// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_signal_enrichment_utils.cpp
// Function: get_binomial_pvalue_per_region_neighborhood_window_control(double*, double*, int, int, double*, double, bool, int, int, int, int)
double get_binomial_pvalue_per_region_neighborhood_window_control(double* signal_track_data, double* control_track_data, int region_start, int region_end, double* _log_factorials, double scaling_factor,
	bool length_normalization, int l_norm_win, int l_signal, int l_control, int n_vicinity_wins)
{
	// Get the total profile signal.
	double total_profile_signal = 0;
	for(int i = region_start; i <= region_end; i++)
	{
		total_profile_signal += floor(signal_track_data[i]);
	} // i loop.

	// If the region size is smaller than 2000 base pairs, get the control signal from a larger region.
	//double total_control_signal = 0;
	int eff_control_region_start = region_start;
	int eff_control_region_end = region_end;
	if((eff_control_region_end - eff_control_region_start+1) <= l_norm_win)
	{
		eff_control_region_start = (region_start+region_end)/2 - l_norm_win;
		eff_control_region_end = (region_start+region_end)/2 + l_norm_win;
	}

	if(eff_control_region_start < 0)
	{
		eff_control_region_start = 1;
	}

	if(eff_control_region_end > l_control)
	{
		eff_control_region_end = l_control;
	}

	if(eff_control_region_end ==eff_control_region_start)
	{
		return(0.0);
		//eff_control_region_end++;
	}

	double total_control_signal = 0;
	for(int cur_start = MAX(1, eff_control_region_start-n_vicinity_wins*(eff_control_region_end-eff_control_region_start)); 
		cur_start < MIN(l_control, eff_control_region_end + n_vicinity_wins*(eff_control_region_end-eff_control_region_start));
		cur_start += (eff_control_region_end-eff_control_region_start))
	{
		double cur_total_control_signal = 0;
		for(int i = cur_start; i <= MIN(l_control, cur_start+(eff_control_region_end-eff_control_region_start)); i++)
		{
			double cur_control_value = control_track_data[i];
			//cur_total_control_signal += floor(cur_control_value);
			cur_total_control_signal += (cur_control_value);
		} // i loop.

		total_control_signal = MAX(total_control_signal, cur_total_control_signal);
	} // i loop.

	// Finally, normalize the control signal from effective window size to the original window size.
	total_control_signal = total_control_signal * (double)(region_end - region_start+1) / (double)(eff_control_region_end - eff_control_region_start+1);

	// Scale the control and profile signals.
	total_control_signal /= scaling_factor;
	total_profile_signal /= scaling_factor;

	// Normalize both signals with respect to normalization region, if they are larger than the region size.
	if(length_normalization && 
		(region_end - region_start+1) > l_norm_win)
	{
		total_profile_signal = total_profile_signal / ((double)(region_end - region_start+1) / l_norm_win);
		total_control_signal = total_control_signal / ((double)(region_end - region_start+1) / l_norm_win);

		if(floor(total_control_signal) == 0)
		{
			total_control_signal = 1.0;
		}

		// The total signal hit 0, return 1.
		if(floor(total_profile_signal) == 0)
		{
			//fprintf(stderr, "Hit 0.\n");
			// Return the most insignificant p-value.
			return(xlog(1.0));
		}
	}
	
	int grand_total_int = (int)(total_profile_signal + total_control_signal);

	// Setup the log factorials.
	double* log_factorials = NULL;
	if(_log_factorials == NULL)
	{
		log_factorials = buffer_log_factorials(grand_total_int+3);
	}
	else
	{
		log_factorials = _log_factorials;
	}

	// Compute the p-values.
	double log_flip = log(.5);
	double cur_region_log_p_val = xlog(0.0);
	for(int i = 0; i <= total_control_signal; i++)
	{
		double log_cur_half_pow = log_flip * grand_total_int;
		double log_cur_perm = 0.0; // = xlog(1.0).

		// Compute the current permutation, using shortcuts, bypassing the function calls from xlog_math library.
		log_cur_perm = xlog_div(log_factorials[grand_total_int], xlog_mul(log_factorials[i], log_factorials[grand_total_int-i]));
		cur_region_log_p_val = xlog_sum(cur_region_log_p_val, xlog_mul(log_cur_perm, log_cur_half_pow));
	} // i loop.

	// Free memory if it is allocated in the function.
	if(_log_factorials == NULL)
	{
		delete [] log_factorials;
	}

	return(cur_region_log_p_val);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movl %r9d, 0x1c(%rsp)
movapd %xmm0, 0x50(%rsp)
movq %r8, 0x48(%rsp)
movq %rsi, %r14
movq %rdi, %r13
movl 0xb8(%rsp), %ebp
movl 0xb0(%rsp), %ebx
movl 0xa0(%rsp), %eax
movl %eax, 0x30(%rsp)
movl %edx, 0x10(%rsp)
movslq %edx, %r15
movl %ecx, 0x20(%rsp)
movslq %ecx, %r12
xorpd %xmm3, %xmm3
cmpq %r12, %r15
jg 0x19d69
movsd (%r13,%r15,8), %xmm0
movapd %xmm3, (%rsp)
callq 0x22b0
movapd (%rsp), %xmm3
addsd %xmm0, %xmm3
incq %r15
jmp 0x19d45
movl 0x20(%rsp), %eax
movl %eax, %ecx
movl 0x10(%rsp), %esi
subl %esi, %ecx
movl 0x30(%rsp), %r11d
cmpl %r11d, %ecx
jge 0x19d8f
addl %esi, %eax
pushq $0x2
popq %rsi
cltd
idivl %esi
movl %eax, %esi
subl %r11d, %esi
addl %r11d, %eax
testl %esi, %esi
pushq $0x1
popq %rdx
cmovsl %edx, %esi
cmpl %ebx, %eax
cmovgel %ebx, %eax
xorpd %xmm2, %xmm2
movl %eax, %r15d
subl %esi, %r15d
je 0x19f99
imull %r15d, %ebp
subl %ebp, %esi
cmpl $0x2, %esi
cmovgel %esi, %edx
addl %eax, %ebp
cmpl %ebx, %ebp
cmovgel %ebx, %ebp
leal 0x1(%rcx), %esi
movslq %r15d, %rdi
xorpd %xmm0, %xmm0
movl %edx, %r8d
cmpl %ebp, %r8d
jge 0x19e01
addl %r15d, %r8d
cmpl %ebx, %r8d
movl %ebx, %r9d
cmovll %r8d, %r9d
movslq %r9d, %r9
xorpd %xmm1, %xmm1
movq %rdx, %r10
cmpq %r9, %r10
jg 0x19df8
addsd (%r14,%r10,8), %xmm1
incq %r10
jmp 0x19de8
maxsd %xmm1, %xmm0
addq %rdi, %rdx
jmp 0x19dcc
cmpl %r11d, %ecx
setge %cl
cvtsi2sd %esi, %xmm1
mulsd %xmm1, %xmm0
incl %r15d
cvtsi2sd %r15d, %xmm2
divsd %xmm2, %xmm0
unpcklpd %xmm0, %xmm3            # xmm3 = xmm3[0],xmm0[0]
movapd 0x50(%rsp), %xmm0
unpcklpd %xmm0, %xmm0            # xmm0 = xmm0[0,0]
divpd %xmm0, %xmm3
testb %cl, 0x1c(%rsp)
je 0x19e94
cvtsi2sd %r11d, %xmm0
divsd %xmm0, %xmm1
unpcklpd %xmm1, %xmm1            # xmm1 = xmm1[0,0]
divpd %xmm1, %xmm3
movapd %xmm3, (%rsp)
movapd %xmm3, %xmm0
callq 0x22b0
movapd %xmm0, 0x30(%rsp)
movapd (%rsp), %xmm0
unpckhpd %xmm0, %xmm0            # xmm0 = xmm0[1,1]
movapd %xmm0, 0x20(%rsp)
callq 0x22b0
movapd 0x30(%rsp), %xmm1
unpcklpd %xmm0, %xmm1            # xmm1 = xmm1[0],xmm0[0]
xorpd %xmm0, %xmm0
cmpeqpd %xmm1, %xmm0
movmskpd %xmm0, %eax
testb $0x2, %al
movq 0x48(%rsp), %r13
jne 0x19e9b
movapd 0x20(%rsp), %xmm0
jmp 0x19ea3
movq 0x48(%rsp), %r13
jmp 0x19ecb
movsd 0xa165(%rip), %xmm0     # 0x24008
testb $0x1, %al
movapd (%rsp), %xmm3
je 0x19ec7
movsd 0xa154(%rip), %xmm0     # 0x24008
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x1f860
unpcklpd %xmm0, %xmm3            # xmm3 = xmm3[0],xmm0[0]
movapd %xmm3, %xmm0
unpckhpd %xmm3, %xmm0            # xmm0 = xmm0[1],xmm3[1]
movapd %xmm0, 0x20(%rsp)
addsd %xmm0, %xmm3
cvttsd2si %xmm3, %ebx
movq %r13, %r14
testq %r13, %r13
jne 0x19ef4
leal 0x3(%rbx), %edi
callq 0x1e201
movq %rax, %r14
xorpd %xmm0, %xmm0
callq 0x1f860
cvtsi2sd %ebx, %xmm1
mulsd 0xe1d7(%rip), %xmm1     # 0x280e0
movsd %xmm1, 0x10(%rsp)
movapd %xmm0, %xmm2
movslq %ebx, %rbx
xorl %r15d, %r15d
movq %rbx, %r12
cvtsi2sd %r15d, %xmm0
movapd 0x20(%rsp), %xmm1
ucomisd %xmm0, %xmm1
movsd %xmm2, (%rsp)
jb 0x19f82
movsd (%r14,%rbx,8), %xmm0
movsd %xmm0, 0x30(%rsp)
movsd (%r14,%r15,8), %xmm0
movsd (%r14,%r12,8), %xmm1
callq 0x1f994
movaps %xmm0, %xmm1
movsd 0x30(%rsp), %xmm0
callq 0x1f9cf
movsd 0x10(%rsp), %xmm1
callq 0x1f994
movapd %xmm0, %xmm1
movsd (%rsp), %xmm0
callq 0x1f8b2
movapd %xmm0, %xmm2
incq %r15
decq %r12
jmp 0x19f1c
testq %r13, %r13
jne 0x19f99
testq %r14, %r14
je 0x19f99
movq %r14, %rdi
callq 0x2210
movsd (%rsp), %xmm2
movapd %xmm2, %xmm0
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq