// File: /workspace/github_c_makefile_star2_O1/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 %r8, 0x80(%rsp)
movq %rcx, 0x50(%rsp)
movq %rdx, 0x68(%rsp)
movslq 0x2c(%rdi), %rdx
testq %rdx, %rdx
movq %rdi, 0x28(%rsp)
movq %r9, 0xc8(%rsp)
jne 0xe214
cmpb $0x0, 0x28(%rdi)
jne 0xe20c
cmpb $0x0, 0x29(%rdi)
je 0xea60
testl %edx, %edx
je 0xe79f
movslq 0xc(%rdi), %r14
movq %r14, %rbx
subq %rdx, %rbx
cmpb $0x0, 0x29(%rdi)
movl 0x18(%rsi), %r8d
movq 0x10(%rsi), %rax
movq %rax, 0xb8(%rsp)
movq %r14, 0xc0(%rsp)
movq %rbx, 0x70(%rsp)
je 0xe5a0
cmpb $0x0, 0xb2d50(%rip)     # 0xc0f9c
jne 0xe27d
movl $0x2, 0xb18bc(%rip)     # 0xbfb14
movl $0x1, 0xb18ba(%rip)     # 0xbfb1c
movl $0x0, 0xb18f4(%rip)     # 0xbfb60
movl $0x3, 0xb18b6(%rip)     # 0xbfb2c
movb $0x1, 0xb2d1f(%rip)     # 0xc0f9c
xorl %r12d, %r12d
cmpb $0x0, 0x28(%rdi)
setne %al
leaq -0x1adc(%rip), %rcx     # 0xc7b2
leaq -0x1aae(%rip), %rsi     # 0xc7e7
cmoveq %rcx, %rsi
movq %rsi, 0x88(%rsp)
movl $0x74, %ecx
movl $0x41, %esi
cmovel %ecx, %esi
movl %esi, 0x98(%rsp)
leaq 0xb4ed4(%rip), %rcx     # 0xc3190
cmoveq 0xb0cf4(%rip), %rcx     # 0xbefb8
movq %rcx, 0x58(%rsp)
cmpl %r14d, %r8d
jl 0xe5f8
movq %rdx, 0x60(%rsp)
movb %al, %r12b
shll $0x4, %r12d
orl $0x4, %r12d
movl %r8d, 0x4c(%rsp)
movl %r8d, %eax
subl %r14d, %eax
incl %eax
movq %rax, 0xd0(%rsp)
movq $0x0, 0x10(%rsp)
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
movl %r12d, 0x38(%rsp)
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0xe34b
testl %r14d, %r14d
setle %bpl
movq 0x50(%rsp), %rax
movq 0x10(%rsp), %rcx
leal (%rcx,%rax), %esi
movl %r14d, %edx
callq 0x1b931
testl %eax, %eax
setne %al
orb %bpl, %al
je 0xe354
jmp 0xe578
testl %r14d, %r14d
jle 0xe578
movq 0xb8(%rsp), %rax
movq 0x10(%rsp), %rcx
addq %rcx, %rax
movq %rax, 0xa8(%rsp)
addq %rbx, %rax
movq %rax, 0xa0(%rsp)
movl 0x4c(%rsp), %eax
subl %ecx, %eax
movl %eax, 0x30(%rsp)
movl $0x1, 0x24(%rsp)
movl $0x1, 0x20(%rsp)
leaq -0x1(%r14), %r13
movq 0xa8(%rsp), %rbp
movsbq -0x1(%rbp,%r14), %r15
movl 0x98(%rsp), %eax
movb %al, -0x1(%rbp,%r14)
movq %rbp, %rdi
movl %ebx, %esi
movq 0x88(%rsp), %rbx
callq *%rbx
movl %eax, 0x40(%rsp)
movq 0xa0(%rsp), %rdi
movq 0x60(%rsp), %rsi
callq *%rbx
movl %eax, %ebx
movq %r14, 0x90(%rsp)
movb %r15b, -0x1(%rbp,%r14)
movq %r13, 0xb0(%rsp)
testq %r13, %r13
je 0xe3fc
movq 0x58(%rsp), %rax
movl (%rax,%r15,4), %eax
movl %eax, 0x18(%rsp)
jmp 0xe404
movl $0xffffffff, 0x18(%rsp) # imm = 0xFFFFFFFF
movl 0x40(%rsp), %ecx
testl %ecx, %ecx
js 0xe531
testl %ebx, %ebx
js 0xe531
xorl %r14d, %r14d
movq 0x90(%rsp), %rax
cmpq 0x70(%rsp), %rax
movl $0x0, %eax
cmovgl 0x24(%rsp), %eax
movl %eax, 0x78(%rsp)
movl 0x20(%rsp), %eax
movl %ecx, %ebp
movl $0x0, %ecx
cmovleq %rax, %rcx
movq %rcx, 0x40(%rsp)
cmpl 0x18(%rsp), %r14d
je 0xe517
movq 0x28(%rsp), %rcx
movq 0x38(%rcx), %rax
movl (%rax,%rbp,4), %r13d
testl %r13d, %r13d
jle 0xe517
movq 0x50(%rcx), %rax
movq (%rax,%rbp,8), %r12
addq $0x4, %r12
movzwl -0x4(%r12), %eax
cmpl %eax, %ebx
jne 0xe50a
movzwl -0x2(%r12), %eax
shll $0x10, %eax
movzwl (%r12), %r15d
orl %eax, %r15d
cmpq $0x0, 0x110(%rsp)
je 0xe4cc
movq 0x28(%rsp), %rdi
movl %r15d, %esi
callq 0xf826
cmpq 0x110(%rsp), %rax
jne 0xe50a
cmpl 0x118(%rsp), %r15d
jl 0xe50a
cmpl 0x120(%rsp), %r15d
jge 0xe50a
movl $0x18, %esi
movq 0x80(%rsp), %rdi
callq 0x2bfa9
movq 0x10(%rsp), %rcx
movl %ecx, 0x8(%rax)
movl %r15d, 0xc(%rax)
addl 0x30(%rsp), %r15d
movl %r15d, 0x10(%rax)
movq (%rsp), %rcx
movq %rcx, (%rax)
movq 0x8(%rsp), %rcx
incl %ecx
movq %rcx, 0x8(%rsp)
movq %rax, (%rsp)
addq $0x6, %r12
decl %r13d
jne 0xe477
addl 0x78(%rsp), %ebx
addq 0x40(%rsp), %rbp
incl %r14d
movl 0x38(%rsp), %r12d
cmpl %r12d, %r14d
jne 0xe44a
movq 0x70(%rsp), %rbx
movq 0x90(%rsp), %rsi
cmpq %rbx, %rsi
movl %r12d, %eax
movl $0x1, %ecx
cmovgl %ecx, %eax
cmovgl %r12d, %ecx
movl 0x20(%rsp), %edx
imull %eax, %edx
movl %edx, 0x20(%rsp)
movl 0x24(%rsp), %eax
imull %ecx, %eax
movl %eax, 0x24(%rsp)
cmpq $0x1, %rsi
movq 0xb0(%rsp), %r14
jg 0xe391
movq 0x10(%rsp), %rcx
incq %rcx
movq %rcx, 0x10(%rsp)
cmpq 0xd0(%rsp), %rcx
movq 0xc0(%rsp), %r14
jne 0xe316
jmp 0xe77a
cmpb $0x0, 0x28(%rdi)
leaq -0x1df9(%rip), %rax     # 0xc7b2
leaq -0x1dcb(%rip), %rcx     # 0xc7e7
cmoveq %rax, %rcx
movq %rcx, 0x30(%rsp)
cmpb $0x0, 0xb29da(%rip)     # 0xc0f9c
jne 0xe5f3
movl $0x2, 0xb1546(%rip)     # 0xbfb14
movl $0x1, 0xb1544(%rip)     # 0xbfb1c
movl $0x0, 0xb157e(%rip)     # 0xbfb60
movl $0x3, 0xb1540(%rip)     # 0xbfb2c
movb $0x1, 0xb29a9(%rip)     # 0xc0f9c
cmpl %r14d, %r8d
jge 0xe60e
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
jmp 0xe77a
movq %rdx, 0x60(%rsp)
movslq %ebx, %rax
movq %rax, 0x18(%rsp)
movl %r8d, 0x4c(%rsp)
movl %r8d, %eax
subl %r14d, %eax
incl %eax
movq %rax, 0x10(%rsp)
xorl %r12d, %r12d
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0xe664
movq 0x50(%rsp), %rax
leal (%r12,%rax), %esi
movl %r14d, %edx
callq 0x1b931
testl %eax, %eax
jne 0xe75f
movq 0xb8(%rsp), %rax
leaq (%rax,%r12), %r13
movq %r13, %rdi
movl %ebx, %esi
movq 0x30(%rsp), %r14
callq *%r14
testl %eax, %eax
js 0xe75f
movl %eax, %r15d
addq 0x18(%rsp), %r13
movq %r13, %rdi
movq 0x60(%rsp), %rsi
callq *%r14
testl %eax, %eax
js 0xe75f
movl %eax, %ebx
movq 0x28(%rsp), %rdx
movq 0x38(%rdx), %rcx
movl %r15d, %eax
movl (%rcx,%rax,4), %ebp
testl %ebp, %ebp
jle 0xe75f
movq 0x50(%rdx), %rcx
movq (%rcx,%rax,8), %r14
movl 0x4c(%rsp), %r13d
subl %r12d, %r13d
addq $0x4, %r14
movzwl -0x4(%r14), %eax
cmpl %eax, %ebx
jne 0xe753
movzwl -0x2(%r14), %eax
shll $0x10, %eax
movzwl (%r14), %r15d
orl %eax, %r15d
cmpq $0x0, 0x110(%rsp)
je 0xe71b
movq 0x28(%rsp), %rdi
movl %r15d, %esi
callq 0xf826
cmpq 0x110(%rsp), %rax
jne 0xe753
cmpl 0x118(%rsp), %r15d
jl 0xe753
cmpl 0x120(%rsp), %r15d
jge 0xe753
movl $0x18, %esi
movq 0x80(%rsp), %rdi
callq 0x2bfa9
movl %r12d, 0x8(%rax)
movl %r15d, 0xc(%rax)
addl %r13d, %r15d
movl %r15d, 0x10(%rax)
movq (%rsp), %rcx
movq %rcx, (%rax)
movq 0x8(%rsp), %rcx
incl %ecx
movq %rcx, 0x8(%rsp)
movq %rax, (%rsp)
addq $0x6, %r14
decl %ebp
jne 0xe6cd
incq %r12
cmpq 0x10(%rsp), %r12
movq 0xc0(%rsp), %r14
movq 0x70(%rsp), %rbx
jne 0xe641
movq 0xc8(%rsp), %rax
movq 0x8(%rsp), %rcx
movl %ecx, (%rax)
movq (%rsp), %rax
addq $0xd8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
cmpb $0x0, 0x29(%rdi)
movl 0x18(%rsi), %edx
movslq 0xc(%rdi), %r8
movq 0x10(%rsi), %rax
movq %rax, 0x88(%rsp)
movq %r8, 0x38(%rsp)
je 0xebde
cmpb $0x0, 0xb27d4(%rip)     # 0xc0f9c
jne 0xe7f9
movl $0x2, 0xb1340(%rip)     # 0xbfb14
movl $0x1, 0xb133e(%rip)     # 0xbfb1c
movl $0x0, 0xb1378(%rip)     # 0xbfb60
movl $0x3, 0xb133a(%rip)     # 0xbfb2c
movb $0x1, 0xb27a3(%rip)     # 0xc0f9c
xorl %ebp, %ebp
cmpb $0x0, 0x28(%rdi)
setne %al
leaq -0x2057(%rip), %rcx     # 0xc7b2
leaq -0x2029(%rip), %rsi     # 0xc7e7
cmoveq %rcx, %rsi
movq %rsi, 0xa8(%rsp)
movl $0x74, %ecx
movl $0x41, %esi
cmovel %ecx, %esi
movl %esi, 0xa0(%rsp)
leaq 0xb4959(%rip), %rcx     # 0xc3190
cmoveq 0xb0779(%rip), %rcx     # 0xbefb8
movq %rcx, 0x60(%rsp)
cmpl %r8d, %edx
jl 0xe5f8
movb %al, %bpl
shll $0x4, %ebp
orl $0x4, %ebp
movl %edx, 0x58(%rsp)
movl %edx, %eax
subl %r8d, %eax
incl %eax
movq %rax, 0x98(%rsp)
movq $0x0, 0x10(%rsp)
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
movl %ebp, 0x40(%rsp)
testl %r8d, %r8d
jle 0xea40
movq 0x88(%rsp), %rax
movq 0x10(%rsp), %rcx
addq %rcx, %rax
movq %rax, 0x70(%rsp)
movq 0x50(%rsp), %rax
addl %ecx, %eax
movl %eax, 0x24(%rsp)
movl 0x58(%rsp), %eax
subl %ecx, %eax
movl %eax, 0x30(%rsp)
movl $0x1, %r15d
movq %r8, %r13
leaq -0x1(%r13), %r12
movq 0x70(%rsp), %r14
movsbq -0x1(%r14,%r13), %rbx
movl 0xa0(%rsp), %eax
movb %al, -0x1(%r14,%r13)
movq %r14, %rdi
movl %r8d, %esi
callq *0xa8(%rsp)
movb %bl, -0x1(%r14,%r13)
movq %r12, 0xb0(%rsp)
testq %r12, %r12
je 0xe90b
movq 0x60(%rsp), %rcx
movl (%rcx,%rbx,4), %ecx
movl %ecx, 0x18(%rsp)
jmp 0xe913
movl $0xffffffff, 0x18(%rsp) # imm = 0xFFFFFFFF
movq %r13, 0x90(%rsp)
testl %eax, %eax
movl %r15d, 0x20(%rsp)
js 0xea1b
movl %eax, %r14d
movl %r15d, %eax
movq %rax, 0x78(%rsp)
xorl %r13d, %r13d
cmpl 0x18(%rsp), %r13d
je 0xea06
movq 0x28(%rsp), %rbx
movq 0x38(%rbx), %rax
movl (%rax,%r14,4), %ebp
testl %ebp, %ebp
jle 0xea06
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0xe976
movl 0x24(%rsp), %esi
movq 0x38(%rsp), %rdx
callq 0x1b931
testl %eax, %eax
jne 0xea06
movq 0x48(%rbx), %rax
movq (%rax,%r14,8), %r15
cmpl $0x2, %ebp
movl $0x1, %eax
cmovll %eax, %ebp
xorl %r12d, %r12d
movl (%r15,%r12,4), %ebx
cmpq $0x0, 0x110(%rsp)
je 0xe9c3
movq 0x28(%rsp), %rdi
movl %ebx, %esi
callq 0xf826
cmpq 0x110(%rsp), %rax
jne 0xe9fe
cmpl 0x118(%rsp), %ebx
jl 0xe9fe
cmpl 0x120(%rsp), %ebx
jge 0xe9fe
movl $0x18, %esi
movq 0x80(%rsp), %rdi
callq 0x2bfa9
movq 0x10(%rsp), %rcx
movl %ecx, 0x8(%rax)
movl %ebx, 0xc(%rax)
addl 0x30(%rsp), %ebx
movl %ebx, 0x10(%rax)
movq (%rsp), %rcx
movq %rcx, (%rax)
movq 0x8(%rsp), %rcx
incl %ecx
movq %rcx, 0x8(%rsp)
movq %rax, (%rsp)
incq %r12
cmpq %r12, %rbp
jne 0xe98c
addq 0x78(%rsp), %r14
incl %r13d
movl 0x40(%rsp), %ebp
cmpl %ebp, %r13d
jne 0xe936
movl 0x20(%rsp), %r15d
imull %ebp, %r15d
cmpq $0x1, 0x90(%rsp)
movq 0xb0(%rsp), %r13
movq 0x38(%rsp), %r8
jg 0xe8c3
movq 0x10(%rsp), %rcx
incq %rcx
movq %rcx, 0x10(%rsp)
cmpq 0x98(%rsp), %rcx
jne 0xe887
jmp 0xe77a
movl 0x18(%rsi), %eax
movl %eax, 0x18(%rsp)
movl 0xc(%rdi), %ecx
leal -0x1(%rcx), %eax
movq 0x10(%rsi), %r10
movl $0x0, %r13d
cmpl $0x2, %ecx
jl 0xea9f
movl %eax, %edx
xorl %esi, %esi
leaq 0xb31e9(%rip), %r9      # 0xc1c70
xorl %r13d, %r13d
movsbq (%r10,%rsi), %r8
shll $0x2, %r13d
addl (%r9,%r8,4), %r13d
incq %rsi
cmpq %rsi, %rdx
jne 0xea8a
cmpl 0x18(%rsp), %ecx
jg 0xe5f8
movl 0x18(%rdi), %ecx
movl %ecx, 0x40(%rsp)
movslq %eax, %r15
movl %eax, %eax
movq %rax, 0x38(%rsp)
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
movq %r10, 0x78(%rsp)
movsbq (%r10,%r15), %rax
shll $0x2, %r13d
leaq 0xb3190(%rip), %rcx     # 0xc1c70
addl (%rcx,%rax,4), %r13d
andl 0x40(%rsp), %r13d
movq 0x28(%rsp), %rbx
movq 0x38(%rbx), %rax
movl (%rax,%r13,4), %r14d
testq %r14, %r14
movq %r15, 0x30(%rsp)
je 0xebc1
movq %r15, %rbp
subq 0x38(%rsp), %rbp
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0xeb2e
movq 0x50(%rsp), %rax
leal (%rax,%rbp), %esi
movl 0xc(%rbx), %edx
callq 0x1b931
testl %eax, %eax
jne 0xebc1
testl %r14d, %r14d
jle 0xebc1
movq 0x48(%rbx), %rax
movq (%rax,%r13,8), %r12
movl 0x18(%rsp), %eax
subl %ebp, %eax
movl %eax, 0x10(%rsp)
xorl %r15d, %r15d
movl (%r12,%r15,4), %ebx
cmpq $0x0, 0x110(%rsp)
je 0xeb83
movq 0x28(%rsp), %rdi
movl %ebx, %esi
callq 0xf826
cmpq 0x110(%rsp), %rax
jne 0xebb9
cmpl 0x118(%rsp), %ebx
jl 0xebb9
cmpl 0x120(%rsp), %ebx
jge 0xebb9
movl $0x18, %esi
movq 0x80(%rsp), %rdi
callq 0x2bfa9
movl %ebp, 0x8(%rax)
movl %ebx, 0xc(%rax)
addl 0x10(%rsp), %ebx
movl %ebx, 0x10(%rax)
movq (%rsp), %rcx
movq %rcx, (%rax)
movq 0x8(%rsp), %rcx
incl %ecx
movq %rcx, 0x8(%rsp)
movq %rax, (%rsp)
incq %r15
cmpq %r15, %r14
jne 0xeb4c
movq 0x30(%rsp), %r15
incq %r15
cmpl %r15d, 0x18(%rsp)
movq 0x78(%rsp), %r10
jne 0xead0
jmp 0xe77a
cmpb $0x0, 0x28(%rdi)
leaq -0x2437(%rip), %rax     # 0xc7b2
leaq -0x2409(%rip), %rcx     # 0xc7e7
cmoveq %rax, %rcx
movq %rcx, 0x10(%rsp)
cmpb $0x0, 0xb239c(%rip)     # 0xc0f9c
jne 0xec31
movl $0x2, 0xb0f08(%rip)     # 0xbfb14
movl $0x1, 0xb0f06(%rip)     # 0xbfb1c
movl $0x0, 0xb0f40(%rip)     # 0xbfb60
movl $0x3, 0xb0f02(%rip)     # 0xbfb2c
movb $0x1, 0xb236b(%rip)     # 0xc0f9c
cmpl %r8d, %edx
jl 0xe5f8
movl %edx, 0x58(%rsp)
movl %edx, %eax
subl %r8d, %eax
incl %eax
movq %rax, 0x30(%rsp)
xorl %r13d, %r13d
movq $0x0, 0x8(%rsp)
movq $0x0, (%rsp)
movq 0x88(%rsp), %rax
leaq (%rax,%r13), %rdi
movq %r8, %r12
movl %r8d, %esi
callq *0x10(%rsp)
testl %eax, %eax
js 0xed4d
movq 0x28(%rsp), %r15
movq 0x38(%r15), %rcx
movl %eax, %ebx
movl (%rcx,%rbx,4), %r14d
testl %r14d, %r14d
jle 0xed4d
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0xecb7
movq 0x50(%rsp), %rax
leal (%rax,%r13), %esi
movl %r12d, %edx
callq 0x1b931
testl %eax, %eax
jne 0xed4d
movq 0x48(%r15), %rax
movq (%rax,%rbx,8), %rbp
movl 0x58(%rsp), %r15d
subl %r13d, %r15d
cmpl $0x2, %r14d
movl $0x1, %eax
cmovll %eax, %r14d
xorl %r12d, %r12d
movl (%rbp,%r12,4), %ebx
cmpq $0x0, 0x110(%rsp)
je 0xed0f
movq 0x28(%rsp), %rdi
movl %ebx, %esi
callq 0xf826
cmpq 0x110(%rsp), %rax
jne 0xed45
cmpl 0x118(%rsp), %ebx
jl 0xed45
cmpl 0x120(%rsp), %ebx
jge 0xed45
movl $0x18, %esi
movq 0x80(%rsp), %rdi
callq 0x2bfa9
movl %r13d, 0x8(%rax)
movl %ebx, 0xc(%rax)
addl %r15d, %ebx
movl %ebx, 0x10(%rax)
movq (%rsp), %rcx
movq %rcx, (%rax)
movq 0x8(%rsp), %rcx
incl %ecx
movq %rcx, 0x8(%rsp)
movq %rax, (%rsp)
incq %r12
cmpq %r12, %r14
jne 0xecd7
incq %r13
cmpq 0x30(%rsp), %r13
movq 0x38(%rsp), %r8
jne 0xec5e
jmp 0xe77a