// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: append_inexact_overlap_region_alloc(overlap_region_alloc*, overlap_region*, long long, long long, int, void*)
int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, 
                                        long long xLen, long long yLen, int add_beg_end, void *km)
{
   
    if (list->length + 1 > list->size)
    {
        uint64_t sl = list->size;
        list->size = list->length + 1;
        kroundup64(list->size);
        if(!km) {
            REALLOC(list->list, list->size);
        } else {
            KREALLOC(km, list->list, list->size);
        }
        /// need to set new space to be 0
        memset(list->list + sl, 0, sizeof(overlap_region)*(list->size - sl));
    }

    if (list->length!=0 && list->list[list->length - 1].y_id==tmp->y_id)
    {    
        ///if(list->list[list->length - 1].shared_seed >= tmp->shared_seed)
        if((list->list[list->length - 1].shared_seed > tmp->shared_seed)
           ||
           ((list->list[list->length - 1].shared_seed == tmp->shared_seed) && 
           (list->list[list->length - 1].overlapLen <= tmp->overlapLen)))
        {
            return 0;
        }
        else
        {
            list->length--;
        }
    }

    if(tmp->x_pos_s <= tmp->y_pos_s)
    {
        tmp->y_pos_s = tmp->y_pos_s - tmp->x_pos_s;
        tmp->x_pos_s = 0;
    }
    else
    {
        tmp->x_pos_s = tmp->x_pos_s - tmp->y_pos_s;
        tmp->y_pos_s = 0;
    }


    long long x_right_length = xLen - tmp->x_pos_e - 1;
    long long y_right_length = yLen - tmp->y_pos_e - 1;

    if(x_right_length <= y_right_length)
    {
        tmp->x_pos_e = xLen - 1;
        tmp->y_pos_e = tmp->y_pos_e + x_right_length;        
    }
    else
    {
        tmp->x_pos_e = tmp->x_pos_e + y_right_length;
        tmp->y_pos_e = yLen - 1;
    }
    
    if (tmp->x_pos_strand == 1)
    {
        list->list[list->length].x_id = tmp->x_id;
        list->list[list->length].x_pos_e = xLen - tmp->x_pos_s - 1;
        list->list[list->length].x_pos_s = xLen - tmp->x_pos_e - 1;
        list->list[list->length].x_pos_strand = 0;

        list->list[list->length].y_id = tmp->y_id;
        list->list[list->length].y_pos_e = yLen - tmp->y_pos_s - 1;
        list->list[list->length].y_pos_s = yLen - tmp->y_pos_e - 1;
        list->list[list->length].y_pos_strand = 1;

        resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
        if(add_beg_end == 1)
        {
            add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
        }
        
        long long distance_gap;
        /****************************may have bugs********************************/
        ///long long pre_distance_gap = 0;
        long long pre_distance_gap = 0xfffffffffffffff;
        /****************************may have bugs********************************/
        long long i = 0;
        for (i = 0; i < (long long)tmp->f_cigar.length; i++)
        {
            distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
            if(distance_gap != pre_distance_gap)
            {
                pre_distance_gap = distance_gap;
                add_fake_cigar(&(list->list[list->length].f_cigar), xLen - get_fake_gap_pos(&(tmp->f_cigar), i) - 1, 
                pre_distance_gap, km);
            }
        }

        if(add_beg_end == 1 && get_fake_gap_pos(&(list->list[list->length].f_cigar), 
            list->list[list->length].f_cigar.length - 1) != (long long)list->list[list->length].x_pos_e)
        {
            add_fake_cigar(&(list->list[list->length].f_cigar), 
            list->list[list->length].x_pos_e, 
            get_fake_gap_shift(&(list->list[list->length].f_cigar), 
            list->list[list->length].f_cigar.length - 1), km);
        }
    }
    else
    {
        list->list[list->length].x_id = tmp->x_id;
        list->list[list->length].x_pos_e = tmp->x_pos_e;
        list->list[list->length].x_pos_s = tmp->x_pos_s;
        list->list[list->length].x_pos_strand = tmp->x_pos_strand;

        list->list[list->length].y_id = tmp->y_id;
        list->list[list->length].y_pos_e = tmp->y_pos_e;
        list->list[list->length].y_pos_s = tmp->y_pos_s;
        list->list[list->length].y_pos_strand = tmp->y_pos_strand;



        resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
        if(add_beg_end == 1)
        {
            add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
        }
        
        long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
        long long distance_pos = tmp->y_pos_e - tmp->y_pos_s;
        long long init_distance_gap = distance_pos - distance_self_pos;
        /****************************may have bugs********************************/
        ///long long pre_distance_gap = init_distance_gap;
        long long pre_distance_gap = 0xfffffffffffffff;
        /****************************may have bugs********************************/
        long long distance_gap;
        long long i = 0;
        for (i = tmp->f_cigar.length - 1; i >= 0; i--)
        {
            distance_gap = get_fake_gap_shift(&(tmp->f_cigar), i);
            if(distance_gap != pre_distance_gap)
            {
                pre_distance_gap = distance_gap;

                add_fake_cigar(&(list->list[list->length].f_cigar), 
                get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap, km);
            }
        }

        if(add_beg_end == 1 && get_fake_gap_pos(&(list->list[list->length].f_cigar), 
        list->list[list->length].f_cigar.length - 1) != (long long)list->list[list->length].x_pos_e)
        {
            add_fake_cigar(&(list->list[list->length].f_cigar), 
            list->list[list->length].x_pos_e, 
            get_fake_gap_shift(&(list->list[list->length].f_cigar), 
            list->list[list->length].f_cigar.length - 1), km);
        } 
    }

    list->list[list->length].shared_seed = tmp->shared_seed;
    list->list[list->length].align_length = 0;
    list->list[list->length].is_match = 0;
    list->list[list->length].non_homopolymer_errors = 0;
    list->list[list->length].strong = 0;

    list->length++;

    return 1;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, %r15
movl %r8d, 0xc(%rsp)
movq %rcx, %r13
movq %rdx, %r12
movq %rsi, %r14
movq %rdi, %rbx
movq 0x8(%rdi), %rbp
movq 0x10(%rdi), %rax
leaq 0x1(%rax), %rcx
cmpq %rbp, %rcx
jbe 0x3e704
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x20, %rax
orq %rcx, %rax
incq %rax
movq %rax, 0x8(%rbx)
imulq $0xa8, %rax, %rdx
movq (%rbx), %rsi
testq %r15, %r15
je 0x3e6d7
movq %r15, %rdi
callq 0x1e3800
jmp 0x3e6e2
movq %rsi, %rdi
movq %rdx, %rsi
callq 0x2370
movq %rax, (%rbx)
imulq $0xa8, %rbp, %rdi
addq %rax, %rdi
movq 0x8(%rbx), %rax
subq %rbp, %rax
imulq $0xa8, %rax, %rdx
xorl %esi, %esi
callq 0x20e0
movq 0x10(%rbx), %rcx
testq %rcx, %rcx
je 0x3e752
movq (%rbx), %rdx
imulq $0xa8, %rcx, %rax
movl -0x98(%rdx,%rax), %esi
cmpl 0x10(%r14), %esi
jne 0x3e752
addq %rax, %rdx
movl 0x24(%r14), %esi
xorl %eax, %eax
cmpl %esi, -0x84(%rdx)
jg 0x3ea7d
jne 0x3e74b
movl -0x88(%rdx), %edx
cmpl 0x20(%r14), %edx
jbe 0x3ea7d
decq %rcx
movq %rcx, 0x10(%rbx)
leaq 0x4(%r14), %rax
movl 0x4(%r14), %edx
movl 0x14(%r14), %esi
leaq 0x14(%r14), %rcx
movl %edx, %edi
subl %esi, %edi
jbe 0x3e76f
movl %edi, (%rax)
movq %rcx, %rax
jmp 0x3e773
subl %edx, %esi
movl %esi, (%rcx)
movl $0x0, (%rax)
movl 0x8(%r14), %edx
movl 0x18(%r14), %ecx
movq %rdx, %rax
notq %rax
addq %r12, %rax
movq %rcx, %rsi
notq %rsi
addq %r13, %rsi
cmpq %rsi, %rax
jle 0x3e7a4
addl %edx, %esi
movl %esi, 0x8(%r14)
leal -0x1(%r13), %eax
jmp 0x3e7af
leal -0x1(%r12), %edx
movl %edx, 0x8(%r14)
addl %ecx, %eax
movl %eax, 0x18(%r14)
movl (%r14), %edi
movl 0xc(%r14), %esi
movq (%rbx), %rcx
imulq $0xa8, 0x10(%rbx), %rdx
movl %edi, (%rcx,%rdx)
cmpl $0x1, %esi
movq %rbx, 0x10(%rsp)
movq %r15, 0x18(%rsp)
jne 0x3e8eb
movl 0x4(%r14), %eax
notl %eax
addl %r12d, %eax
leaq (%rcx,%rdx), %rdi
addq $0x38, %rdi
movl %eax, -0x30(%rdi)
movl 0x8(%r14), %eax
notl %eax
addl %r12d, %eax
movl %eax, -0x34(%rdi)
movl $0x0, -0x2c(%rdi)
movl 0x10(%r14), %eax
movl %eax, -0x28(%rdi)
movl 0x14(%r14), %eax
notl %eax
addl %r13d, %eax
movl %eax, -0x20(%rdi)
movl 0x18(%r14), %eax
notl %eax
addl %r13d, %eax
movl %eax, -0x24(%rdi)
movl $0x1, -0x1c(%rdi)
movl 0x40(%r14), %esi
addl $0x2, %esi
movq %r15, %rdx
callq 0x3e604
cmpl $0x1, 0xc(%rsp)
jne 0x3e85e
movq (%rbx), %rax
imulq $0xa8, 0x10(%rbx), %rcx
leaq (%rax,%rcx), %rdi
addq $0x38, %rdi
movl -0x34(%rdi), %esi
xorl %edx, %edx
movq %r15, %rcx
callq 0x3dd21
cmpl $0x0, 0x40(%r14)
je 0x3e9e9
movabsq $0xfffffffffffffff, %rax # imm = 0xFFFFFFFFFFFFFFF
xorl %r13d, %r13d
movabsq $0x100000000, %rbp      # imm = 0x100000000
xorl %r15d, %r15d
movq 0x38(%r14), %rcx
movq %r13, %rdx
sarq $0x1d, %rdx
movq (%rcx,%rdx), %rsi
movl %esi, %ecx
shrl %ecx
movl %ecx, %edx
negl %edx
testb $0x1, %sil
cmovel %ecx, %edx
movslq %edx, %rbx
cmpq %rbx, %rax
je 0x3e8d7
movq 0x10(%rsp), %rcx
movq (%rcx), %rax
imulq $0xa8, 0x10(%rcx), %rcx
leaq (%rax,%rcx), %rdi
addq $0x38, %rdi
shrq $0x20, %rsi
notl %esi
addl %r12d, %esi
movq 0x18(%rsp), %rcx
callq 0x3dd21
movq %rbx, %rax
incq %r15
movl 0x40(%r14), %ecx
addq %rbp, %r13
cmpq %rcx, %r15
jb 0x3e883
jmp 0x3e9e9
movl 0x8(%r14), %r8d
leaq (%rcx,%rdx), %rdi
addq $0x38, %rdi
movl %r8d, -0x30(%rdi)
movl 0x4(%r14), %ecx
movl %ecx, -0x34(%rdi)
movl %esi, -0x2c(%rdi)
movl 0x10(%r14), %ecx
movl %ecx, -0x28(%rdi)
movl %eax, -0x20(%rdi)
movl 0x14(%r14), %eax
movl %eax, -0x24(%rdi)
movl 0x1c(%r14), %eax
movl %eax, -0x1c(%rdi)
movl 0x40(%r14), %esi
addl $0x2, %esi
movq %r15, %rdx
callq 0x3e604
cmpl $0x1, 0xc(%rsp)
jne 0x3e953
movq (%rbx), %rax
imulq $0xa8, 0x10(%rbx), %rcx
leaq (%rax,%rcx), %rdi
addq $0x38, %rdi
movl -0x34(%rdi), %esi
xorl %edx, %edx
movq %r15, %rcx
callq 0x3dd21
movabsq $0xfffffffffffffff, %rax # imm = 0xFFFFFFFFFFFFFFF
movl 0x4(%r14), %ecx
movl 0x8(%r14), %r13d
movl 0x40(%r14), %ebp
addl 0x18(%r14), %ecx
movl %ecx, 0x24(%rsp)
addl 0x14(%r14), %r13d
decl %ebp
leaq 0x1(%rbp), %r15
shlq $0x20, %rbp
movabsq $-0x100000000, %rbx     # imm = 0xFFFFFFFF00000000
movq 0x38(%r14), %rcx
movq %rbp, %rdx
sarq $0x1d, %rdx
movq (%rcx,%rdx), %rsi
movl %esi, %edx
shrl %edx
movl %edx, %ecx
negl %ecx
testb $0x1, %sil
cmovel %edx, %ecx
movslq %ecx, %r12
cmpq %r12, %rax
je 0x3e9e1
movq 0x10(%rsp), %rdx
movq (%rdx), %rax
imulq $0xa8, 0x10(%rdx), %rdx
leaq (%rax,%rdx), %rdi
addq $0x38, %rdi
shrq $0x20, %rsi
addl %r13d, %ecx
movl 0x24(%rsp), %edx
subl %ecx, %edx
movq 0x18(%rsp), %rcx
callq 0x3dd21
movq %r12, %rax
addq %rbx, %rbp
decq %r15
jg 0x3e989
cmpl $0x1, 0xc(%rsp)
movq 0x10(%rsp), %rbx
jne 0x3ea49
imulq $0xa8, 0x10(%rbx), %rcx
movq (%rbx), %rax
movl 0x40(%rax,%rcx), %edx
decl %edx
movq 0x38(%rax,%rcx), %rsi
movslq %edx, %rdx
movslq 0x4(%rsi,%rdx,8), %rdx
movl 0x8(%rax,%rcx), %esi
cmpq %rsi, %rdx
je 0x3ea49
addq %rcx, %rax
leaq 0x38(%rax), %rdi
movl 0x40(%rax), %ecx
decl %ecx
movq 0x38(%rax), %rax
movslq %ecx, %rcx
movl (%rax,%rcx,8), %eax
movl %eax, %ecx
shrl %ecx
movl %ecx, %edx
negl %edx
testb $0x1, %al
cmovel %ecx, %edx
movq 0x18(%rsp), %rcx
callq 0x3dd21
movl 0x24(%r14), %eax
movq (%rbx), %rcx
movq 0x10(%rbx), %rdx
imulq $0xa8, %rdx, %rsi
movl %eax, 0x24(%rcx,%rsi)
xorl %eax, %eax
movl %eax, 0x28(%rcx,%rsi)
movb %al, 0x2c(%rcx,%rsi)
movl %eax, 0x30(%rcx,%rsi)
movb %al, 0x2e(%rcx,%rsi)
incq %rdx
movq %rdx, 0x10(%rbx)
movl $0x1, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq