// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/genoFind.c
// Function: gfFindHitsWithQmask
static struct gfHit *gfFindHitsWithQmask(struct genoFind *gf, bioSeq *seq,
	Bits *qMaskBits, int qMaskOffset, struct lm *lm, int *retHitCount, 
	struct gfSeqSource *target, int tMin, int tMax)
/* Find hits associated with one sequence soft-masking seq according to qMaskBits.
 * The hits will be in genome rather than chromosome coordinates. */
{
struct gfHit *hitList = NULL;
if (gf->segSize == 0 && !gf->isPep && !gf->allowOneMismatch)
    {
    hitList = gfFastFindDnaHits(gf, seq, qMaskBits, qMaskOffset, lm, retHitCount,
	target, tMin, tMax);
    }
else
    {
    if (gf->segSize == 0)
	{
	if (gf->allowOneMismatch)
	    {
	    hitList = gfStraightFindNearHits(gf, seq, qMaskBits, qMaskOffset, lm, 
		retHitCount, target, tMin, tMax);
	    }
	else
	    {
	    hitList = gfStraightFindHits(gf, seq, qMaskBits, qMaskOffset, lm, retHitCount, 
		target, tMin, tMax);
	    }
	}
    else
	{
	if (gf->allowOneMismatch)
	    {
	    hitList = gfSegmentedFindNearHits(gf, seq, qMaskBits, qMaskOffset, lm, retHitCount,
		target, tMin, tMax);
	    }
	else
	    {
	    hitList = gfSegmentedFindHits(gf, seq, qMaskBits, qMaskOffset, lm, retHitCount,
		target, tMin, tMax);
	    }
	}
    }
return hitList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xd8, %rsp
movq %r9, 0xc0(%rsp)
movq %r8, 0x78(%rsp)
movq %rcx, 0x58(%rsp)
movq %rdx, %r14
movq %rdi, %rbp
movl 0x2c(%rdi), %eax
testl %eax, %eax
movq %rdx, 0x70(%rsp)
movq %rdi, 0x40(%rsp)
je 0xc40c
movl 0x18(%rsi), %ebx
movslq 0xc(%rbp), %rcx
movl %ebx, 0x84(%rsp)
subl %ecx, %ebx
movq %rcx, 0x88(%rsp)
movl %ecx, %r12d
movl %eax, 0x60(%rsp)
subl %eax, %r12d
cmpb $0x0, 0x29(%rbp)
movq 0x10(%rsi), %rax
movq %rax, 0xb8(%rsp)
movl %r12d, (%rsp)
je 0xc568
callq 0xd4c6
xorl %r13d, %r13d
cmpb $0x0, 0x28(%rbp)
leaq -0x176a(%rip), %rax     # 0xa9b4
leaq -0x173f(%rip), %rcx     # 0xa9e6
cmoveq %rax, %rcx
movq %rcx, 0x90(%rsp)
pushq $0x74
popq %rax
pushq $0x41
popq %rcx
cmovel %eax, %ecx
movl %ecx, 0xb4(%rsp)
leaq 0xab068(%rip), %rax     # 0xb71b0
cmoveq 0xa6e68(%rip), %rax     # 0xb2fb8
movq %rax, 0xd0(%rsp)
setne %r13b
shll $0x4, %r13d
orl $0x4, %r13d
movslq %r12d, %rax
movq %rax, 0x68(%rsp)
movslq %ebx, %rax
movq %rax, 0xc8(%rsp)
xorl %eax, %eax
movq $0x0, 0x10(%rsp)
movl $0x0, 0x4(%rsp)
movl %r13d, 0x50(%rsp)
cmpq 0xc8(%rsp), %rax
jg 0xcaff
movq %rax, 0x8(%rsp)
testq %r14, %r14
je 0xc1cc
movq 0x58(%rsp), %rax
movq 0x8(%rsp), %rcx
leal (%rcx,%rax), %esi
movq %r14, %rdi
movq 0x88(%rsp), %rdx
callq 0x1856c
testl %eax, %eax
jne 0xc3ff
movq 0xb8(%rsp), %rax
movq 0x8(%rsp), %rcx
