// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/rcr.c
// Function: gt_rcr_encoder_new
GtRcrEncoder *gt_rcr_encoder_new(const GtEncseq *ref,
                                 const char *filename,
                                 bool vquals,
                                 bool mquals,
                                 bool quals,
                                 bool ureads,
                                 bool descs,
                                 GtTimer *timer,
                                 GtError *err)
{
  int had_err = 0;
  GtRcrEncoder *rcr_enc;

  gt_error_check(err);
  gt_assert(ref && filename);

  if (timer != NULL)
    gt_timer_show_progress(timer, "Initializing RcrEncoder", stdout);

  rcr_enc = gt_rcr_encoder_init(filename, ref);

  if (quals) {
    gt_assert(!vquals);
    rcr_enc->store_all_qual = true;
  }
  if (vquals) {
    gt_assert(!quals);
    rcr_enc->store_var_qual = true;
  }
  if (mquals)
    rcr_enc->store_mapping_qual = true;
  if (ureads)
    rcr_enc->store_unmmaped_reads = true;

  if (!(gt_alphabet_is_dna(gt_encseq_alphabet(ref)))) {
    gt_error_set(err, "alphabet has to be DNA");
    had_err = -1;
  }

  if (!had_err)
    had_err = gt_rcr_analyse_alignment_data(rcr_enc, timer, err);

  if (!had_err)
    had_err = rcr_initialize_encoders(rcr_enc, timer, err);

  if (!had_err && descs)
    had_err = gt_rcr_init_desc_encoding(rcr_enc, timer, err);

  if (!had_err)
    return rcr_enc;
  else {
    gt_rcr_encoder_delete(rcr_enc);
    return NULL;
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
movl %r9d, %ebp
movl %r8d, %r13d
movl %ecx, %r14d
movl %edx, %r12d
movq %rsi, %rbx
movq %rdi, %r15
movq 0xd0(%rsp), %rdi
testq %rdi, %rdi
je 0x108ed9
callq 0x89eb7
testb %al, %al
jne 0x1099e1
testq %r15, %r15
je 0x1099b3
testq %rbx, %rbx
je 0x1099b3
movl %r13d, 0x30(%rsp)
movl %r14d, 0x60(%rsp)
movl %ebp, 0x28(%rsp)
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x108f1c
movq 0x32efa3(%rip), %rax    # 0x437eb0
movq (%rax), %rdx
leaq 0x22613f(%rip), %rsi    # 0x32f056
callq 0xaf86f
movq %r15, %rdi
callq 0x754dd
movq %rax, %rdi
callq 0x56cd2
movl %eax, %ebp
leaq 0x2260fe(%rip), %r13    # 0x32f033
movl $0x1c0, %edi            # imm = 0x1C0
movq %r13, %rsi
movl $0x3c6, %edx            # imm = 0x3C6
callq 0x93160
movq %rax, %r14
movq %r15, 0x98(%rax)
movq %rbx, 0xa0(%rax)
callq 0x9e2bc
movq %rax, 0xb0(%r14)
callq 0x6d958
movq %rax, 0x38(%r14)
callq 0x6d958
movq %rax, 0x40(%r14)
callq 0x6d958
movq %rax, 0x20(%r14)
callq 0x6d958
movq %rax, 0x28(%r14)
callq 0x6d958
movq %rax, 0x30(%r14)
pushq $0x1
popq %rdi
pushq $0x38
popq %rsi
callq 0x174c0
movq %rax, 0x90(%r14)
andq $0x0, 0x18(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x48(%r14)
movups %xmm0, 0x58(%r14)
movups %xmm0, 0x68(%r14)
movups %xmm0, 0x78(%r14)
andq $0x0, 0x88(%r14)
movb $0x1, 0x1b8(%r14)
incl %ebp
movups %xmm0, 0x180(%r14)
movups %xmm0, 0x190(%r14)
movups %xmm0, 0x1a0(%r14)
andq $0x0, 0x1b0(%r14)
andl $0x0, 0x1ba(%r14)
movb $0x0, 0x1be(%r14)
pushq $0x8
popq %rsi
movq %rbp, %rdi
movq %r13, %rdx
movq %r14, %r13
movl $0x3ea, %ecx            # imm = 0x3EA
callq 0x9334a
movq %rax, 0xa8(%r14)
xorl %ecx, %ecx
cmpq %rcx, %rbp
je 0x10902f
andq $0x0, (%rax,%rcx,8)
incq %rcx
jmp 0x109020
movq %r13, %rcx
addq $0xf0, %rcx
pushq $0x1e
popq %rax
cmpq $0x28, %rax
je 0x10904d
andq $0x0, (%r13,%rax,8)
incq %rax
jmp 0x10903c
cmpb $0x0, 0x30(%rsp)
je 0x109067
testb %r12b, %r12b
jne 0x109a12
movb $0x1, 0x1bb(%r13)
jmp 0x109074
testb %r12b, %r12b
je 0x109074
movb $0x1, 0x1be(%r13)
cmpb $0x0, 0x60(%rsp)
je 0x109083
movb $0x1, 0x1bc(%r13)
movq %rcx, 0x68(%rsp)
cmpb $0x0, 0x28(%rsp)
je 0x109097
movb $0x1, 0x1bd(%r13)
movq %r15, %rdi
callq 0x754dd
movq %rax, %rdi
callq 0x5741b
testb %al, %al
je 0x1096e4
movq 0xa0(%r13), %rdi
leaq 0x23c9e0(%rip), %rsi    # 0x345a9d
xorl %edx, %edx
callq 0x1f7bdc
movq %rax, 0x38(%rsp)
cmpq $0x0, 0x90(%r13)
je 0x109a43
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x1090fa
movq 0x32edc5(%rip), %rax    # 0x437eb0
movq (%rax), %rdx
leaq 0x226135(%rip), %rsi    # 0x32f22a
callq 0xaf86f
cmpq $0x0, 0x38(%rsp)
setne %dl
jne 0x109126
movl %edx, %ebx
movq 0xa0(%r13), %rdx
leaq 0x226134(%rip), %rsi    # 0x32f249
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0x89dbb
movl %ebx, %edx
movl $0x0, 0x24(%rsp)
movq %r13, 0x8(%rsp)
testb $0x1, %dl
je 0x1096ff
movq 0x90(%r13), %rsi
movq 0x38(%rsp), %rdi
callq 0x1f809f
testl %eax, %eax
js 0x10971c
movq 0x90(%r13), %r14
testq %r14, %r14
je 0x10994f
movl (%r14), %ebx
cmpl %ebx, 0x24(%rsp)
je 0x109197
movslq %ebx, %rsi
andq $0x0, 0x1a8(%r13)
movq 0x98(%r13), %rdi
callq 0x74d9c
movq %rax, 0x188(%r13)
movq 0x90(%r13), %r14
movl %ebx, 0x24(%rsp)
movslq 0x4(%r14), %rax
cmpq %rax, 0x1a8(%r13)
setbe %dl
ja 0x109247
movl (%r14), %eax
movl %eax, 0x24(%rsp)
xorl %eax, %eax
movabsq $0x400000000, %rcx      # imm = 0x400000000
testq %rcx, 0x8(%r14)
setne %al
incq 0x198(%r13,%rax,8)
movq 0x8(%r14), %r15
