// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/core/encseq.c
// Function: fillViadirectaccess
static int fillViadirectaccess(GtEncseq *encseq,
                               GtDustMasker *dust_masker, /* NULL if not used */
                               Gtssptaboutinfo *ssptaboutinfo,
                               GtSequenceBuffer *fb,
                               GtError *err)
{
  GtUword currentposition,
                fillexceptionrangeidx = 0,
                mapposition = 0,
                nextcheckpos = GT_UNDEF_UWORD,
                pagenumber = 0,
                lastexceptionrangelength = 0;
  int retval;
  GtUchar cc;
  char orig;
  GtSWtable_uint32 *exceptiontable = &(encseq->exceptiontable.st_uint32);
  gt_error_check(err);

  if (encseq->has_exceptiontable) {
    exceptiontable->positions = gt_malloc(sizeof (*exceptiontable->positions) *
                                         exceptiontable->numofpositionstostore);
    exceptiontable->rangelengths =
                               gt_malloc(sizeof(*exceptiontable->rangelengths) *
                                         exceptiontable->numofpositionstostore);
    exceptiontable->endidxinpage =
                               gt_malloc(sizeof(*exceptiontable->endidxinpage) *
                                         exceptiontable->numofpages);
    exceptiontable->mappositions =
                              gt_malloc(sizeof (*exceptiontable->mappositions) *
                                        exceptiontable->numofpositionstostore);

    nextcheckpos = exceptiontable->maxrangevalue;
  }

  encseq->plainseq = gt_malloc(sizeof (*encseq->plainseq) *
                               encseq->totallength);
  encseq->hasplainseqptr = false;
  for (currentposition=0; /* Nothing */; currentposition++) {
    retval = gt_sequence_buffer_next_with_original(fb, dust_masker, &cc,
                                                   &orig, err);
    if (retval == 1) {
      if (encseq->has_exceptiontable && cc != (GtUchar) GT_SEPARATOR) {
        if (orig == encseq->maxchars[cc]) {
          if (lastexceptionrangelength > 0) {
            exceptiontable->rangelengths[fillexceptionrangeidx-1]
              = (uint32_t) (lastexceptionrangelength-1);
            lastexceptionrangelength = 0;
          }
        }
        else {
          /* at beginning of exception range */
          if (lastexceptionrangelength == 0) {
            /* store remainder of currentposition: this value is not larger
               than maxrangevalue and this can be stored in a page */
            exceptiontable->positions[fillexceptionrangeidx++]
              = (uint32_t) (currentposition & exceptiontable->maxrangevalue);
            exceptiontable->mappositions[fillexceptionrangeidx-1]
              = mapposition;
            lastexceptionrangelength = 1UL;
          }
          else /* extend exception range */ {
