// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_recompute_alignment
void gt_querymatch_recompute_alignment(GtQuerymatch *querymatch,
                                       const GtSeedExtendDisplayFlag
                                         *out_display_flag,
                                       bool match_has_cigar,
                                       bool dtrace,
                                       GtUword trace_delta,
                                       bool match_has_seed,
                                       const GtEncseq *db_encseq,
                                       const GtEncseq *query_encseq,
                                       const GtKarlinAltschulStat
                                         *karlin_altschul_stat,
                                       double evalue,
                                       double bitscore)
{
  GtSeqorEncseq db_seqorencseq, query_seqorencseq;

  GT_SEQORENCSEQ_INIT_ENCSEQ(&db_seqorencseq,db_encseq);
  GT_SEQORENCSEQ_INIT_ENCSEQ(&query_seqorencseq,query_encseq);
  if (match_has_cigar || trace_delta > 0)
  {
    if (querymatch->ref_querymatchoutoptions != NULL &&
        gt_querymatch_alignment_display(out_display_flag))
    {
      gt_querymatchoutoptions_extract_seq(querymatch->ref_querymatchoutoptions,
                                          &db_seqorencseq,
                                          querymatch->dbstart_relative,
                                          gt_querymatch_dbstart(querymatch),
                                          gt_querymatch_dblen(querymatch),
                                          querymatch->query_readmode,
                                          &query_seqorencseq,
                                          querymatch->querystart,
                                          querymatch->query_seqstart +
                                            querymatch->querystart_fwdstrand,
                                          gt_querymatch_querylen(querymatch),
                                          false);
    }
    if (querymatch->ref_eoplist != NULL && trace_delta > 0)
    {
      gt_eoplist_trace2cigar(querymatch->ref_eoplist,dtrace,trace_delta);
    }
  } else
  {
    if (match_has_seed)
    {
      gt_querymatch_seed_alignment(querymatch,&db_seqorencseq,
                                   &query_seqorencseq);
    } else
    {
      gt_querymatch_full_alignment(querymatch,&db_seqorencseq,
                                   &query_seqorencseq);
    }
  }
  if ((evalue == DBL_MAX || bitscore == DBL_MAX) &&
      karlin_altschul_stat != NULL)
  {
    gt_querymatch_evalue_bit_score(&evalue, &bitscore, karlin_altschul_stat,
                                   querymatch);
  }
  gt_querymatch_prettyprint(evalue,bitscore,out_display_flag,querymatch);
}

// Assembly:
pushq %rbp