testq %rcx, %r15
jne 0x109133
movb %dl, 0x7(%rsp)
movq 0x30(%r14), %rax
movq %rax, 0x50(%rsp)
movl 0x10(%r14), %ebp
cmpb $0x1, 0x1bc(%r13)
movl %ebp, %eax
jne 0x10920d
movq 0x40(%r13), %rdi
movl %r15d, %eax
shrl $0x10, %eax
movzbl %al, %esi
callq 0x6d96d
movl 0x10(%r14), %eax
movslq %eax, %rbx
movq 0x20(%r13), %rdi
movq %rbx, %rsi
callq 0x6d96d
movq 0x1b0(%r13), %rax
testq %rax, %rax
je 0x10926d
cmpq %rbx, %rax
je 0x10927b
cmpq %rbx, 0x190(%r13)
jae 0x10923d
movq %rbx, 0x190(%r13)
movb $0x0, 0x1b8(%r13)
jmp 0x10927b
movl %edx, %ebx
movq 0xa0(%r13), %rdx
movq 0xd0(%rsp), %rdi
leaq 0x226002(%rip), %rsi    # 0x32f261
xorl %eax, %eax
callq 0x89dbb
movl %ebx, %edx
jmp 0x109133
movq %rbx, 0x1b0(%r13)
movq %rbx, 0x190(%r13)
movq %r14, 0x40(%rsp)
movq %r15, %r14
shrq $0x30, %r14
shrl $0x18, %r15d
movq 0x50(%rsp), %rax
addq %r15, %rax
movq %rax, 0x70(%rsp)
leaq (%rax,%r14,4), %rax
incl %ebp
sarl %ebp
movslq %ebp, %r12
movq %rax, 0x30(%rsp)
addq %r12, %rax
movq %rax, 0x58(%rsp)
cmpb $0x1, 0x1bb(%r13)
jne 0x1092e3
xorl %r13d, %r13d
cmpq %r13, %rbx
je 0x1092e3
movq 0x58(%rsp), %rax
movzbl (%rax,%r13), %esi
addq $0x21, %rsi
movq 0x8(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0x6d96d
incq %r13
jmp 0x1092bd
shlq $0x2, %r14
movq 0x40(%rsp), %rbx
movslq 0x4(%rbx), %rbp
movq %rbp, %rsi
movq 0x8(%rsp), %r13
subq 0x1a8(%r13), %rsi
movq 0x28(%r13), %rdi
callq 0x6d96d
movq %rbp, 0x48(%rsp)
movq %rbp, 0x1a8(%r13)
addq %r12, %r14
addq %r15, %r14
addq %r14, 0x50(%rsp)
movq %rbx, %r14
movb $0x1, %al
movl %eax, (%rsp)
xorl %r12d, %r12d
xorl %ebx, %ebx
xorl %ecx, %ecx
movzwl 0xe(%r14), %eax
cmpq %rax, %rcx
jae 0x1096a7
movq %rbx, 0x10(%rsp)
movq 0x98(%r13), %rdi
movq %rcx, %rbx
callq 0x754dd
movq %rax, %r15
movq %rax, %rdi
callq 0x56cd2
movq %rax, 0x18(%rsp)
movq 0x70(%rsp), %rax
movq %rbx, 0x80(%rsp)
movl (%rax,%rbx,4), %edx
movl %edx, %eax
andl $0xf, %eax
leal -0x7(%rax), %ecx
cmpl $0x2, %ecx
movl $0x0, %ecx
cmovbl %ecx, %eax
cmpl $0x4, %eax
ja 0x109677
shrl $0x4, %edx
leaq 0x225c3e(%rip), %rcx    # 0x32efd4
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
movl %edx, %ebp
movq %r12, 0x28(%rsp)
jmpq *%rax
movq 0x50(%rsp), %rax
addq %r12, %rax
movq %rax, 0x78(%rsp)
leal (,%r12,4), %ebp
movq %r12, %r13
movq 0x48(%rsp), %r14
movq 0x10(%rsp), %rax
movq %rax, 0x18(%rsp)
xorl %r12d, %r12d
movq %rdx, 0x60(%rsp)
cmpq %r12, %rdx
je 0x1095f8
movq %r13, %rax
shrq %rax
movq 0x30(%rsp), %rcx
movb (%rcx,%rax), %al
movl %ebp, %ecx
notb %cl
andb $0x4, %cl
shrb %cl, %al
andb $0xf, %al
movzbl %al, %edi
movq %r15, %rsi
callq 0x10ca09
movl %eax, %ebx
movq 0x8(%rsp), %rax
movq 0x98(%rax), %rdi
movq 0x188(%rax), %rsi
addq %r14, %rsi
xorl %edx, %edx
callq 0x705e4
cmpb %bl, %al
je 0x10945d
movq 0x8(%rsp), %rax
incq 0xf0(%rax)
cmpb $0x1, 0x1be(%rax)
jne 0x109451
movq 0x78(%rsp), %rcx
movzbl (%rcx,%r12), %esi
addq $0x21, %rsi
movq 0x38(%rax), %rdi
callq 0x6d96d
movl $0x0, (%rsp)
movq %r13, 0x18(%rsp)
incq %r12
incq %r14
incq %r13
addb $0x4, %bpl
movq 0x60(%rsp), %rdx
jmp 0x1093d5
incq 0x110(%r13)
movq 0x18(%rsp), %rax
leal -0x1(%rax), %r14d
leal (,%r12,4), %r12d
xorl %r13d, %r13d
cmpq %r13, %rbp
je 0x1094fc
movq 0x28(%rsp), %rax
addq %r13, %rax
shrq %rax
movq 0x30(%rsp), %rcx
movb (%rcx,%rax), %al
movl %r12d, %ecx
notb %cl
andb $0x4, %cl
shrb %cl, %al
andb $0xf, %al
movzbl %al, %edi
movq %r15, %rsi
callq 0x10ca09
movl %eax, %ebx
movq %r15, %rdi
callq 0x56d5a
movsbl %al, %esi
movq %r15, %rdi
callq 0x57552
cmpb %al, %bl
je 0x1094dc
movzbl %bl, %eax
jmp 0x1094e0
movzbl %r14b, %eax
movq 0x8(%rsp), %rcx
movq 0xa8(%rcx), %rcx
movzbl %al, %eax
incq (%rcx,%rax,8)
incq %r13
addb $0x4, %r12b
jmp 0x10948f
movq 0x8(%rsp), %r13
cmpb $0x1, 0x1be(%r13)
movq 0x10(%rsp), %r15
movq 0x28(%rsp), %r12
jne 0x109666
movq 0x58(%rsp), %rax
leaq (%rax,%r12), %rbx
xorl %r14d, %r14d
cmpq %r14, %rbp
je 0x109666
movzbl (%rbx,%r14), %esi
addq $0x21, %rsi
movq 0x38(%r13), %rdi
callq 0x6d96d
incq %r14
jmp 0x109525
incq 0x100(%r13)
jmp 0x109555
incq 0x108(%r13)
addq %rbp, 0x48(%rsp)
movl $0x0, (%rsp)
movq %r12, %rbp
jmp 0x109614
incq 0xf8(%r13)
movq 0x18(%rsp), %rax
leal -0x1(%rax), %r14d
leal (,%r12,4), %r13d
xorl %ebx, %ebx
cmpq %rbx, %rbp
je 0x10961b
leaq (%r12,%rbx), %rax
shrq %rax
movq 0x30(%rsp), %rcx
movb (%rcx,%rax), %al
movl %r13d, %ecx
notb %cl
andb $0x4, %cl
shrb %cl, %al
andb $0xf, %al
movzbl %al, %edi
movq %r15, %rsi
callq 0x10ca09
movl %eax, %r12d
movq %r15, %rdi
callq 0x56d5a
movsbl %al, %esi
movq %r15, %rdi
callq 0x57552
cmpb %al, %r12b
je 0x1095d3
movzbl %r12b, %eax
jmp 0x1095d7
movzbl %r14b, %eax
movq 0x8(%rsp), %rcx
movq 0xa8(%rcx), %rcx
movzbl %al, %eax
incq (%rcx,%rax,8)
incq %rbx
addb $0x4, %r13b
movq 0x28(%rsp), %r12
jmp 0x109583
movq 0x28(%rsp), %rbp
addq %rdx, %rbp
addq %rdx, 0x48(%rsp)
movq 0x18(%rsp), %r12
movq 0x8(%rsp), %r13
movq 0x40(%rsp), %r14
movq 0x10(%rsp), %r15
jmp 0x109682
movq 0x8(%rsp), %r13
movq 0xa8(%r13), %rax
movl 0x18(%rsp), %ecx
incq (%rax,%rcx,8)
cmpb $0x1, 0x1be(%r13)
movq 0x10(%rsp), %r15
jne 0x109666
movq 0x58(%rsp), %rax
leaq (%rax,%r12), %rbx
xorl %r14d, %r14d
cmpq %r14, %rbp
je 0x109666
movzbl (%rbx,%r14), %esi
addq $0x21, %rsi
movq 0x38(%r13), %rdi
callq 0x6d96d
incq %r14
jmp 0x10964a
addq %r12, %rbp
movl $0x0, (%rsp)
movq 0x40(%rsp), %r14
jmp 0x109682
movq %r12, %rbp
movq 0x10(%rsp), %r15
movq %r15, %r12
movq %r12, %rbx
movq %r12, %rsi
subq %r15, %rsi
movq 0x30(%r13), %rdi
callq 0x6d96d
movq 0x80(%rsp), %rcx
incq %rcx
movq %rbp, %r12
jmp 0x10932e
testb $0x1, (%rsp)
jne 0x1096c0
movq 0xb0(%r13), %rdi
movq 0x180(%r13), %rsi
callq 0x9e2d1
movslq 0x4(%r14), %rax
testq %rax, %rax
js 0x109987
movq %rax, 0x1a8(%r13)
incq 0x180(%r13)
movb 0x7(%rsp), %dl
jmp 0x109133
leaq 0x22598b(%rip), %rsi    # 0x32f076
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0x89dbb
jmp 0x10992f
movq 0x198(%r13), %rax
movq %rax, 0x138(%r13)
movq 0x38(%rsp), %rdi
callq 0x1f8059
jmp 0x10992f
movq 0x198(%r13), %rax
movq %rax, 0x138(%r13)
movq 0x38(%rsp), %rdi
callq 0x1f8059
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x109757
movq 0x32e768(%rip), %rax    # 0x437eb0
movq (%rax), %rdx
leaq 0x225b25(%rip), %rsi    # 0x32f277
callq 0xaf86f
movq 0x28(%r13), %rdi
callq 0x10ca4e
cmpq $-0x1, %rax
je 0x109912
cmpq $0x1, %rax
adcq $0x0, %rax
movq %rax, %rdi
callq 0xe6f70
movq %rax, 0x50(%r13)
movq 0x30(%r13), %rdi
callq 0x10ca4e
cmpq $-0x1, %rax
je 0x1097a1
cmpq $0x1, %rax
adcq $0x0, %rax
movq %rax, %rdi
callq 0xe6f70
movq %rax, 0x58(%r13)
cmpb $0x0, 0x1b8(%r13)
jne 0x1097c9
movq 0x20(%r13), %rdi
movq 0x190(%r13), %rdx
incq %rdx
leaq 0x32fc(%rip), %rsi      # 0x10cabc
callq 0xf04b4
movq %rax, 0x60(%r13)
cmpb $0x0, 0x1bb(%r13)
jne 0x1097dd
cmpb $0x1, 0x1be(%r13)
jne 0x1097f6
movq 0x38(%r13), %rdi
leaq 0x32d4(%rip), %rsi      # 0x10cabc
movl $0x100, %edx            # imm = 0x100
callq 0xf04b4
movq %rax, 0x68(%r13)
cmpb $0x1, 0x1bc(%r13)
jne 0x109819
movq 0x40(%r13), %rdi
leaq 0x32b1(%rip), %rsi      # 0x10cabc
movl $0x100, %edx            # imm = 0x100
callq 0xf04b4
movq %rax, 0x70(%r13)
leaq 0x32a1(%rip), %rsi      # 0x10cac1
pushq $0xa
popq %rdx
movq 0x68(%rsp), %rdi
callq 0xf04b4
movq %rax, 0x78(%r13)
testq %rax, %rax
je 0x109906
movq 0x98(%r13), %rdi
movq 0xa8(%r13), %rbx
callq 0x754dd
movq %rax, %rdi
callq 0x56cd2
movl %eax, %edx
incq %rdx
leaq 0x3260(%rip), %rsi      # 0x10cac1
movq %rbx, %rdi
callq 0xf04b4
movq %rax, 0x80(%r13)
testq %rax, %rax
je 0x109906
cmpb $0x0, 0xc0(%rsp)
je 0x10993a
