// File: /workspace/github_c_makefile_star2_O3/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, %ebx
movl %r8d, %r13d
movl %ecx, %ebp
movl %edx, %r15d
movq %rsi, %r14
movq %rdi, %r12
movq 0xd0(%rsp), %rdi
testq %rdi, %rdi
je 0x168160
callq 0xfcc32
testb %al, %al
jne 0x168cfa
testq %r12, %r12
je 0x168cf5
testq %r14, %r14
je 0x168cf5
movl %r13d, 0x20(%rsp)
movl %ebp, 0x28(%rsp)
movl %ebx, 0x48(%rsp)
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x1681a2
movq 0x350d45(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x226b59(%rip), %rsi    # 0x38ecf6
callq 0x11cc90
movq %r12, %rdi
callq 0xebcd9
movq %rax, %rdi
callq 0xd11cf
movl %eax, %ebp
leaq 0x226b18(%rip), %r13    # 0x38ecd3
movl $0x1c0, %edi            # imm = 0x1C0
movq %r13, %rsi
movl $0x3c6, %edx            # imm = 0x3C6
callq 0x104226
movq %rax, %rbx
movq %r12, 0x98(%rax)
movq %r14, 0xa0(%rax)
callq 0x10d640
movq %rax, 0xb0(%rbx)
callq 0xe54e0
movq %rax, 0x38(%rbx)
callq 0xe54e0
movq %rax, 0x40(%rbx)
callq 0xe54e0
movq %rax, 0x20(%rbx)
callq 0xe54e0
movq %rax, 0x28(%rbx)
callq 0xe54e0
movq %rax, 0x30(%rbx)
movl $0x1, %edi
movl $0x38, %esi
callq 0x174e0
movq %rax, 0x90(%rbx)
xorl %eax, %eax
movq %rax, 0x18(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x48(%rbx)
movups %xmm0, 0x58(%rbx)
movups %xmm0, 0x68(%rbx)
movups %xmm0, 0x78(%rbx)
movq %rax, 0x88(%rbx)
movb $0x1, 0x1b8(%rbx)
leal 0x1(%rbp), %r14d
movups %xmm0, 0x180(%rbx)
movups %xmm0, 0x190(%rbx)
movups %xmm0, 0x1a0(%rbx)
movq %rax, 0x1b0(%rbx)
movl $0x0, 0x1ba(%rbx)
movb $0x0, 0x1be(%rbx)
movl $0x8, %esi
movq %r14, %rdi
movq %r13, %rdx
movl $0x3ea, %ecx            # imm = 0x3EA
callq 0x10436a
movq %rbx, 0x10(%rsp)
movq %rax, 0xa8(%rbx)
incl %ebp
je 0x1682bb
shlq $0x3, %r14
movq %rax, %rdi
xorl %esi, %esi
movq %r14, %rdx
callq 0x173a0
movq 0x10(%rsp), %rbp
xorps %xmm0, %xmm0
movups %xmm0, 0x130(%rbp)
movups %xmm0, 0x120(%rbp)
movups %xmm0, 0x110(%rbp)
movups %xmm0, 0x100(%rbp)
movups %xmm0, 0xf0(%rbp)
cmpb $0x0, 0x20(%rsp)
je 0x1682ff
testb %r15b, %r15b
jne 0x168cff
movb $0x1, 0x1bb(%rbp)
jmp 0x16830b
testb %r15b, %r15b
je 0x16830b
movb $0x1, 0x1be(%rbp)
cmpb $0x0, 0x28(%rsp)
je 0x168319
movb $0x1, 0x1bc(%rbp)
cmpb $0x0, 0x48(%rsp)
je 0x168327
movb $0x1, 0x1bd(%rbp)
movq %r12, %rdi
callq 0xebcd9
movq %rax, %rdi
callq 0xd1749
testb %al, %al
je 0x168c50
movq 0xa0(%rbp), %rdi
leaq 0x23d3d0(%rip), %rsi    # 0x3a571d
xorl %edx, %edx
callq 0x24759a
cmpq $0x0, 0x90(%rbp)
je 0x168d04
movq %rax, %r14
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x168388
movq 0x350b5f(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x226b47(%rip), %rsi    # 0x38eeca
callq 0x11cc90
testq %r14, %r14
je 0x168c68
movq 0x90(%rbp), %rsi
movq %r14, %rdi
callq 0x247a55
testl %eax, %eax
js 0x168a5a
movabsq $0x400000000, %r15      # imm = 0x400000000
xorl %r12d, %r12d
movq %r14, 0x78(%rsp)
movq 0x90(%rbp), %r13
testq %r13, %r13
je 0x168ceb
movslq (%r13), %rsi
cmpl %esi, %r12d
je 0x1683f8
movq $0x0, 0x1a8(%rbp)
movq 0x98(%rbp), %rdi
callq 0xeb6ee
movq %rax, 0x188(%rbp)
movq 0x90(%rbp), %r13
movslq 0x4(%r13), %rax
cmpq %rax, 0x1a8(%rbp)
ja 0x168c71
movl (%r13), %r12d
xorl %eax, %eax
testq %r15, 0x8(%r13)
setne %al
incq 0x198(%rbp,%rax,8)
movq 0x8(%r13), %rbx
testq %r15, %rbx
jne 0x168a47
movl %r12d, 0x64(%rsp)
movq 0x30(%r13), %rax
movq %rax, 0x58(%rsp)
movq %rbp, %r15
movl 0x10(%r13), %ebp
cmpb $0x1, 0x1bc(%r15)
movl %ebp, %r12d
jne 0x168462
movq 0x40(%r15), %rdi
movl %ebx, %eax
shrl $0x10, %eax
movzbl %al, %esi
callq 0xe54fb
movl 0x10(%r13), %r12d
movslq %r12d, %r14
movq 0x20(%r15), %rdi
movq %r14, %rsi
callq 0xe54fb
movq 0x1b0(%r15), %rax
testq %rax, %rax
je 0x1684a0
cmpq %r14, %rax
je 0x1684ae
movq 0x10(%rsp), %rax
cmpq %r14, 0x190(%rax)
jae 0x168497
movq %r14, 0x190(%rax)
movb $0x0, 0x1b8(%rax)
jmp 0x1684ae
movq %r14, 0x1b0(%r15)
movq %r14, 0x190(%r15)
movq %r13, 0x30(%rsp)
movq %rbx, %r15
shrq $0x30, %r15
shrl $0x18, %ebx
movq 0x58(%rsp), %rax
addq %rbx, %rax
movq %rax, 0x80(%rsp)
leaq (%rax,%r15,4), %rax
incl %ebp
sarl %ebp
movslq %ebp, %rcx
movq %rax, 0x48(%rsp)
movq %rcx, 0x20(%rsp)
leaq (%rax,%rcx), %r13
testl %r12d, %r12d
movq 0x10(%rsp), %rbp
je 0x168517
cmpb $0x0, 0x1bb(%rbp)
je 0x168517
xorl %r12d, %r12d
movzbl (%r13,%r12), %esi
addq $0x21, %rsi
movq 0x38(%rbp), %rdi
callq 0xe54fb
incq %r12
cmpq %r12, %r14
jne 0x1684fc
movq %r13, 0x68(%rsp)
movq 0x30(%rsp), %r14
movslq 0x4(%r14), %r12
movq %r12, %rsi
subq 0x1a8(%rbp), %rsi
movq 0x28(%rbp), %rdi
callq 0xe54fb
movq %r12, 0x50(%rsp)
movq %r12, 0x1a8(%rbp)
cmpw $0x0, 0xe(%r14)
movl $0x0, %r12d
je 0x168a0c
shlq $0x2, %r15
addq 0x20(%rsp), %r15
addq %rbx, %r15
addq %r15, 0x58(%rsp)
movb $0x1, %al
movl %eax, 0xc(%rsp)
xorl %r14d, %r14d
movq $0x0, 0x28(%rsp)
xorl %r15d, %r15d
movq 0x30(%rsp), %r13
movq 0x98(%rbp), %rdi
callq 0xebcd9
movq %rax, 0x20(%rsp)
movq %rax, %rdi
callq 0xd11cf
movq 0x80(%rsp), %rcx
movl (%rcx,%r14,4), %ecx
movl %ecx, %edx
andl $0xf, %edx
leal -0x7(%rdx), %esi
cmpl $0x2, %esi
cmovbl %r12d, %edx
cmpl $0x4, %edx
ja 0x16877a
movl %ecx, %edi
shrl $0x4, %edi
leaq 0x22660a(%rip), %rsi    # 0x38ebd4
movslq (%rsi,%rdx,4), %rdx
addq %rsi, %rdx
jmpq *%rdx
movq %rdi, 0x70(%rsp)
movq %r14, 0x40(%rsp)
cmpl $0x10, %ecx
movq %r15, 0x18(%rsp)
jae 0x168787
movq 0x28(%rsp), %rax
