// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-align.c
// Function: gt_querymatchoutoptions_seededmatch2eoplist
void gt_querymatchoutoptions_seededmatch2eoplist(
                                GtQuerymatchoutoptions *querymatchoutoptions,
                                const GtSeqorEncseq *dbes,
                                GtUword dbstart_relative,
                                GtUword db_seqstart,
                                GtUword dblen,
                                GtReadmode query_readmode,
                                const GtSeqorEncseq *queryes,
                                GtUword query_seqstart,
                                GtUword query_seqlen,
                                GtUword querystart_rel,
                                GtUword querylen,
                                GtUword db_seedpos_rel,
                                GtUword query_seedpos_rel,
                                GtUword seedlen,
                                bool verify_alignment,
                                bool greedyextension)
{
  GtUword ulen, vlen, ustart, vstart;
  GtFtPolished_point right_best_polished_point = {0,0,0,0,0},
                     left_best_polished_point = {0,0,0,0,0};
  GtUword pol_size;
  GtSeqpaircoordinates *coords;
  GtUword leftcolumn, rightcolumn;

  gt_assert(querymatchoutoptions != NULL &&
            querymatchoutoptions->pol_info != NULL);
  pol_size = GT_MULT2(querymatchoutoptions->pol_info->cut_depth);
  gt_eoplist_reset(querymatchoutoptions->eoplist);
  ustart = db_seedpos_rel + seedlen;
  vstart = query_seedpos_rel + seedlen;
  gt_assert(dbstart_relative + dblen >= ustart);
  ulen = dbstart_relative + dblen - ustart;
  gt_assert(querystart_rel + querylen >= vstart);
  vlen = querystart_rel + querylen - vstart;
  if (ulen > 0 && vlen > 0)
  {
    gt_align_front_prune_edist(true,
                               &right_best_polished_point,
                               querymatchoutoptions->front_trace,
                               dbes,
                               queryes,
                               query_readmode,
                               query_seqstart,
                               query_seqlen,
                               querymatchoutoptions->ggemi,
                               greedyextension,
                               seedlen,
                               db_seqstart + ustart,
                               ulen,
                               query_seqstart + vstart,
                               vlen);
    if (querymatchoutoptions->front_trace != NULL)
    {
      front_trace2eoplist(querymatchoutoptions->always_polished_ends,
                          querymatchoutoptions->eoplist,
                          querymatchoutoptions->front_trace,
                          &right_best_polished_point,
                          pol_size,
                          querymatchoutoptions->pol_info->match_score,
                          querymatchoutoptions->pol_info->difference_score,
                          NULL,
                          ulen,
                          NULL,
                          vlen);
      front_trace_reset(querymatchoutoptions->front_trace,ulen+vlen);
    }
  }
  gt_eoplist_match_add(querymatchoutoptions->eoplist,seedlen);
  if (db_seedpos_rel > dbstart_relative && query_seedpos_rel > querystart_rel)
  {
    ulen = db_seedpos_rel - dbstart_relative;
    vlen = query_seedpos_rel - querystart_rel;
    gt_align_front_prune_edist(false,
                               &left_best_polished_point,
                               querymatchoutoptions->front_trace,
                               dbes,
                               queryes,
                               query_readmode,
                               query_seqstart,
                               query_seqlen,
                               querymatchoutoptions->ggemi,
                               greedyextension,
                               seedlen,
                               db_seqstart + dbstart_relative,
                               ulen,
                               query_seqstart + querystart_rel,
                               vlen);
    if (querymatchoutoptions->front_trace != NULL)
    {
      GtUword previous_eoplistlen
        = gt_eoplist_length(querymatchoutoptions->eoplist);
      front_trace2eoplist(querymatchoutoptions->always_polished_ends,
                          querymatchoutoptions->eoplist,
                          querymatchoutoptions->front_trace,
                          &left_best_polished_point,
                          pol_size,
                          querymatchoutoptions->pol_info->match_score,
                          querymatchoutoptions->pol_info->difference_score,
                          NULL,
                          ulen,
                          NULL,
                          vlen);
      gt_eoplist_reverse_end(querymatchoutoptions->eoplist,previous_eoplistlen);
      front_trace_reset(querymatchoutoptions->front_trace,ulen+vlen);
    }
  }
  coords = &querymatchoutoptions->correction_info;
  gt_assert(db_seedpos_rel >= dbstart_relative + left_best_polished_point.row);
  coords->uoffset = db_seedpos_rel - left_best_polished_point.row -
                                     dbstart_relative;
  coords->ulen = seedlen + left_best_polished_point.row +
                 right_best_polished_point.row;
  leftcolumn = left_best_polished_point.alignedlen -
               left_best_polished_point.row;
  rightcolumn = right_best_polished_point.alignedlen -
                right_best_polished_point.row;
  gt_assert(query_seedpos_rel >= leftcolumn + querystart_rel);
  coords->voffset = query_seedpos_rel - leftcolumn - querystart_rel;
  coords->vlen = seedlen + leftcolumn + rightcolumn;
  coords->sumdist = left_best_polished_point.distance +
                    right_best_polished_point.distance;
  coords->sum_max_mismatches = left_best_polished_point.max_mismatches +
                               right_best_polished_point.max_mismatches;
  gt_eoplist_reverse_end(querymatchoutoptions->eoplist,0);
  if (verify_alignment)
  {
    gt_querymtch_alignment_verification(querymatchoutoptions,
                                        db_seqstart + dbstart_relative,
                                        coords->ulen,
                                        query_seqstart + querystart_rel,
                                        coords->vlen,
                                        coords->sumdist);
  }
  gt_eoplist_set_seedoffset(querymatchoutoptions->eoplist,
                            db_seedpos_rel - dbstart_relative,
                            seedlen);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
movl %r9d, 0x8(%rsp)
movq %rcx, 0x18(%rsp)
movq %rsi, 0x20(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x70(%rsp)
movaps %xmm0, 0x60(%rsp)
xorl %eax, %eax
movq %rax, 0x80(%rsp)
movq %rax, 0x50(%rsp)
movaps %xmm0, 0x40(%rsp)
movaps %xmm0, 0x30(%rsp)
testq %rdi, %rdi
je 0x1c2464
