movq 0xb0(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x2146f
jmp 0x214a7
movq 0x61ab2a(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f4b93(%rip), %rsi    # 0x516013
leaq 0x4f4d38(%rip), %rdx    # 0x5161bf
leaq 0x4f72a2(%rip), %rcx    # 0x518730
leaq 0x4f6f66(%rip), %r8     # 0x5183fb
movl $0x9e, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x214a9
jmp 0x214ab
cmpq $0x0, 0xa8(%rsp)
jne 0x214ee
movq 0x61aae3(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f4b4c(%rip), %rsi    # 0x516013
leaq 0x559691(%rip), %rdx    # 0x57ab5f
leaq 0x4f725b(%rip), %rcx    # 0x518730
leaq 0x4f6f1f(%rip), %r8     # 0x5183fb
movl $0x9f, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x214f0
callq 0x11aa90
testb $0x1, %al
jne 0x214fb
jmp 0x21563
leaq 0x55324f(%rip), %rdi    # 0x574751
callq 0x1213a0
movq %rax, 0x98(%rsp)
movq 0x98(%rsp), %rdi
callq 0x1213f0
cmpq $0x0, 0x98(%rsp)
jne 0x2155f
movq 0x61aa72(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f4adb(%rip), %rsi    # 0x516013
leaq 0x51500d(%rip), %rdx    # 0x53654c
leaq 0x4f71ea(%rip), %rcx    # 0x518730
leaq 0x4f6eae(%rip), %r8     # 0x5183fb
movl $0xa3, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x21561
jmp 0x21563
cmpl $0x0, 0xa4(%rsp)
jne 0x2193a
cmpq $0x0, 0x98(%rsp)
je 0x2159a
movq 0x98(%rsp), %rdi
movq 0x61a9ad(%rip), %rax    # 0x63bf38
movq (%rax), %rdx
leaq 0x5401ff(%rip), %rsi    # 0x561794
callq 0x121930
movq 0xa8(%rsp), %rax
movq 0x8(%rax), %rdi
callq 0x11dfa0
cmpq $0x0, %rax
jne 0x216ce
callq 0x11afb0
movq %rax, 0x78(%rsp)
movq 0xa8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11e280
movq %rax, 0x70(%rsp)
movq 0x78(%rsp), %rax
movq %rax, 0x58(%rsp)
movq 0x70(%rsp), %rdi
callq 0x11dee0
movq %rax, 0x60(%rsp)
movq 0x70(%rsp), %rdi
callq 0x11dfa0
movq 0x58(%rsp), %rdi
movq 0x60(%rsp), %rsi
movq %rax, %rdx
movl $0x2e, %ecx
callq 0x11afd0
movq $0x0, 0x68(%rsp)
movq 0x68(%rsp), %rax
movq %rax, 0x50(%rsp)
movq 0x78(%rsp), %rdi
callq 0x11b5b0
movq %rax, %rcx
movq 0x50(%rsp), %rax
subq $0x1, %rcx
cmpq %rcx, %rax
jae 0x216ba
movq 0xa8(%rsp), %rax
movq 0x8(%rax), %rax
movq %rax, 0x40(%rsp)
movq 0x78(%rsp), %rdi
movq 0x68(%rsp), %rsi
callq 0x11b4c0
movq 0x40(%rsp), %rdi
movq %rax, %rsi
callq 0x11d550
movq 0x68(%rsp), %rax
movq %rax, 0x48(%rsp)
movq 0x78(%rsp), %rdi
callq 0x11b5b0
movq %rax, %rcx
movq 0x48(%rsp), %rax
subq $0x2, %rcx
cmpq %rcx, %rax
jae 0x216a5
movq 0xa8(%rsp), %rax
movq 0x8(%rax), %rdi
movl $0x2e, %esi
callq 0x11da70
jmp 0x216a7
movq 0x68(%rsp), %rax
addq $0x1, %rax
movq %rax, 0x68(%rsp)