movq %rax, 0x38(%rsp)
jmp 0x168879
movq %r15, 0x18(%rsp)
movq %r14, 0x40(%rsp)
incq 0x110(%rbp)
movl %edi, %ebx
cmpl $0x10, %ecx
jb 0x1689b3
decl %eax
movl %eax, 0xc(%rsp)
movq 0x18(%rsp), %r12
leal (,%r12,4), %r15d
movq %rbx, %r13
movq %r12, %rax
shrq %rax
movq 0x48(%rsp), %rcx
movzbl (%rcx,%rax), %eax
movl %r15d, %ecx
notb %cl
andb $0x4, %cl
shrl %cl, %eax
andl $0xf, %eax
leal -0x1(%rax), %ecx
cmpl $0x7, %ecx
ja 0x168664
leaq 0x2265b1(%rip), %rdx    # 0x38ec08
movslq (%rdx,%rcx,4), %rax
addq %rdx, %rax
jmpq *%rax
movb $0x41, %al
jmp 0x16867a
movb $-0x2, %r14b
cmpl $0xf, %eax
je 0x16868a
movb $0x4e, %al
jmp 0x16867a
movb $0x47, %al
jmp 0x16867a
movb $0x54, %al
jmp 0x16867a
movb $0x43, %al
movzbl %al, %esi
movq 0x20(%rsp), %rdi
callq 0xd185d
movl %eax, %r14d
movq 0x20(%rsp), %rbp
movq %rbp, %rdi
callq 0xd11f1
movsbl %al, %esi
movq %rbp, %rdi
callq 0xd185d
cmpb %al, %r14b
je 0x1686ad
movzbl %r14b, %eax
jmp 0x1686b2
movzbl 0xc(%rsp), %eax
movq 0x10(%rsp), %rcx
movq 0xa8(%rcx), %rcx
movzbl %al, %eax
incq (%rcx,%rax,8)
addb $0x4, %r15b
incq %r12
decq %r13
jne 0x16862c
movq 0x10(%rsp), %rbp
cmpb $0x1, 0x1be(%rbp)
movl $0x0, %r12d
movq 0x30(%rsp), %r13
jne 0x1689b3
movq 0x68(%rsp), %rax
movq 0x18(%rsp), %rcx
leaq (%rax,%rcx), %r14
xorl %r15d, %r15d
movzbl (%r14,%r15), %esi
addq $0x21, %rsi
movq 0x38(%rbp), %rdi
callq 0xe54fb
incq %r15
cmpq %r15, %rbx
jne 0x168703
jmp 0x1689b3
incq 0x100(%rbp)
jmp 0x168732
incq 0x108(%rbp)
movl %edi, %eax
addq %rax, 0x50(%rsp)
movl $0x0, 0xc(%rsp)
movq %r15, %rbx
jmp 0x1689c8
movq %r15, 0x18(%rsp)
movq %r14, 0x40(%rsp)
incq 0xf8(%rbp)
movl %edi, %edx
movl %eax, %ebx
cmpl $0xf, %ecx
ja 0x1688a2
movq 0xa8(%rbp), %rax
incq (%rax,%rbx,8)
movq %rdx, %rbx
jmp 0x1689b3
movq %r15, %rbx
movq 0x28(%rsp), %r15
jmp 0x1689c8
movq 0x58(%rsp), %rax
leaq (%rax,%r15), %r12
movq %r15, %rbp
leal (,%r15,4), %r15d
movq 0x50(%rsp), %rbx
movq 0x70(%rsp), %r13
movq 0x28(%rsp), %rax
movq %rax, 0x38(%rsp)
movq %rbp, %rax
shrq %rax
movq 0x48(%rsp), %rcx
movzbl (%rcx,%rax), %eax
movl %r15d, %ecx
notb %cl
andb $0x4, %cl
shrl %cl, %eax
andl $0xf, %eax
leal -0x1(%rax), %ecx
cmpl $0x7, %ecx
ja 0x1687e7
leaq 0x22644e(%rip), %rdx    # 0x38ec28
movslq (%rdx,%rcx,4), %rax
addq %rdx, %rax
jmpq *%rax
movb $0x41, %al
jmp 0x1687fd
movb $-0x2, %r14b
cmpl $0xf, %eax
je 0x16880d
movb $0x4e, %al
jmp 0x1687fd
movb $0x47, %al
jmp 0x1687fd
movb $0x54, %al
jmp 0x1687fd
movb $0x43, %al
movzbl %al, %esi
movq 0x20(%rsp), %rdi
callq 0xd185d
movl %eax, %r14d
movq 0x10(%rsp), %rax
movq 0x98(%rax), %rdi
movq 0x188(%rax), %rsi
addq %rbx, %rsi
xorl %edx, %edx
callq 0xe7bbc
cmpb %r14b, %al
je 0x168863