            if (lastexceptionrangelength == exceptiontable->maxrangevalue) {
              gt_assert(fillexceptionrangeidx > 0);
              exceptiontable->rangelengths[fillexceptionrangeidx-1]
                = (uint32_t) exceptiontable->maxrangevalue;
              lastexceptionrangelength = 0;
            }
            else {
              lastexceptionrangelength++;
            }
          }
          bitpackarray_store_uint32(encseq->exceptions,
                                   (BitOffset) mapposition,
                                   (uint32_t) encseq->subsymbolmap[(int) orig]);
          mapposition++;
        }
      }
      encseq->plainseq[currentposition] = cc;
      if (cc == (GtUchar) GT_SEPARATOR)
        ssptaboutinfo_processseppos(ssptaboutinfo, currentposition);
      ssptaboutinfo_processanyposition(ssptaboutinfo, currentposition);
    }
    else {
      if (retval < 0) {
        gt_free(encseq->plainseq);
        encseq->plainseq = NULL;
        return -1;
      }
      gt_assert(retval == 0);
      if (encseq->has_exceptiontable && lastexceptionrangelength > 0) {
        /* note that we store one less than the length to prevent overflows */
        gt_assert(fillexceptionrangeidx > 0 &&
                  fillexceptionrangeidx <=
                  exceptiontable->numofpositionstostore);
        exceptiontable->rangelengths[fillexceptionrangeidx-1]
          = (uint32_t) (lastexceptionrangelength-1);
      }
      break;
    }
    if (encseq->has_exceptiontable && currentposition == nextcheckpos) {
      exceptiontable->endidxinpage[pagenumber] = fillexceptionrangeidx;
      pagenumber++;
      nextcheckpos += 1UL + exceptiontable->maxrangevalue;
    }
  }
  if (encseq->has_exceptiontable) {
    while (pagenumber < exceptiontable->numofpages) {
      exceptiontable->endidxinpage[pagenumber] = fillexceptionrangeidx;
      pagenumber++;
    }
  }
  ssptaboutinfo_finalize(ssptaboutinfo);
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movq %r8, %r12
movq %rcx, 0x20(%rsp)
movq %rdx, %r14
movq %rsi, 0x18(%rsp)
movq %rdi, %rbx
testq %r8, %r8
je 0xd033b
movq %r12, %rdi
callq 0x34fea
testb %al, %al
jne 0xd06a9
movq $-0x1, %r15
cmpb $0x1, 0x2f0(%rbx)
jne 0xd03d9
movq 0x320(%rbx), %rdi
shlq $0x2, %rdi
leaq 0x325b9(%rip), %rbp     # 0x10291a
movq %rbp, %rsi
movl $0x886, %edx            # imm = 0x886
callq 0x35862
movq %rax, 0x2f8(%rbx)
movq 0x320(%rbx), %rdi
shlq $0x2, %rdi
movq %rbp, %rsi
movl $0x889, %edx            # imm = 0x889
callq 0x35862
movq %rax, 0x300(%rbx)
movq 0x318(%rbx), %rdi
shlq $0x3, %rdi
movq %rbp, %rsi
movl $0x88c, %edx            # imm = 0x88C
callq 0x35862
movq %rax, 0x308(%rbx)
movq 0x320(%rbx), %rdi
shlq $0x3, %rdi
movq %rbp, %rsi
movl $0x88f, %edx            # imm = 0x88F
callq 0x35862
movq %rax, 0x310(%rbx)
movq 0x328(%rbx), %r15
movq 0x30(%rbx), %rdi
leaq 0x32536(%rip), %rsi     # 0x10291a
movl $0x895, %edx            # imm = 0x895
callq 0x35862
movq %rax, 0x290(%rbx)