jmp 0x21618
movq 0x78(%rsp), %rdi
callq 0x11b600
movq 0x70(%rsp), %rdi
callq 0x11f560
callq 0xb7a40
movq %rax, 0x80(%rsp)
movq 0x80(%rsp), %rdi
callq 0xba590
movq 0x80(%rsp), %rdi
callq 0xbacc0
movq 0x80(%rsp), %rax
movq %rax, 0x38(%rsp)
movq 0xa8(%rsp), %rax
movq 0x10(%rax), %rdi
callq 0x11dee0
movq 0x38(%rsp), %rdi
movq %rax, %rsi
movq 0xb0(%rsp), %rdx
callq 0xb7aa0
movq %rax, 0x90(%rsp)
movq 0x80(%rsp), %rdi
callq 0xb7e50
cmpq $0x0, 0x90(%rsp)
jne 0x21787
movq 0xb0(%rsp), %rax
movq %rax, 0x30(%rsp)
movq 0xa8(%rsp), %rax
movq 0x10(%rax), %rdi
callq 0x11dee0
movq 0x30(%rsp), %rdi
movq %rax, %rdx
leaq 0x4f6fdb(%rip), %rsi    # 0x518750
movb $0x0, %al
callq 0xd88c0
movl $0xffffffff, 0xa4(%rsp) # imm = 0xFFFFFFFF
cmpl $0x0, 0xa4(%rsp)
jne 0x2192d
movq 0x90(%rsp), %rdi
callq 0xb0f00
movq %rax, %rdi
callq 0x7f400
testb $0x1, %al
jne 0x217ed
movq 0xb0(%rsp), %rax
movq %rax, 0x28(%rsp)
movq 0xa8(%rsp), %rax
movq 0x10(%rax), %rdi
callq 0x11dee0
movq 0x28(%rsp), %rdi
movq %rax, %rdx
leaq 0x4f6f90(%rip), %rsi    # 0x51876b
movb $0x0, %al
callq 0xd88c0
movl $0xffffffff, 0xa4(%rsp) # imm = 0xFFFFFFFF
cmpl $0x0, 0xa4(%rsp)
jne 0x2192b
movq 0x90(%rsp), %rax
movq %rax, 0x20(%rsp)
movq 0xa8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dee0
movq 0x20(%rsp), %rdi
movq %rax, %rsi
movq 0xa8(%rsp), %rax
movb 0x1(%rax), %dl
movq 0xa8(%rsp), %rax
movb 0x2(%rax), %cl
movq 0xa8(%rsp), %rax
movb 0x3(%rax), %r8b
movq 0xa8(%rsp), %rax
movb 0x4(%rax), %r9b
movq 0xa8(%rsp), %rax
movb 0x5(%rax), %r11b
movq 0x98(%rsp), %r10
movq 0xb0(%rsp), %rax
andb $0x1, %dl
andb $0x1, %cl
andb $0x1, %r8b
andb $0x1, %r9b
andb $0x1, %r11b
movzbl %dl, %edx
movzbl %cl, %ecx
movzbl %r8b, %r8d
movzbl %r9b, %r9d
movzbl %r11b, %r11d
movl %r11d, (%rsp)
movq %r10, 0x8(%rsp)
movq %rax, 0x10(%rsp)
callq 0x1bc240
movq %rax, 0x88(%rsp)
cmpq $0x0, 0x88(%rsp)
jne 0x218c2
movl $0xffffffff, 0xa4(%rsp) # imm = 0xFFFFFFFF
jmp 0x2191e
movq 0xa8(%rsp), %rax
testb $0x1, (%rax)
je 0x218dc
movq 0x88(%rsp), %rdi
callq 0x1bd340
movq 0x88(%rsp), %rax
movq %rax, 0x18(%rsp)
movq 0xa8(%rsp), %rax
movq 0x8(%rax), %rdi
callq 0x11dee0
movq 0x18(%rsp), %rdi
movq %rax, %rsi
movq 0x98(%rsp), %rdx
movq 0xb0(%rsp), %rcx
callq 0x1bcf80
movl %eax, 0xa4(%rsp)
movq 0x88(%rsp), %rdi
callq 0x1bce30
jmp 0x2192d
movq 0x90(%rsp), %rdi
callq 0xae070
cmpq $0x0, 0x98(%rsp)
je 0x21969
movq 0x98(%rsp), %rdi
movq 0x61a5e4(%rip), %rax    # 0x63bf38
movq (%rax), %rsi
callq 0x121d70
movq 0x98(%rsp), %rdi
callq 0x121f00
movl 0xa4(%rsp), %eax
addq $0xd8, %rsp
retq
nopl (%rax,%rax)