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movb %r9b, %al
movq 0x130(%rsp), %r9
movq 0x128(%rsp), %r9
movq 0x120(%rsp), %r9
movq %rdi, 0x100(%rsp)
movq %rsi, 0xf8(%rsp)
andb $0x1, %dl
movb %dl, 0xf7(%rsp)
andb $0x1, %cl
movb %cl, 0xf6(%rsp)
movq %r8, 0xe8(%rsp)
andb $0x1, %al
movb %al, 0xe7(%rsp)
movsd %xmm0, 0xd8(%rsp)
movsd %xmm1, 0xd0(%rsp)
movq 0x120(%rsp), %rax
movq %rax, 0xa0(%rsp)
movq $0x0, 0x98(%rsp)
movq $0x0, 0xa8(%rsp)
movq $-0x1, 0xb8(%rsp)
movq $-0x1, 0xb0(%rsp)
movq $0x0, 0xc0(%rsp)
movb $0x0, 0xc8(%rsp)
movb $0x1, 0xc9(%rsp)
movq 0x128(%rsp), %rax
movq %rax, 0x68(%rsp)
movq $0x0, 0x60(%rsp)
movq $0x0, 0x70(%rsp)
movq $-0x1, 0x80(%rsp)
movq $-0x1, 0x78(%rsp)
movq $0x0, 0x88(%rsp)
movb $0x0, 0x90(%rsp)
movb $0x1, 0x91(%rsp)
testb $0x1, 0xf7(%rsp)
jne 0x26abc0
cmpq $0x0, 0xe8(%rsp)
jbe 0x26ad1b
movq 0x100(%rsp), %rax
cmpq $0x0, 0x90(%rax)
je 0x26acd4
movq 0xf8(%rsp), %rdi
callq 0x265cd0
testb $0x1, %al
jne 0x26abec
jmp 0x26acd4
movq 0x100(%rsp), %rax
movq 0x90(%rax), %rax
movq %rax, 0x28(%rsp)
movq 0x100(%rsp), %rax
movq 0x8(%rax), %rax
movq %rax, 0x30(%rsp)
movq 0x100(%rsp), %rdi
callq 0x2676b0
movq %rax, 0x38(%rsp)
movq 0x100(%rsp), %rdi
callq 0x2676e0
movq %rax, 0x40(%rsp)
movq 0x100(%rsp), %rax
movl 0x88(%rax), %eax
movl %eax, 0x4c(%rsp)
movq 0x100(%rsp), %rax
movq 0x30(%rax), %rax
movq %rax, 0x50(%rsp)
movq 0x100(%rsp), %rax
movq 0x50(%rax), %rax
movq 0x100(%rsp), %rcx
addq 0x38(%rcx), %rax
movq %rax, 0x58(%rsp)
movq 0x100(%rsp), %rdi
callq 0x2676a0
movq 0x28(%rsp), %rdi
movq 0x30(%rsp), %rdx
movq 0x38(%rsp), %rcx
movq 0x40(%rsp), %r8
movl 0x4c(%rsp), %r9d
movq 0x50(%rsp), %r11
movq 0x58(%rsp), %r10
leaq 0x98(%rsp), %rsi
leaq 0x60(%rsp), %rbx
xorl %ebp, %ebp
movq %rbx, (%rsp)
movq %r11, 0x8(%rsp)
movq %r10, 0x10(%rsp)
movq %rax, 0x18(%rsp)
movl $0x0, 0x20(%rsp)
callq 0x264d30
movq 0x100(%rsp), %rax
cmpq $0x0, 0xb0(%rax)
je 0x26ad19
cmpq $0x0, 0xe8(%rsp)
jbe 0x26ad19
movq 0x100(%rsp), %rax
movq 0xb0(%rax), %rdi
movb 0xf6(%rsp), %al
movq 0xe8(%rsp), %rdx
andb $0x1, %al
movzbl %al, %esi
callq 0x4c39f0
jmp 0x26ad5d
testb $0x1, 0xe7(%rsp)
je 0x26ad41
movq 0x100(%rsp), %rdi
leaq 0x98(%rsp), %rsi
leaq 0x60(%rsp), %rdx
callq 0x26ae00
jmp 0x26ad5b
movq 0x100(%rsp), %rdi
leaq 0x98(%rsp), %rsi
leaq 0x60(%rsp), %rdx
callq 0x26af00
jmp 0x26ad5d
movsd 0xd8(%rsp), %xmm0
movsd 0x2adfe2(%rip), %xmm1   # 0x518d50
ucomisd %xmm1, %xmm0
jne 0x26ad78
jp 0x26ad78
jmp 0x26ad91
movsd 0xd0(%rsp), %xmm0
movsd 0x2adfc7(%rip), %xmm1   # 0x518d50
ucomisd %xmm1, %xmm0
jne 0x26adc1
jp 0x26adc1
cmpq $0x0, 0x130(%rsp)
je 0x26adc1
movq 0x130(%rsp), %rdx
movq 0x100(%rsp), %rcx
leaq 0xd8(%rsp), %rdi
leaq 0xd0(%rsp), %rsi
callq 0x26b150
movsd 0xd8(%rsp), %xmm0
movsd 0xd0(%rsp), %xmm1
movq 0xf8(%rsp), %rdi
movq 0x100(%rsp), %rsi
callq 0x267bd0
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %rbp
retq
nopw %cs:(%rax,%rax)