// File: /workspace/github_c_makefile_star2_O2/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 %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xa8, %rsp
movl %ecx, %ebp
movq %rsi, %r14
movq %rdi, %rbx
xorb $0x1, %dl
movq 0xe0(%rsp), %rax
movq %rax, 0x78(%rsp)
andq $0x0, 0x70(%rsp)
movq 0xe8(%rsp), %rax
andq $0x0, 0x80(%rsp)
movq %xmm0, 0x28(%rsp)
movsd %xmm1, 0x30(%rsp)
pcmpeqd %xmm2, %xmm2
movdqu %xmm2, 0x88(%rsp)
andq $0x0, 0x98(%rsp)
movw $0x100, %cx             # imm = 0x100
movq %rax, 0x40(%rsp)
andq $0x0, 0x38(%rsp)
movw %cx, 0xa0(%rsp)
andq $0x0, 0x48(%rsp)
movdqu %xmm2, 0x50(%rsp)
andq $0x0, 0x60(%rsp)
movw %cx, 0x68(%rsp)
testq %r8, %r8
sete %al
testb %dl, %al
movapd %xmm1, 0x10(%rsp)
movdqa %xmm0, (%rsp)
jne 0x16bec2
movq %r8, %r15
cmpq $0x0, 0x90(%rbx)
je 0x16be8b
movq %r14, %rdi
callq 0x169236
movdqa (%rsp), %xmm0
movapd 0x10(%rsp), %xmm1
testb %al, %al
je 0x16be8b
movq 0x90(%rbx), %rdi
movq 0x8(%rbx), %rdx
movq 0x10(%rbx), %r8
movq 0x20(%rbx), %rcx
addq %rdx, %rcx
movl 0x88(%rbx), %r9d
movq 0x38(%rbx), %rax
addq 0x50(%rbx), %rax
subq $0x8, %rsp
leaq 0x40(%rsp), %r10
leaq 0x78(%rsp), %rsi
pushq $0x0
pushq 0x40(%rbx)
pushq %rax
pushq 0x30(%rbx)
pushq %r10
callq 0x168b06
movdqa 0x30(%rsp), %xmm0
movapd 0x40(%rsp), %xmm1
addq $0x30, %rsp
testq %r15, %r15
sete %al
movq 0xb0(%rbx), %rdi
testq %rdi, %rdi
sete %cl
orb %al, %cl
jne 0x16bfc7
movzbl %bpl, %esi
movq %r15, %rdx
callq 0x2b8ad9
movdqa (%rsp), %xmm0
movapd 0x10(%rsp), %xmm1
jmp 0x16bfc7
testb %r9b, %r9b
je 0x16bf29
leaq 0x70(%rsp), %r15
leaq 0x38(%rsp), %rdx
pushq $0x1
popq %rcx
movq %rbx, %rdi
movq %r15, %rsi
callq 0x16b943
cmpq $0x0, 0x8(%r15)
je 0x16c075
movdqu 0x18(%rbx), %xmm0
pshufd $0x4e, %xmm0, %xmm0     # xmm0 = xmm0[2,3,0,1]
movdqu %xmm0, 0x88(%rsp)
cmpq $0x0, 0x40(%rsp)
je 0x16c0a3
movdqu 0x48(%rbx), %xmm0
pshufd $0x4e, %xmm0, %xmm0     # xmm0 = xmm0[2,3,0,1]
movdqu %xmm0, 0x50(%rsp)
movapd 0x10(%rsp), %xmm1
movdqa (%rsp), %xmm0
jmp 0x16bfc7
movq 0x90(%rbx), %rdi
testq %rdi, %rdi
je 0x16bfc7
movl 0x88(%rbx), %ebp
movq 0x8(%rbx), %rdx
movq 0x10(%rbx), %rcx
addq 0x20(%rbx), %rdx
movzbl 0x8d(%rbx), %eax
subq $0x8, %rsp
leaq 0x78(%rsp), %r12
leaq 0x40(%rsp), %r15
movq %r12, %rsi
movq %r15, %r8
movl %ebp, %r9d
pushq %rax
pushq 0x40(%rbx)
pushq 0x30(%rbx)
pushq 0x48(%rbx)
pushq 0x50(%rbx)
callq 0x1688e4
addq $0x30, %rsp
movq 0x90(%rbx), %rdi
movq 0x8(%rbx), %rdx
movq 0x10(%rbx), %r8
movq 0x20(%rbx), %rcx
addq %rdx, %rcx
movq 0x38(%rbx), %rax
addq 0x50(%rbx), %rax
subq $0x8, %rsp
movq %r12, %rsi
movl %ebp, %r9d
pushq $0x1
pushq 0x40(%rbx)
pushq %rax
pushq 0x30(%rbx)
pushq %r15
callq 0x168b06
movdqa 0x30(%rsp), %xmm0
movapd 0x40(%rsp), %xmm1
addq $0x30, %rsp
cmpq $0x0, 0xf0(%rsp)
je 0x16c058
movsd 0x17bd32(%rip), %xmm3   # 0x2e7d10
movapd %xmm1, %xmm2
cmpeqpd %xmm3, %xmm2
cmpeqpd %xmm0, %xmm3
orpd %xmm2, %xmm3
movd %xmm3, %eax
testb $0x1, %al
je 0x16c058
movq 0x40(%rbx), %rdi
movq 0x48(%rbx), %r12
addq 0x10(%rbx), %rdi
movq 0x70(%rbx), %rsi
movq 0x78(%rbx), %rdx
callq 0x16adf8
movq %rax, %r13
movq 0x78(%rbx), %rbp
movq %rbx, %rdi
callq 0x16ac5c
subq $0x8, %rsp
leaq 0x30(%rsp), %rdi
leaq 0x38(%rsp), %r15
movq %r15, %rsi
movq 0xf8(%rsp), %rdx
movq %r12, %rcx
movq %r13, %r8
movq %rbp, %r9
pushq %rax
callq 0x16ae82
popq %rax
popq %rcx
leaq 0x28(%rsp), %rax
movsd (%rax), %xmm0
movsd (%r15), %xmm1
movq %r14, %rdi
movq %rbx, %rsi
callq 0x16a2d0
addq $0xa8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2cbeec(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x178f8d(%rip), %rsi    # 0x2e5013
leaq 0x1e00ff(%rip), %rdx    # 0x34c18c
leaq 0x1e0119(%rip), %rcx    # 0x34c1ad
leaq 0x1df9fd(%rip), %r8     # 0x34ba98
movl $0x4fa, %r9d            # imm = 0x4FA
jmp 0x16c0cf
movq 0x2cbebe(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x178f5f(%rip), %rsi    # 0x2e5013
leaq 0x1e010f(%rip), %rdx    # 0x34c1ca
leaq 0x1e00eb(%rip), %rcx    # 0x34c1ad
leaq 0x1df9cf(%rip), %r8     # 0x34ba98
movl $0x4fc, %r9d            # imm = 0x4FC
xorl %eax, %eax
callq 0x17a50
callq 0x17390
nop