movq 0x10(%rsp), %rax
incq 0xf0(%rax)
cmpb $0x1, 0x1be(%rax)
jne 0x168856
movzbl (%r12), %esi
addq $0x21, %rsi
movq 0x38(%rax), %rdi
callq 0xe54fb
movl $0x0, 0xc(%rsp)
movq %rbp, 0x38(%rsp)
incq %rbx
incq %rbp
incq %r12
addb $0x4, %r15b
decq %r13
jne 0x1687af
movq 0x18(%rsp), %rbx
movq 0x70(%rsp), %rax
addq %rax, %rbx
addq %rax, 0x50(%rsp)
movq 0x38(%rsp), %r15
movq 0x10(%rsp), %rbp
xorl %r12d, %r12d
movq 0x30(%rsp), %r13
jmp 0x1689c3
decl %eax
movl %eax, 0xc(%rsp)
movq 0x18(%rsp), %r13
leal (,%r13,4), %r12d
movq %rdx, 0x38(%rsp)
movq %rdx, %rbp
movq %r13, %rax
shrq %rax
movq 0x48(%rsp), %rcx
movzbl (%rcx,%rax), %eax
movl %r12d, %ecx
notb %cl
andb $0x4, %cl
shrl %cl, %eax
andl $0xf, %eax
leal -0x1(%rax), %ecx
cmpl $0x7, %ecx
ja 0x1688f5
leaq 0x226300(%rip), %rdx    # 0x38ebe8
movslq (%rdx,%rcx,4), %rax
addq %rdx, %rax
jmpq *%rax
movb $0x41, %al
jmp 0x16890b
movb $-0x2, %r14b
cmpl $0xf, %eax
je 0x16891b
movb $0x4e, %al
jmp 0x16890b
movb $0x47, %al
jmp 0x16890b
movb $0x54, %al
jmp 0x16890b
movb $0x43, %al
movzbl %al, %esi
movq 0x20(%rsp), %rdi
callq 0xd185d
movl %eax, %r14d
movq 0x20(%rsp), %r15
movq %r15, %rdi
callq 0xd11f1
movsbl %al, %esi
movq %r15, %rdi
callq 0xd185d
cmpb %al, %r14b
je 0x16893e
movzbl %r14b, %ecx
jmp 0x168943
movzbl 0xc(%rsp), %ecx
movq 0x10(%rsp), %rax
movq 0xa8(%rax), %rax
movzbl %cl, %ecx
incq (%rax,%rcx,8)
addb $0x4, %r12b
incq %r13
decq %rbp
jne 0x1688bd
incq (%rax,%rbx,8)
movq 0x10(%rsp), %rbp
cmpb $0x1, 0x1be(%rbp)
movl $0x0, %r12d
movq 0x30(%rsp), %r13
movq 0x38(%rsp), %rbx
jne 0x1689b3
movq 0x68(%rsp), %rax
movq 0x18(%rsp), %rcx
leaq (%rax,%rcx), %r14
xorl %r15d, %r15d
movzbl (%r14,%r15), %esi
addq $0x21, %rsi
movq 0x38(%rbp), %rdi
callq 0xe54fb
incq %r15
cmpq %r15, %rbx
jne 0x168999
movq 0x18(%rsp), %r15
addq %r15, %rbx
movl $0x0, 0xc(%rsp)
movq 0x40(%rsp), %r14
movq %r15, %rsi
subq 0x28(%rsp), %rsi
movq 0x30(%rbp), %rdi
callq 0xe54fb
incq %r14
movzwl 0xe(%r13), %eax
movq %r15, 0x28(%rsp)
movq %rbx, %r15
cmpq %rax, %r14
jb 0x168581
testb $0x1, 0xc(%rsp)
jne 0x168a0c
movq 0xb0(%rbp), %rdi
movq 0x180(%rbp), %rsi
callq 0x10d65b
movq 0x30(%rsp), %rax
movslq 0x4(%rax), %rax
testq %rax, %rax
js 0x168cf0
movq %rax, 0x1a8(%rbp)
incq 0x180(%rbp)
movq 0x90(%rbp), %r13
movq 0x78(%rsp), %r14
movabsq $0x400000000, %r15      # imm = 0x400000000
movl 0x64(%rsp), %r12d
movq %r14, %rdi
movq %r13, %rsi
callq 0x247a55
testl %eax, %eax
jns 0x1683ba
movq 0x198(%rbp), %rax
movq %rax, 0x138(%rbp)
movq %r14, %rdi
callq 0x247a0f
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x168a93
movq 0x350454(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x226489(%rip), %rsi    # 0x38ef17
