// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/hpol_processor.c
// Function: gt_hpol_processor_run
int gt_hpol_processor_run(GtHpolProcessor *hpp, GtLogger *logger, GtError *err)
{
  int had_err = 0;
  GtUword i, hlen, tlen;
  GtUchar prev, c;
  bool coding = false;
  bool end_of_annotation = true;
  GtEncseqReader *esr;
  gt_assert(hpp != NULL);
  gt_assert(hpp->encseq != NULL);
  esr = gt_encseq_create_reader_with_readmode(hpp->encseq,
      GT_READMODE_FORWARD, 0);
  tlen = gt_encseq_total_length(hpp->encseq);
  prev = gt_encseq_reader_next_encoded_char(esr);
  hlen = 1UL;
  if (hpp->cds_oracle != NULL)
    had_err = gt_seqpos_classifier_position_is_inside_feature(
        hpp->cds_oracle, 0, &coding, &end_of_annotation, err);
  for (i = 1UL; i < tlen && !had_err; i++)
  {
    if (hpp->cds_oracle != NULL)
    {
      had_err = gt_seqpos_classifier_position_is_inside_feature(
          hpp->cds_oracle, i, &coding, &end_of_annotation, err);
    }
    if (!had_err)
    {
      c = gt_encseq_reader_next_encoded_char(esr);
      if (prev == c)
      {
        hlen++;
      }
      else
      {
        if (hlen >= hpp->hmin && (hpp->cds_oracle == NULL || coding))
          gt_hpol_processor_process_hpol_end(hpp, prev, i - 1UL, hlen);
        hlen = 1UL;
      }
      prev = c;
    }
  }
  if (!had_err)
  {
    if (hlen >= hpp->hmin && (hpp->cds_oracle == NULL || coding))
      gt_hpol_processor_process_hpol_end(hpp, prev, i - 1UL, hlen);
  }
  gt_encseq_reader_delete(esr);
  gt_aligned_segments_pile_flush(hpp->asp, true);
  if (!had_err && hpp->processed_segments != NULL)
  {
    for (i = 0; i < hpp->nfiles; i++)
      had_err = gt_hpol_processor_output_sorted_segments(hpp,
          hpp->reads_iters[i], hpp->outfiles[i], err);
  }
  if (logger != NULL && !had_err)
    gt_hpol_processor_show_hdist(hpp, logger);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %rdx, 0x38(%rsp)
movq %rsi, 0x20(%rsp)
movb $0x0, 0x6(%rsp)
movb $0x1, 0x7(%rsp)
testq %rdi, %rdi
je 0xef46d
movq %rdi, %r14
movq (%rdi), %rdi
testq %rdi, %rdi
je 0xef49b
xorl %r12d, %r12d
xorl %esi, %esi
xorl %edx, %edx
callq 0x72260
movq %rax, %rbx
movq (%r14), %rdi
callq 0x7055e
movq %rax, 0x30(%rsp)
movq %rbx, 0x28(%rsp)
movq %rbx, %rdi
callq 0x70f55
movl %eax, %ebx
movq %r14, 0x10(%rsp)
movq 0x60(%r14), %rdi
testq %rdi, %rdi
je 0xeedf8
leaq 0x6(%rsp), %rdx
leaq 0x7(%rsp), %rcx
xorl %esi, %esi
movq 0x38(%rsp), %r8
callq 0x117765
movl %eax, %r12d
pushq $0x1
popq %rax
xorl %r14d, %r14d
movq %rax, 0x8(%rsp)
movq %r14, %r15
incq %r14
movzbl %bl, %ebp
cmpq 0x30(%rsp), %r14
jae 0xeeeac
testl %r12d, %r12d
jne 0xeeeac
movq 0x10(%rsp), %rax
movq 0x60(%rax), %rdi
testq %rdi, %rdi
je 0xeee4e
movq %r14, %rsi
leaq 0x6(%rsp), %rdx
leaq 0x7(%rsp), %rcx
movq 0x38(%rsp), %r8
callq 0x117765