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x1098aa
movq 0x32e615(%rip), %rax    # 0x437eb0
movq (%rax), %rdx
leaq 0x225a32(%rip), %rsi    # 0x32f2d7
callq 0xaf86f
callq 0xd1220
movq %rax, 0x48(%r13)
movq %rax, %rdi
callq 0xd12c2
movq 0x98(%r13), %rdi
movq 0xa0(%r13), %rbx
callq 0x754dd
movq %rbx, %rdi
movq %rax, %rsi
movq 0xd0(%rsp), %rbx
movq %rbx, %rdx
callq 0x113c3c
movq %rax, 0x88(%r13)
testq %rax, %rax
je 0x10992f
movq %rax, %rdi
movq %rbx, %rsi
callq 0x11379c
movq %rax, 0x18(%r13)
testq %rax, %rax
jne 0x10993a
jmp 0x10992f
leaq 0x22599e(%rip), %rsi    # 0x32f2ab
jmp 0x1096eb
movq 0xa0(%r13), %rdx
leaq 0x22596d(%rip), %rsi    # 0x32f28d
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0x89dbb
movq %r13, %rdi
callq 0x109a74
xorl %r13d, %r13d
movq %r13, %rax
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x32e612(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1db6b3(%rip), %rsi    # 0x2e5013
leaq 0x22588a(%rip), %rdx    # 0x32f1f1
leaq 0x22589e(%rip), %rcx    # 0x32f20c
leaq 0x2256be(%rip), %r8     # 0x32f033
movl $0x409, %r9d            # imm = 0x409
xorl %eax, %eax
callq 0x17a50
callq 0x17390
movq 0x32e5da(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1df41f(%rip), %rsi    # 0x2e8db7
leaq 0x225694(%rip), %rdx    # 0x32f033
movl $0x3bb, %ecx            # imm = 0x3BB
xorl %eax, %eax
callq 0x17a50
pushq $0x1
popq %rdi
callq 0x178f0
movq 0x32e5ae(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1db64f(%rip), %rsi    # 0x2e5013
leaq 0x22567b(%rip), %rdx    # 0x32f046
leaq 0x22564e(%rip), %rcx    # 0x32f020
leaq 0x22565a(%rip), %r8     # 0x32f033
movl $0x44f, %r9d            # imm = 0x44F
jmp 0x10997b
movq 0x32e580(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1db621(%rip), %rsi    # 0x2e5013
leaq 0x1db7c6(%rip), %rdx    # 0x2e51bf
leaq 0x225620(%rip), %rcx    # 0x32f020
leaq 0x22562c(%rip), %r8     # 0x32f033
movl $0x44e, %r9d            # imm = 0x44E
jmp 0x10997b
movq 0x32e54f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1db5f0(%rip), %rsi    # 0x2e5013
leaq 0x225644(%rip), %rdx    # 0x32f06e
leaq 0x2255ef(%rip), %rcx    # 0x32f020
leaq 0x2255fb(%rip), %r8     # 0x32f033
movl $0x457, %r9d            # imm = 0x457
jmp 0x10997b
movq 0x32e51e(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1db5bf(%rip), %rsi    # 0x2e5013
leaq 0x225796(%rip), %rdx    # 0x32f1f1
leaq 0x2257aa(%rip), %rcx    # 0x32f20c
leaq 0x2255ca(%rip), %r8     # 0x32f033
movl $0x3fc, %r9d            # imm = 0x3FC
jmp 0x10997b