callq 0x11cc90
movq 0x28(%rbp), %rdi
callq 0x16b6de
cmpq $-0x1, %rax
je 0x168caf
cmpq $0x1, %rax
adcq $0x0, %rax
movq %rax, %rdi
callq 0x14c39c
movq %rax, 0x50(%rbp)
movq 0x30(%rbp), %rdi
callq 0x16b6de
cmpq $-0x1, %rax
je 0x168add
cmpq $0x1, %rax
adcq $0x0, %rax
movq %rax, %rdi
callq 0x14c39c
movq %rax, 0x58(%rbp)
cmpb $0x0, 0x1b8(%rbp)
jne 0x168b04
movq 0x20(%rbp), %rdi
movq 0x190(%rbp), %rdx
incq %rdx
leaq 0x2c56(%rip), %rsi      # 0x16b751
callq 0x153ff8
movq %rax, 0x60(%rbp)
cmpb $0x0, 0x1bb(%rbp)
jne 0x168b16
cmpb $0x1, 0x1be(%rbp)
jne 0x168b2f
movq 0x38(%rbp), %rdi
leaq 0x2c30(%rip), %rsi      # 0x16b751
movl $0x100, %edx            # imm = 0x100
callq 0x153ff8
movq %rax, 0x68(%rbp)
movq %rbp, %r14
addq $0xf0, %r14
cmpb $0x1, 0x1bc(%rbp)
jne 0x168b5b
movq 0x40(%rbp), %rdi
leaq 0x2c04(%rip), %rsi      # 0x16b751
movl $0x100, %edx            # imm = 0x100
callq 0x153ff8
movq %rax, 0x70(%rbp)
leaq 0x2bf4(%rip), %rsi      # 0x16b756
movl $0xa, %edx
movq %r14, %rdi
callq 0x153ff8
movq %rax, 0x78(%rbp)
testq %rax, %rax
je 0x168ca6
movq 0x98(%rbp), %rdi
movq 0xa8(%rbp), %r14
callq 0xebcd9
movq %rax, %rdi
callq 0xd11cf
movl %eax, %edx
incq %rdx
leaq 0x2bb3(%rip), %rsi      # 0x16b756
movq %r14, %rdi
callq 0x153ff8
movq %rax, 0x80(%rbp)
testq %rax, %rax
je 0x168ca6
cmpb $0x0, 0xc0(%rsp)
je 0x168cd6
movq 0xc8(%rsp), %rdi
testq %rdi, %rdi
je 0x168bec
movq 0x3502fb(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x226390(%rip), %rsi    # 0x38ef77
callq 0x11cc90
callq 0x13ad24
movq %rax, 0x48(%rbp)
movq %rax, %rdi
callq 0x13ad9a
movq 0x98(%rbp), %rdi
movq 0xa0(%rbp), %r14
callq 0xebcd9
movq %r14, %rdi
movq %rax, %rsi
movq 0xd0(%rsp), %rbx
movq %rbx, %rdx
callq 0x170ae8
movq %rax, 0x88(%rbp)
testq %rax, %rax
je 0x168ccc
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1706d5
movq %rax, 0x18(%rbp)
testq %rax, %rax
jne 0x168cd6
jmp 0x168ccc
leaq 0x2260bf(%rip), %rsi    # 0x38ed16
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0xfcb67
jmp 0x168ccc
leaq 0x22627a(%rip), %rsi    # 0x38eee9
jmp 0x168c78
leaq 0x226289(%rip), %rsi    # 0x38ef01
movq 0xa0(%rbp), %rdx
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0xfcb67
movq 0x198(%rbp), %rax
movq %rax, 0x138(%rbp)
movq %r14, %rdi
callq 0x247a0f
jmp 0x168ccc
leaq 0x22629e(%rip), %rsi    # 0x38ef4b
jmp 0x168c57
movq 0xa0(%rbp), %rdx
leaq 0x226270(%rip), %rsi    # 0x38ef2d
movq 0xd0(%rsp), %rdi
xorl %eax, %eax
callq 0xfcb67
movq %rbp, %rdi
callq 0x168d09
xorl %ebp, %ebp
movq %rbp, %rax
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x4f8ba
callq 0x4f88d
callq 0x4f854
callq 0x4f81b
callq 0x4f92c
callq 0x4f8f3