movb $0x0, 0x298(%rbx)
leaq 0x6(%rsp), %rdx
leaq 0x7(%rsp), %rcx
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
movq %r12, %r8
callq 0x7f610
cmpl $0x1, %eax
jne 0xd05f2
movq %r12, 0x30(%rsp)
xorl %ebp, %ebp
xorl %r13d, %r13d
xorl %r12d, %r12d
movq $0x0, 0x10(%rsp)
movq $0x0, 0x8(%rsp)
movq %r14, 0x28(%rsp)
movb 0x6(%rsp), %cl
cmpb $-0x1, %cl
setne %al
andb 0x2f0(%rbx), %al
cmpb $0x1, %al
jne 0xd055a
movzbl %cl, %edx
movsbq 0x7(%rsp), %rax
movq 0x348(%rbx), %rsi
cmpb (%rsi,%rdx), %al
jne 0xd0493
testq %r13, %r13
je 0xd048b
decl %r13d
movq 0x300(%rbx), %rax
movq 0x8(%rsp), %rdx
movl %r13d, -0x4(%rax,%rdx,4)
xorl %r13d, %r13d
jmp 0xd055a
movq 0x328(%rbx), %rcx
testq %r13, %r13
je 0xd04c8
cmpq %rcx, %r13
jne 0xd04c3
movq 0x8(%rsp), %rdx
testq %rdx, %rdx
je 0xd06a4
movq 0x300(%rbx), %rcx
movl %r13d, -0x4(%rcx,%rdx,4)
xorl %r13d, %r13d
jmp 0xd04f8
incq %r13
jmp 0xd04f8
andl %ebp, %ecx
movq 0x2f8(%rbx), %rdx
movq 0x8(%rsp), %rsi
movl %ecx, (%rdx,%rsi,4)
movq 0x310(%rbx), %rcx
movq 0x10(%rsp), %rdx
movq %rdx, (%rcx,%rsi,8)
leaq 0x1(%rsi), %rcx
movl $0x1, %r13d
movq %rcx, 0x8(%rsp)
movq 0x330(%rbx), %rsi
testq %rsi, %rsi
je 0xd069f
movq 0x10(%rsp), %rcx
cmpq %rcx, 0x8(%rsi)
jbe 0xd069f
movl 0x10(%rsi), %edx
cmpq $0x21, %rdx
jae 0xd069f
movq %r13, %r14
movq 0x358(%rbx), %rcx
movzbl (%rcx,%rax), %ecx
movq (%rsi), %rdi
movq %rdx, %rsi
movq 0x10(%rsp), %r13
imulq %r13, %rsi
callq 0xde284
incq %r13
movq %r13, 0x10(%rsp)
movb 0x6(%rsp), %cl
movq %r14, %r13
movq 0x28(%rsp), %r14
movq 0x290(%rbx), %rax
movb %cl, (%rax,%rbp)
cmpb $-0x1, 0x6(%rsp)
jne 0xd0576
movq %r14, %rdi
movq %rbp, %rsi
callq 0xc4427
testq %r14, %r14
je 0xd0591
cmpq %rbp, 0x10(%r14)
jne 0xd0591
movq %r14, %rdi
callq 0xcf47b
movq 0x18(%r14), %rax
addq %rax, 0x10(%r14)
cmpb $0x1, 0x2f0(%rbx)
jne 0xd05c1
cmpq %r15, %rbp
jne 0xd05c1
movq 0x308(%rbx), %rax
movq 0x8(%rsp), %rcx
movq %rcx, (%rax,%r12,8)
incq %r12
incq %rbp
movq 0x328(%rbx), %r15
addq %rbp, %r15
jmp 0xd05c4
incq %rbp
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
leaq 0x6(%rsp), %rdx
leaq 0x7(%rsp), %rcx
movq 0x30(%rsp), %r8
callq 0x7f610
cmpl $0x1, %eax
je 0xd0445
movq 0x8(%rsp), %rdx
jmp 0xd05fa
xorl %edx, %edx
xorl %r12d, %r12d
xorl %r13d, %r13d
testl %eax, %eax
js 0xd0668
jne 0xd06ae
movb 0x2f0(%rbx), %al
cmpb $0x1, %al
jne 0xd0638
testq %r13, %r13
je 0xd0638
testq %rdx, %rdx
je 0xd06b3
cmpq 0x320(%rbx), %rdx
ja 0xd06b3
decl %r13d
movq 0x300(%rbx), %rcx
movl %r13d, -0x4(%rcx,%rdx,4)
testb %al, %al
je 0xd065c
cmpq 0x318(%rbx), %r12
jae 0xd065c
movq 0x308(%rbx), %rax
movq %rdx, (%rax,%r12,8)
incq %r12
cmpq 0x318(%rbx), %r12
jb 0xd064c
movq %r14, %rdi
callq 0xc4493
xorl %eax, %eax
jmp 0xd0690
movq 0x290(%rbx), %rdi
leaq 0x322a4(%rip), %rsi     # 0x10291a
movl $0x8c6, %edx            # imm = 0x8C6
callq 0x35c27
movq $0x0, 0x290(%rbx)
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x2ec7d
callq 0x2ec44
callq 0x2ec0b
callq 0x2ecb4
callq 0x2eced