movq %rdi, %rbx
movq 0xb0(%rdi), %rax
testq %rax, %rax
je 0x1c2464
movq %r8, %r12
movq %rdx, %r14
movq 0xf8(%rsp), %r13
movq 0xe8(%rsp), %rbp
movq 0x8(%rax), %rax
movq %rax, 0x10(%rsp)
movq 0x28(%rbx), %rdi
callq 0x322120
movq %r13, %rax
addq %rbp, %rax
movq %r14, 0x28(%rsp)
addq %r14, %r12
movq %r12, %r14
subq %rax, %r14
jb 0x1c2469
movq 0xf0(%rsp), %r15
leaq (%r15,%r13), %r10
movq 0xe0(%rsp), %r13
addq 0xd8(%rsp), %r13
cmpq %r10, %r13
jb 0x1c246e
movq 0x10(%rsp), %rcx
addq %rcx, %rcx
movq %rcx, 0x10(%rsp)
cmpq %rax, %r12
sete %cl
subq %r10, %r13
sete %dl
orb %cl, %dl
movq 0xf8(%rsp), %r12
jne 0x1c2257
movq 0x40(%rbx), %rdx
addq 0x18(%rsp), %rax
movq 0xc8(%rsp), %r12
addq %r12, %r10
subq $0x8, %rsp
movzbl 0x110(%rsp), %r11d
leaq 0x68(%rsp), %rsi
movl $0x1, %edi
movq 0x28(%rsp), %rcx
movq 0xc8(%rsp), %r8
movl 0x10(%rsp), %r9d
pushq %r13
pushq %r10
pushq %r14
pushq %rax
pushq 0x120(%rsp)
pushq %r11
pushq 0x48(%rbx)
pushq 0x110(%rsp)
pushq %r12
movq 0x148(%rsp), %r12
callq 0x1ea4d2
addq $0x50, %rsp
movq 0x40(%rbx), %rdx
testq %rdx, %rdx
je 0x1c2257
movzbl 0xa8(%rbx), %edi
movq 0x28(%rbx), %rsi
movq 0xb0(%rbx), %rax
movq 0x28(%rax), %r9
subq $0x8, %rsp
xorl %r10d, %r10d
leaq 0x68(%rsp), %rcx
movq 0x18(%rsp), %r8
pushq %r13
pushq %r10
pushq %r14
pushq %r10
pushq 0x20(%rax)
callq 0x32462e
addq $0x30, %rsp
movq 0x40(%rbx), %rdi
addq %r13, %r14
movq %r14, %rsi
callq 0x3243af
movq 0x28(%rbx), %rdi
movq %r12, %rsi
callq 0x322783
movq %rbp, %r14
movq 0x28(%rsp), %r13
subq %r13, %r14
setbe %al
movq %r15, %r12
subq 0xd8(%rsp), %r12
setbe %cl
orb %al, %cl
jne 0x1c2368
movq 0x40(%rbx), %rdx
movq 0x18(%rsp), %rax
addq %r13, %rax
movq 0xd8(%rsp), %rcx
movq 0xc8(%rsp), %rsi
leaq (%rcx,%rsi), %r10
subq $0x8, %rsp
movzbl 0x110(%rsp), %r11d
leaq 0x38(%rsp), %rsi
xorl %edi, %edi
movq 0x28(%rsp), %rcx
movq 0xc8(%rsp), %r8
movl 0x10(%rsp), %r9d
pushq %r12
pushq %r10
pushq %r14
pushq %rax
pushq 0x120(%rsp)
pushq %r11
pushq 0x48(%rbx)
pushq 0x110(%rsp)
pushq 0x110(%rsp)
callq 0x1ea4d2
addq $0x50, %rsp
cmpq $0x0, 0x40(%rbx)
je 0x1c2368
movq 0x28(%rbx), %rdi
callq 0x322a1c
movq %rax, 0x8(%rsp)
movzbl 0xa8(%rbx), %edi
movq 0x28(%rbx), %rsi
movq 0x40(%rbx), %rdx
movq 0xb0(%rbx), %rax
movq 0x28(%rax), %r9
subq $0x8, %rsp
xorl %r10d, %r10d
leaq 0x38(%rsp), %rcx
movq 0x18(%rsp), %r8
pushq %r12
pushq %r10
pushq %r14
pushq %r10
pushq 0x20(%rax)
callq 0x32462e
addq $0x30, %rsp
movq 0x28(%rbx), %rdi
movq 0x8(%rsp), %rsi
callq 0x322a28
movq 0x40(%rbx), %rdi
addq %r14, %r12
movq %r12, %rsi
callq 0x3243af
movq 0x38(%rsp), %rax
leaq (%rax,%r13), %rcx
subq %rcx, %rbp
jb 0x1c2473
movq %rbp, 0x78(%rbx)
movq 0xf8(%rsp), %r12
leaq (%rax,%r12), %rdx
movq 0x68(%rsp), %rcx
addq %rcx, %rdx
movq %rdx, 0x88(%rbx)
movq 0x30(%rsp), %rdx
subq %rax, %rdx
movq 0xd8(%rsp), %rax
addq %rdx, %rax
subq %rax, %r15
jb 0x1c2478
movq %r12, %rax
subq %rcx, %rax
addq %rdx, %rax
addq 0x60(%rsp), %rax
movb 0x100(%rsp), %bpl
movq %r15, 0x80(%rbx)
movq %rax, 0x90(%rbx)
movq 0x70(%rsp), %rax
addq 0x40(%rsp), %rax
movq %rax, 0x98(%rbx)
movq 0x80(%rsp), %rax
addq 0x50(%rsp), %rax
movq %rax, 0xa0(%rbx)
movq 0x28(%rbx), %rdi
xorl %esi, %esi
callq 0x322a28
testb %bpl, %bpl
je 0x1c2443
movq 0x18(%rsp), %rsi
addq %r13, %rsi
movq 0xd8(%rsp), %rcx
addq 0xc8(%rsp), %rcx
movq 0x88(%rbx), %rdx
movq 0x90(%rbx), %r8
movq 0x98(%rbx), %r9
movq %rbx, %rdi
callq 0x1c247d
movq 0x28(%rbx), %rdi
movq %r14, %rsi
movq %r12, %rdx
callq 0x32429e
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x68d6e
callq 0x68d35
callq 0x68cfc
callq 0x68cc3
callq 0x68c8a