// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_readjoiner_assembly.c
// Function: gt_readjoiner_assembly_paths2seq
static int gt_readjoiner_assembly_paths2seq(const char *readset,
    GtUword lengthcutoff, bool showpaths, bool astat,
    double coverage, bool load_copynum, GtUword buffersize,
    GtLogger *default_logger, GtTimer **timer, GtError *err)
{
  int had_err;
  GtEncseqLoader *el = gt_encseq_loader_new();
  GtEncseq *reads;

  if (gt_showtime_enabled())
  {
    gt_assert(timer != NULL);
    if (*timer == NULL) /* paths2seq */
    {
      *timer = gt_timer_new_with_progress_description(
          GT_READJOINER_ASSEMBLY_MSG_PUMPENCSEQ);
      gt_timer_show_cpu_time_by_progress(*timer);
      gt_timer_start(*timer);
    }
    else
      gt_timer_show_progress(*timer, GT_READJOINER_ASSEMBLY_MSG_PUMPENCSEQ,
          stdout);
  }
  gt_logger_log(default_logger, GT_READJOINER_ASSEMBLY_MSG_PUMPENCSEQ);
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  gt_encseq_loader_mirror(el);
  reads = gt_encseq_loader_load(el, readset, err);
  gt_assert(reads != NULL);
  gt_readjoiner_assembly_pump_encseq_through_cache(reads);
  if (gt_showtime_enabled())
    gt_timer_show_progress(*timer, GT_READJOINER_ASSEMBLY_MSG_OUTPUTCONTIGS,
        stdout);
  gt_logger_log(default_logger, GT_READJOINER_ASSEMBLY_MSG_OUTPUTCONTIGS);
  had_err = gt_contigpaths_to_fasta(readset, GT_READJOINER_SUFFIX_CONTIG_PATHS,
      GT_READJOINER_SUFFIX_CONTIGS, reads, lengthcutoff, showpaths,
      astat, coverage, load_copynum, (size_t)buffersize, default_logger, err);
  gt_encseq_delete(reads);
  gt_encseq_loader_delete(el);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %rbx
subq $0x78, %rsp
movb %r8b, %al
movq 0xa0(%rsp), %r8
movq 0x98(%rsp), %r8
movq 0x90(%rsp), %r8
movq %rdi, 0x70(%rsp)
movq %rsi, 0x68(%rsp)
andb $0x1, %dl
movb %dl, 0x67(%rsp)
andb $0x1, %cl
movb %cl, 0x66(%rsp)
movsd %xmm0, 0x58(%rsp)
andb $0x1, %al
movb %al, 0x57(%rsp)
movq %r9, 0x48(%rsp)
callq 0xb7a40
movq %rax, 0x38(%rsp)
callq 0x11aa90
testb $0x1, %al
jne 0x4edc2
jmp 0x4ee76
jmp 0x4edc4
cmpq $0x0, 0x98(%rsp)
jne 0x4ee07
movq 0x5ed1ca(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4c7233(%rip), %rsi    # 0x516013
leaq 0x4d5366(%rip), %rdx    # 0x52414d
leaq 0x4d536d(%rip), %rcx    # 0x52415b
leaq 0x4d4b64(%rip), %r8     # 0x523959
movl $0x166, %r9d            # imm = 0x166
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x4ee09
movq 0x98(%rsp), %rax
cmpq $0x0, (%rax)
jne 0x4ee53
leaq 0x4d535e(%rip), %rdi    # 0x52417c
callq 0x1213a0
movq %rax, %rcx
movq 0x98(%rsp), %rax
movq %rcx, (%rax)
movq 0x98(%rsp), %rax
movq (%rax), %rdi
callq 0x121ec0
movq 0x98(%rsp), %rax
movq (%rax), %rdi
callq 0x1213f0
jmp 0x4ee74
movq 0x98(%rsp), %rax
movq (%rax), %rdi
movq 0x5ed0d3(%rip), %rax    # 0x63bf38
movq (%rax), %rdx
leaq 0x4d530d(%rip), %rsi    # 0x52417c
callq 0x121930
jmp 0x4ee76
movq 0x90(%rsp), %rdi
leaq 0x4d52f7(%rip), %rsi    # 0x52417c
movb $0x0, %al
callq 0xe7cd0
movq 0x38(%rsp), %rdi
callq 0xba570
movq 0x38(%rsp), %rdi
callq 0xba760
movq 0x38(%rsp), %rdi
callq 0xba710
movq 0x38(%rsp), %rdi
movq 0x70(%rsp), %rsi
movq 0xa0(%rsp), %rdx
callq 0xb7aa0
movq %rax, 0x30(%rsp)
cmpq $0x0, 0x30(%rsp)
jne 0x4ef06
movq 0x5ed0cb(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4c7134(%rip), %rsi    # 0x516013
leaq 0x530898(%rip), %rdx    # 0x57f77e
leaq 0x4d526e(%rip), %rcx    # 0x52415b
leaq 0x4d4a65(%rip), %r8     # 0x523959
movl $0x177, %r9d            # imm = 0x177
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x4ef08
movq 0x30(%rsp), %rdi
callq 0x4f180
callq 0x11aa90
testb $0x1, %al
jne 0x4ef1d
jmp 0x4ef3e
movq 0x98(%rsp), %rax
movq (%rax), %rdi
movq 0x5ed009(%rip), %rax    # 0x63bf38
movq (%rax), %rdx
leaq 0x4d525d(%rip), %rsi    # 0x524196
callq 0x121930
movq 0x90(%rsp), %rdi
leaq 0x4d5249(%rip), %rsi    # 0x524196
movb $0x0, %al
callq 0xe7cd0
movq 0x70(%rsp), %rdi
movq 0x30(%rsp), %rcx
movq 0x68(%rsp), %r8
movb 0x67(%rsp), %r9b
movb 0x66(%rsp), %bpl
movsd 0x58(%rsp), %xmm0
movb 0x57(%rsp), %bl
movq 0x48(%rsp), %r11
movq 0x90(%rsp), %r10
movq 0xa0(%rsp), %rax
leaq 0x4d54f3(%rip), %rsi    # 0x524486
leaq 0x4d4c29(%rip), %rdx    # 0x523bc3
andb $0x1, %r9b
andb $0x1, %bpl
andb $0x1, %bl
movzbl %r9b, %r9d
movzbl %bpl, %ebp
movl %ebp, (%rsp)
movzbl %bl, %ebx
movl %ebx, 0x8(%rsp)
movq %r11, 0x10(%rsp)
movq %r10, 0x18(%rsp)
movq %rax, 0x20(%rsp)
callq 0x27ca70
movl %eax, 0x44(%rsp)
movq 0x30(%rsp), %rdi
callq 0xae070
movq 0x38(%rsp), %rdi
callq 0xb7e50
movl 0x44(%rsp), %eax
addq $0x78, %rsp
popq %rbx
popq %rbp
retq
nop