leaq (%rax,%rcx), %rdx
movq 0x68(%rsp), %rax
movq %rdx, 0xa0(%rsp)
addq %rdx, %rax
movq %rax, 0x98(%rsp)
movl 0x84(%rsp), %r14d
subl %ecx, %r14d
movq 0x88(%rsp), %rcx
pushq $0x1
popq %rax
movl %eax, 0x3c(%rsp)
movl %eax, 0x38(%rsp)
testq %rcx, %rcx
jle 0xc3fa
movq %rcx, 0x48(%rsp)
leaq -0x1(%rcx), %rbp
movq 0xa0(%rsp), %r15
movsbq (%r15,%rbp), %rbx
movl 0xb4(%rsp), %eax
movb %al, (%r15,%rbp)
movq %r15, %rdi
movl %r12d, %esi
movq 0x90(%rsp), %r12
callq *%r12
movl %eax, 0x20(%rsp)
movq 0x98(%rsp), %rdi
movl 0x60(%rsp), %esi
callq *%r12
movl %eax, %r12d
movb %bl, (%r15,%rbp)
pushq $-0x1
popq %rax
movl %eax, 0x18(%rsp)
movq %rbp, 0xa8(%rsp)
testq %rbp, %rbp
je 0xc28b
movq 0xd0(%rsp), %rax
movl (%rax,%rbx,4), %eax
movl %eax, 0x18(%rsp)
movl 0x20(%rsp), %esi
movl %esi, %eax
orl %r12d, %eax
movq 0x40(%rsp), %rcx
js 0xc3bc
xorl %ebx, %ebx
movq 0x48(%rsp), %rax
cmpq 0x68(%rsp), %rax
movl $0x0, %edx
cmovgl 0x38(%rsp), %edx
movl 0x3c(%rsp), %eax
movl %esi, %esi
movl $0x0, %edi
cmovleq %rax, %rdi
movl %edx, 0x30(%rsp)
movq %rdi, 0x28(%rsp)
cmpl %r13d, %ebx
je 0xc3bc
cmpl 0x18(%rsp), %ebx
je 0xc3af
movq 0x38(%rcx), %rax
movq 0x50(%rcx), %rcx
movl (%rax,%rsi,4), %r13d
movq %rsi, 0x20(%rsp)
movq (%rcx,%rsi,8), %rbp
testl %r13d, %r13d
movl $0x0, %eax
cmovlel %eax, %r13d
addq $0x4, %rbp
subl $0x1, %r13d
jb 0xc397
movzwl -0x4(%rbp), %eax
cmpl %eax, %r12d
jne 0xc38e
movzwl -0x2(%rbp), %eax
shll $0x10, %eax
movzwl (%rbp), %r15d
orl %eax, %r15d
cmpq $0x0, 0x110(%rsp)
je 0xc35d
movq 0x40(%rsp), %rdi
movl %r15d, %esi
callq 0xd4fc
cmpq 0x110(%rsp), %rax
jne 0xc38e
cmpl 0x118(%rsp), %r15d
jl 0xc38e
cmpl 0x120(%rsp), %r15d
jge 0xc38e
movq 0x78(%rsp), %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movq 0x8(%rsp), %rcx
movl %ecx, 0x8(%rax)
movl %r15d, 0xc(%rax)
addl %r14d, %r15d
movl %r15d, 0x10(%rax)
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
incl 0x4(%rsp)
movq %rax, 0x10(%rsp)
addq $0x6, %rbp
jmp 0xc305
movq 0x40(%rsp), %rcx
movl 0x50(%rsp), %r13d
movl 0x30(%rsp), %edx
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdi
addl %edx, %r12d
addq %rdi, %rsi
incl %ebx
jmp 0xc2cd
movq 0x48(%rsp), %rax
cmpq 0x68(%rsp), %rax
movl %r13d, %eax
pushq $0x1
popq %rcx
cmovgl %ecx, %eax
cmovgl %r13d, %ecx
movl 0x3c(%rsp), %edx
imull %eax, %edx
movl %edx, 0x3c(%rsp)
movl 0x38(%rsp), %eax
imull %ecx, %eax
movl %eax, 0x38(%rsp)
movq 0xa8(%rsp), %rcx
movl (%rsp), %r12d
jmp 0xc213
movq 0x70(%rsp), %r14
movq 0x8(%rsp), %rax
incq %rax
jmp 0xc18f
movb 0x28(%rbp), %al
movb 0x29(%rbp), %cl
testb %al, %al
je 0xc70e
testb %cl, %cl
jne 0xc716
movl 0x18(%rsi), %ebx
movl 0xc(%rbp), %r12d
movl %ebx, 0x20(%rsp)