testl %eax, %eax
je 0xeee4e
movl %eax, %r12d
jmp 0xeee64
movq 0x28(%rsp), %rdi
callq 0x70f55
cmpb %al, %bl
jne 0xeee69
incq 0x8(%rsp)
xorl %r12d, %r12d
movl %ebx, %r13d
jmp 0xeeea4
movl %eax, %r13d
xorl %r12d, %r12d
movq 0x10(%rsp), %rax
movq 0x8(%rsp), %rcx
cmpq 0x8(%rax), %rcx
jb 0xeee9c
cmpq $0x0, 0x60(%rax)
je 0xeee8d
cmpb $0x1, 0x6(%rsp)
jne 0xeee9c
movq 0x10(%rsp), %rdi
movl %ebp, %esi
movq %r15, %rdx
callq 0xef4fa
pushq $0x1
popq %rax
movq %rax, 0x8(%rsp)
movl %r13d, %ebx
jmp 0xeee03
testl %r12d, %r12d
je 0xeeede
movq 0x28(%rsp), %rdi
callq 0x722ae
movq 0x10(%rsp), %rax
movq 0x68(%rax), %rdi
pushq $0x1
popq %rsi
callq 0xb4d61
movl %r12d, %eax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x10(%rsp), %rbx
movq 0x8(%rsp), %rax
cmpq 0x8(%rbx), %rax
jb 0xeef0e
cmpq $0x0, 0x60(%rbx)
je 0xeeefc
cmpb $0x1, 0x6(%rsp)
jne 0xeef0e
movq %rbx, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq 0x8(%rsp), %rcx
callq 0xef4fa
movq 0x28(%rsp), %rdi
callq 0x722ae
movq 0x68(%rbx), %rdi
pushq $0x1
popq %rsi
callq 0xb4d61
cmpq $0x0, 0xe8(%rbx)
movq %rbx, %rbp
je 0xef044
leaq 0x40(%rsp), %r14
xorl %ecx, %ecx
xorl %r12d, %r12d
cmpq 0xe0(%rbp), %rcx
jae 0xef047
cmpq $0x0, 0xe8(%rbp)
je 0xef407
movq 0xd8(%rbp), %rax
movq (%rax,%rcx,8), %rbx
testq %rbx, %rbx
je 0xef435
movq 0xd0(%rbp), %rax
movq %rcx, 0x30(%rsp)
movq (%rax,%rcx,8), %r15
callq 0xacb84
movq %rax, %r13
movq %rbx, %rdi
leaq 0x50(%rsp), %rsi
leaq 0x48(%rsp), %rdx
movq %r14, %rcx
movq 0x38(%rsp), %r8
callq 0xa62e5
testl %eax, %eax
jle 0xef02c
movq 0x40(%rsp), %rsi
movq %r13, %rdi
callq 0xacc8b
xorl %ebp, %ebp
movq 0x40(%rsp), %r12
movq %r12, %rdi
callq 0x172d0
cmpq %rax, %rbp
jae 0xeefda
cmpb $0x20, (%r12,%rbp)
jne 0xeefd5
movb $0x0, (%r12,%rbp)
incq %rbp
jmp 0xeefb7
movq 0x10(%rsp), %rbp
movq 0xe8(%rbp), %rdi
movq %r12, %rsi
callq 0x8f482
testq %rax, %rax
je 0xef014
movq %rax, %r12
movq %r13, %rdi
callq 0xad1fa
movq %r12, %rdi
pushq $0x1
popq %rsi
movq %r15, %rdx
movq %rax, %rcx
callq 0xefcc3
jmp 0xeef86
movq 0x40(%rsp), %rsi
leaq 0x23546d(%rip), %rdi    # 0x32448d
xorl %eax, %eax
callq 0xb2cd0
jmp 0xeef86
movl %eax, %r12d
movq %r13, %rdi
callq 0xae103
movq 0x30(%rsp), %rcx
incq %rcx
jmp 0xeef3f
xorl %r12d, %r12d
movq 0x20(%rsp), %rbx
testq %rbx, %rbx
je 0xeeecc
testl %r12d, %r12d
jne 0xeeecc
cmpq $0x0, 0x50(%rbp)
je 0xef4c9
movq 0x8(%rbp), %rdx
cmpq $0x0, 0x60(%rbp)
leaq 0x1ff77f(%rip), %rax    # 0x2ee7f8
leaq 0x23547f(%rip), %rcx    # 0x3244ff
cmoveq %rax, %rcx
leaq 0x235443(%rip), %rsi    # 0x3244ce
movq %rbx, %rdi
xorl %eax, %eax
callq 0x92e71
leaq 0x235477(%rip), %rsi    # 0x324513
movq %rbx, %rdi
xorl %eax, %eax
callq 0x92e71
movq 0x8(%rbp), %rbx
leaq 0x23547c(%rip), %r14    # 0x32452d
cmpq 0xa0(%rbp), %rbx
ja 0xef15f
movq 0x50(%rbp), %rdi
movq %rbx, %rsi
callq 0x6da5e
testq %rax, %rax
je 0xef157
movq %rax, %r15
movq 0x58(%rbp), %rdi
movq %rbx, %rsi
callq 0x6da5e
movq %rax, %r12
movq 0x58(%rbp), %rdi
movq %rbx, %rsi
callq 0x6da5e
movq %rax, %xmm1
movq 0x1f87e2(%rip), %xmm3   # 0x2e78e0
punpckldq %xmm3, %xmm1    # xmm1 = xmm1[0],xmm3[0],xmm1[1],xmm3[1]
movapd 0x1f87e6(%rip), %xmm2   # 0x2e78f0
subpd %xmm2, %xmm1
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa6be(%rip), %xmm0   # 0x2e97e0
movq %r15, %xmm1
punpckldq %xmm3, %xmm1    # xmm1 = xmm1[0],xmm3[0],xmm1[1],xmm3[1]
subpd %xmm2, %xmm1
movapd %xmm1, %xmm2
unpckhpd %xmm1, %xmm2            # xmm2 = xmm2[1],xmm1[1]
addsd %xmm1, %xmm2
divsd %xmm2, %xmm0
movq 0x20(%rsp), %rdi
movq %r14, %rsi
movq %rbx, %rdx
movq %r15, %rcx
movq %r12, %r8
movb $0x1, %al
callq 0x92e71
incq %rbx
jmp 0xef0b1
movq 0x98(%rbp), %rcx
movq %rcx, %xmm1
movq 0x1f876d(%rip), %xmm3   # 0x2e78e0
punpckldq %xmm3, %xmm1    # xmm1 = xmm1[0],xmm3[0],xmm1[1],xmm3[1]
movapd 0x1f8771(%rip), %xmm2   # 0x2e78f0
subpd %xmm2, %xmm1
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa649(%rip), %xmm0   # 0x2e97e0
movq 0x90(%rbp), %rdx
movq %rdx, %xmm1
punpckldq %xmm3, %xmm1    # xmm1 = xmm1[0],xmm3[0],xmm1[1],xmm3[1]
subpd %xmm2, %xmm1
movapd %xmm1, %xmm2
unpckhpd %xmm1, %xmm2            # xmm2 = xmm2[1],xmm1[1]
addsd %xmm1, %xmm2
divsd %xmm2, %xmm0
leaq 0x235387(%rip), %rsi    # 0x324549
movq 0x20(%rsp), %rbx
movq %rbx, %rdi
movb $0x1, %al
callq 0x92e71
movq 0x60(%rbp), %rdi
testq %rdi, %rdi
je 0xef1f3
callq 0x117b53
leaq 0x235380(%rip), %rsi    # 0x324566
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x92e71
xorl %r12d, %r12d
cmpb $0x1, 0xb8(%rbp)
jne 0xeeecc
movq 0x78(%rbp), %rbx
addq 0x70(%rbp), %rbx
movq 0x80(%rbp), %r14
addq %rbx, %r14
addq 0x88(%rbp), %r14
leaq 0x235359(%rip), %rsi    # 0x32457c
xorl %r12d, %r12d
movq 0x20(%rsp), %rdi
movq %r14, %rdx
xorl %eax, %eax
callq 0x92e71
movq %rbx, %xmm1
movq 0x1f869e(%rip), %xmm0   # 0x2e78e0
punpckldq %xmm0, %xmm1    # xmm1 = xmm1[0],xmm0[0],xmm1[1],xmm0[1]
movdqa %xmm0, %xmm2
movapd 0x1f869e(%rip), %xmm0   # 0x2e78f0
subpd %xmm0, %xmm1
movapd %xmm0, %xmm3
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
movsd 0x1fa572(%rip), %xmm1   # 0x2e97e0
mulsd %xmm1, %xmm0
movq %r14, %xmm1
movq 0x20(%rsp), %r14
punpckldq %xmm2, %xmm1    # xmm1 = xmm1[0],xmm2[0],xmm1[1],xmm2[1]
subpd %xmm3, %xmm1
movapd %xmm1, %xmm2
unpckhpd %xmm1, %xmm2            # xmm2 = xmm2[1],xmm1[1]
addsd %xmm1, %xmm2
movapd %xmm2, 0x10(%rsp)
divsd %xmm2, %xmm0
leaq 0x2352fb(%rip), %rsi    # 0x32459c
movq %r14, %rdi
movq %rbx, %rdx
movb $0x1, %al
callq 0x92e71
movq 0x78(%rbp), %rdx
movq %rdx, %xmm1
punpckldq 0x1f8621(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x1f8629(%rip), %xmm1   # 0x2e78f0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa505(%rip), %xmm0   # 0x2e97e0
divsd 0x10(%rsp), %xmm0
leaq 0x2352df(%rip), %rsi    # 0x3245c7
movq %r14, %rdi
movb $0x1, %al
callq 0x92e71
movq 0x70(%rbp), %rdx
movq %rdx, %xmm1
punpckldq 0x1f85dd(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x1f85e5(%rip), %xmm1   # 0x2e78f0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa4c1(%rip), %xmm0   # 0x2e97e0
divsd 0x10(%rsp), %xmm0
leaq 0x2352c6(%rip), %rsi    # 0x3245f2
movq %r14, %rdi
movb $0x1, %al
callq 0x92e71
movq 0x80(%rbp), %rdx
movq %rdx, %xmm1
punpckldq 0x1f8596(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x1f859e(%rip), %xmm1   # 0x2e78f0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa47a(%rip), %xmm0   # 0x2e97e0
divsd 0x10(%rsp), %xmm0
leaq 0x2352aa(%rip), %rsi    # 0x32461d
movq %r14, %rdi
movb $0x1, %al
callq 0x92e71
movq 0x88(%rbp), %rdx
movq %rdx, %xmm1
punpckldq 0x1f854f(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x1f8557(%rip), %xmm1   # 0x2e78f0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x1fa433(%rip), %xmm0   # 0x2e97e0
divsd 0x10(%rsp), %xmm0
leaq 0x23528e(%rip), %rsi    # 0x324648
movq %r14, %rdi
movb $0x1, %al
callq 0x92e71
cmpq $0x0, 0xe8(%rbp)
je 0xeeecc
movq 0xa8(%rbp), %rdx
leaq 0x235293(%rip), %rsi    # 0x324673
xorl %r12d, %r12d
movq %r14, %rdi
xorl %eax, %eax
callq 0x92e71
movq 0xb0(%rbp), %rsi
leaq 0x23529a(%rip), %rdi    # 0x324695
xorl %eax, %eax
callq 0x92a82
jmp 0xeeecc
movq 0x348b5a(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1f5bfb(%rip), %rsi    # 0x2e5013
leaq 0x23503b(%rip), %rdx    # 0x32445a
leaq 0x23500b(%rip), %rcx    # 0x324431
leaq 0x234594(%rip), %r8     # 0x3239c1
movl $0x38d, %r9d            # imm = 0x38D
jmp 0xef461
movq 0x348b2c(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1f5bcd(%rip), %rsi    # 0x2e5013
leaq 0x23502d(%rip), %rdx    # 0x32447a
leaq 0x234fdd(%rip), %rcx    # 0x324431
leaq 0x234566(%rip), %r8     # 0x3239c1
movl $0x38e, %r9d            # imm = 0x38E
xorl %eax, %eax
callq 0x17a50
callq 0x17390
movq 0x348af4(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1f5b95(%rip), %rsi    # 0x2e5013
leaq 0x234579(%rip), %rdx    # 0x3239fe
leaq 0x2346bd(%rip), %rcx    # 0x323b49
leaq 0x23452e(%rip), %r8     # 0x3239c1
movl $0x3ae, %r9d            # imm = 0x3AE
jmp 0xef461
movq 0x348ac6(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1f5b67(%rip), %rsi    # 0x2e5013
leaq 0x2346ac(%rip), %rdx    # 0x323b5f
leaq 0x23468f(%rip), %rcx    # 0x323b49
leaq 0x234500(%rip), %r8     # 0x3239c1
movl $0x3af, %r9d            # imm = 0x3AF
jmp 0xef461
movq 0x348a98(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1f5b39(%rip), %rsi    # 0x2e5013
leaq 0x234fda(%rip), %rdx    # 0x3244bb
leaq 0x234fb6(%rip), %rcx    # 0x32449e
leaq 0x2344d2(%rip), %r8     # 0x3239c1
movl $0x34f, %r9d            # imm = 0x34F
jmp 0xef461