subl %r12d, %ebx
testb %al, %al
movq 0x10(%rsi), %r13
leaq -0x1a89(%rip), %rax     # 0xa9b4
leaq -0x1a5e(%rip), %rcx     # 0xa9e6
cmoveq %rax, %rcx
movq %rcx, 0x18(%rsp)
callq 0xd4c6
movslq %ebx, %rax
movq %rax, 0x8(%rsp)
xorl %r14d, %r14d
movq $0x0, 0x10(%rsp)
movl $0x0, 0x4(%rsp)
movl %r12d, 0x30(%rsp)
movq %r13, 0x28(%rsp)
cmpq 0x8(%rsp), %r14
jg 0xcaff
leaq (%r14,%r13), %rdi
movl %r12d, %esi
callq *0x18(%rsp)
testl %eax, %eax
js 0xc560
movq 0x38(%rbp), %rcx
movl %eax, %r15d
movslq (%rcx,%r15,4), %rbx
testq %rbx, %rbx
jle 0xc560
movq 0x70(%rsp), %rdi
testq %rdi, %rdi
je 0xc4cd
movq 0x58(%rsp), %rax
leal (%r14,%rax), %esi
movl %r12d, %edx
callq 0x1856c
testl %eax, %eax
jne 0xc560
movq 0x48(%rbp), %rax
movq (%rax,%r15,8), %r13
movl 0x20(%rsp), %ebp
subl %r14d, %ebp
xorl %r15d, %r15d
cmpq %r15, %rbx
je 0xc551
movl (%r13,%r15,4), %r12d
cmpq $0x0, 0x110(%rsp)
je 0xc51f
movq 0x40(%rsp), %rdi
movl %r12d, %esi
callq 0xd4fc
cmpq 0x110(%rsp), %rax
jne 0xc54c
cmpl 0x118(%rsp), %r12d
jl 0xc54c
cmpl 0x120(%rsp), %r12d
jge 0xc54c
movq 0x78(%rsp), %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movl %r14d, 0x8(%rax)
movl %r12d, 0xc(%rax)
addl %ebp, %r12d
movl %r12d, 0x10(%rax)
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
incl 0x4(%rsp)
movq %rax, 0x10(%rsp)
incq %r15
jmp 0xc4df
movq 0x40(%rsp), %rbp
movl 0x30(%rsp), %r12d
movq 0x28(%rsp), %r13
incq %r14
jmp 0xc478
cmpb $0x0, 0x28(%rbp)
leaq -0x1bbf(%rip), %rax     # 0xa9b4
leaq -0x1b94(%rip), %r13     # 0xa9e6
cmoveq %rax, %r13
callq 0xd4c6
movslq %r12d, %rax
movq %rax, 0x20(%rsp)
movslq %ebx, %rax
movq %rax, 0x18(%rsp)
xorl %r15d, %r15d
movq $0x0, 0x10(%rsp)
movl $0x0, 0x4(%rsp)
movl 0x60(%rsp), %ebx
movq %r13, 0x30(%rsp)
cmpq 0x18(%rsp), %r15
jg 0xcaff
testq %r14, %r14
je 0xc5e1
movq 0x58(%rsp), %rax
leal (%r15,%rax), %esi
movq %r14, %rdi
movq 0x88(%rsp), %rdx
callq 0x1856c
testl %eax, %eax
jne 0xc706
movq 0xb8(%rsp), %rax
movq %r15, 0x8(%rsp)
addq %rax, %r15
movq %r15, %rdi
movl %r12d, %esi
callq *%r13
testl %eax, %eax
js 0xc6ed
movl %eax, %r12d
addq 0x20(%rsp), %r15
movq %r15, %rdi
movl %ebx, %esi
callq *%r13
testl %eax, %eax
js 0xc6f8
movl %eax, %r15d
movl %r12d, %eax
movq 0x38(%rbp), %rcx
movq 0x50(%rbp), %rdx
movl (%rcx,%rax,4), %ebx
movq (%rdx,%rax,8), %r14
movl 0x84(%rsp), %r13d
subl 0x8(%rsp), %r13d
testl %ebx, %ebx
movl $0x0, %eax
cmovlel %eax, %ebx
addq $0x4, %r14
movl (%rsp), %r12d
subl $0x1, %ebx
jb 0xc6e2
movzwl -0x4(%r14), %eax
cmpl %eax, %r15d
jne 0xc6d9
movzwl -0x2(%r14), %eax
shll $0x10, %eax
movzwl (%r14), %r12d
orl %eax, %r12d
cmpq $0x0, 0x110(%rsp)
je 0xc6a4
movq %rbp, %rdi
movl %r12d, %esi
callq 0xd4fc
cmpq 0x110(%rsp), %rax
jne 0xc6d5
cmpl 0x118(%rsp), %r12d
jl 0xc6d5
cmpl 0x120(%rsp), %r12d
jge 0xc6d5
movq 0x78(%rsp), %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movq 0x8(%rsp), %rcx
movl %ecx, 0x8(%rax)
movl %r12d, 0xc(%rax)
addl %r13d, %r12d
movl %r12d, 0x10(%rax)
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
incl 0x4(%rsp)
movq %rax, 0x10(%rsp)
movl (%rsp), %r12d
addq $0x6, %r14
jmp 0xc64e
movq 0x70(%rsp), %r14
movl 0x60(%rsp), %ebx
jmp 0xc6fc
movl (%rsp), %r12d
movq 0x8(%rsp), %r15
jmp 0xc706
movl (%rsp), %r12d
movq 0x8(%rsp), %r15
movq 0x30(%rsp), %r13
incq %r15
jmp 0xc5b0
testb %cl, %cl
je 0xc977
movslq 0x18(%rsi), %rax
movslq 0xc(%rbp), %rcx
movq %rax, 0x60(%rsp)
movq %rcx, 0x50(%rsp)
subq %rcx, %rax
movq %rax, 0x98(%rsp)
movq 0x10(%rsi), %rax
movq %rax, 0x90(%rsp)
callq 0xd4c6
xorl %r15d, %r15d
cmpb $0x0, 0x28(%rbp)
setne %r15b
leaq -0x1da2(%rip), %rax     # 0xa9b4
leaq -0x1d77(%rip), %rcx     # 0xa9e6
cmoveq %rax, %rcx
movq %rcx, 0x68(%rsp)
pushq $0x74
popq %rax
pushq $0x41
popq %rcx
cmovel %eax, %ecx
movl %ecx, (%rsp)
leaq 0xaaa37(%rip), %rax     # 0xb71b0
cmoveq 0xa6837(%rip), %rax     # 0xb2fb8
movq %rax, 0xa0(%rsp)
shll $0x4, %r15d
orl $0x4, %r15d
xorl %r14d, %r14d
movq $0x0, 0x10(%rsp)
movl $0x0, 0x4(%rsp)
movl %r15d, 0x38(%rsp)
cmpq 0x98(%rsp), %r14
jg 0xcaff
movq 0x90(%rsp), %rax
addq %r14, %rax
movq %rax, 0xa8(%rsp)
movq 0x58(%rsp), %rax
addl %r14d, %eax
movl %eax, 0x3c(%rsp)
movq 0x60(%rsp), %rax
movq %r14, %rcx
movl %eax, %r14d
movq %rcx, 0x8(%rsp)
subl %ecx, %r14d
movq 0x50(%rsp), %rdx
pushq $0x1
popq %rax
movl %eax, 0x48(%rsp)
testq %rdx, %rdx
jle 0xc96a
decq %rdx
movq %rdx, 0x28(%rsp)
movq 0xa8(%rsp), %r12
movq 0x28(%rsp), %rax
movsbq (%r12,%rax), %rbx
movl (%rsp), %eax
movq 0x28(%rsp), %rcx
movb %al, (%r12,%rcx)
movq %r12, %rdi
movq 0x50(%rsp), %rsi
callq *0x68(%rsp)
movq 0x28(%rsp), %rcx
movb %bl, (%r12,%rcx)
movq 0x28(%rsp), %rdx
pushq $-0x1
popq %rcx
testq %rdx, %rdx
je 0xc852
movq 0xa0(%rsp), %rcx
movl (%rcx,%rbx,4), %ecx
testl %eax, %eax
js 0xc95d
movl %eax, %edx
movl 0x48(%rsp), %eax
xorl %r12d, %r12d
movl %ecx, 0x20(%rsp)
movq %rax, 0x30(%rsp)
cmpl %r15d, %r12d
je 0xc958
cmpl %ecx, %r12d
je 0xc94d
movq 0x38(%rbp), %rax
movq %rdx, 0x18(%rsp)
movslq (%rax,%rdx,4), %r13
testq %r13, %r13
jle 0xc93f
movq 0x70(%rsp), %rdi
testq %rdi, %rdi
je 0xc8b4
movl 0x3c(%rsp), %esi
movq 0x50(%rsp), %rdx
callq 0x1856c
testl %eax, %eax
jne 0xc93f
movq 0x48(%rbp), %rax
movq 0x18(%rsp), %rcx
movq (%rax,%rcx,8), %rbp
xorl %r15d, %r15d
cmpq %r15, %r13
je 0xc935
movl (%rbp,%r15,4), %ebx
cmpq $0x0, 0x110(%rsp)
je 0xc901
movq 0x40(%rsp), %rdi
movl %ebx, %esi
callq 0xd4fc
cmpq 0x110(%rsp), %rax
jne 0xc930
cmpl 0x118(%rsp), %ebx
jl 0xc930
cmpl 0x120(%rsp), %ebx
jge 0xc930
movq 0x78(%rsp), %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movq 0x8(%rsp), %rcx
movl %ecx, 0x8(%rax)
movl %ebx, 0xc(%rax)
addl %r14d, %ebx
movl %ebx, 0x10(%rax)
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
incl 0x4(%rsp)
movq %rax, 0x10(%rsp)
incq %r15
jmp 0xc8c4
movq 0x40(%rsp), %rbp
movl 0x38(%rsp), %r15d
movl 0x20(%rsp), %ecx
movq 0x18(%rsp), %rdx
movq 0x30(%rsp), %rax
addq %rax, %rdx
incl %r12d
jmp 0xc86c
movq 0x28(%rsp), %rdx
movl 0x48(%rsp), %eax
imull %r15d, %eax
jmp 0xc7f2
movq 0x8(%rsp), %r14
incq %r14
jmp 0xc7aa
movslq 0x18(%rsi), %rax
movq %rax, 0x18(%rsp)
movslq 0xc(%rbp), %r15
leal -0x1(%r15), %edx
movl 0x18(%rbp), %r13d
movq 0x10(%rsi), %rsi
xorl %eax, %eax
testl %edx, %edx
movl $0x0, %ecx
movl %edx, 0x30(%rsp)
cmovgl %edx, %ecx
leaq 0xa92e9(%rip), %rdi     # 0xb5c90
xorl %r8d, %r8d
cmpq %rax, %rcx
je 0xc9c1
movsbq (%rsi,%rax), %rdx
shll $0x2, %r8d
addl (%rdi,%rdx,4), %r8d
incq %rax
jmp 0xc9aa
decq %r15
movq $0x0, 0x10(%rsp)
movl $0x0, 0x4(%rsp)
movl %r13d, 0x50(%rsp)
movq %rsi, 0x28(%rsp)
cmpq 0x18(%rsp), %r15
jge 0xcaff
movsbq (%rsi,%r15), %rax
shll $0x2, %r8d
addl (%rdi,%rax,4), %r8d
andl %r13d, %r8d
movq 0x38(%rbp), %rax
movl (%rax,%r8,4), %r12d
testl %r12d, %r12d
je 0xcaf7
movq %r8, 0x8(%rsp)
movl %r15d, %ebx
subl 0x30(%rsp), %ebx
testq %r14, %r14
je 0xca37
movq 0x58(%rsp), %rax
leal (%rbx,%rax), %esi
movl 0xc(%rbp), %edx
movq %r14, %rdi
callq 0x1856c
testl %eax, %eax
jne 0xcae6
movq %r15, 0x20(%rsp)
movq 0x48(%rbp), %rax
movq 0x8(%rsp), %rcx
movq (%rax,%rcx,8), %r13
movq 0x18(%rsp), %rax
movl %eax, %ebp
subl %ebx, %ebp
testl %r12d, %r12d
movl $0x0, %eax
cmovlel %eax, %r12d
xorl %r14d, %r14d
cmpq %r14, %r12
je 0xcad2
movl (%r13,%r14,4), %r15d
cmpq $0x0, 0x110(%rsp)
je 0xcaa1
movq 0x40(%rsp), %rdi
movl %r15d, %esi
callq 0xd4fc
cmpq 0x110(%rsp), %rax
jne 0xcacd
cmpl 0x118(%rsp), %r15d
jl 0xcacd
cmpl 0x120(%rsp), %r15d
jge 0xcacd
movq 0x78(%rsp), %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movl %ebx, 0x8(%rax)
movl %r15d, 0xc(%rax)
addl %ebp, %r15d
movl %r15d, 0x10(%rax)
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
incl 0x4(%rsp)
movq %rax, 0x10(%rsp)
incq %r14
jmp 0xca61
movq 0x70(%rsp), %r14
movq 0x40(%rsp), %rbp
movq 0x20(%rsp), %r15
movl 0x50(%rsp), %r13d
movq 0x28(%rsp), %rsi
leaq 0xa919e(%rip), %rdi     # 0xb5c90
movq 0x8(%rsp), %r8
incq %r15
jmp 0xc9df
movq 0xc0(%rsp), %rax
movl 0x4(%rsp), %ecx
movl %ecx, (%rax)
movq 0x10(%rsp), %rax
addq $0xd8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq