LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_top_region_per_total_coverage(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, double)
vector<t_annot_region*>* get_top_region_per_total_coverage(vector<t_annot_region*>* regions, double max_covg)
{
	double cur_total_covg = 0;
	vector<t_annot_region*>* top_regions = new vector<t_annot_region*>();
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		cur_total_covg += (regions->at(i_reg)->end - regions->at(i_reg)->start + 1);
		top_regions->push_back(regions->at(i_reg));
		if(max_covg == 0 ||
			max_covg <= cur_total_covg)
		{
			break;
		}
	} // i_reg loop.

	return(top_regions);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x18, %rsp
movsd %xmm0, 0x8(%rsp)
movq %rdi, %rbx
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r14
xorpd %xmm0, %xmm0
andq $0x0, 0x10(%rax)
movupd %xmm0, (%rax)
xorl %r15d, %r15d
xorpd %xmm1, %xmm1
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x123a1
movq %rbx, %rdi
movq %r15, %rsi
movsd %xmm1, 0x10(%rsp)
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %ebp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
subl 0xc(%rax), %ebp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq %r14, %rdi
movq %rax, %rsi
callq 0x7448
movsd 0x10(%rsp), %xmm1
movsd 0x8(%rsp), %xmm0
ucomisd 0x11d28(%rip), %xmm0    # 0x240b0
jne 0x1238c
jnp 0x123a1
incl %ebp
cvtsi2sd %ebp, %xmm0
incq %r15
addsd %xmm0, %xmm1
ucomisd 0x8(%rsp), %xmm1
jb 0x12324
movq %r14, %rax
addq $0x18, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: sort_set_sorting_info(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, bool (*)(t_annot_region*, t_annot_region*))
void sort_set_sorting_info(vector<t_annot_region*>* regions, bool (sort_regions_callback)(t_annot_region*, t_annot_region*))
{
	// Set the sorting info for each region.
	if(regions->size() == 0)
	{
		return;
	}

	// Sort the regions.
	if(sort_regions_callback != NULL)
	{
		sort(regions->begin(), regions->end(), sort_regions_callback);
	}

		// Set the cumulative start positions for each region: Cumulative start from the end of the list.
	int current_cumulative_start = regions->back()->start;
	for(int i_reg = regions->size()-1; i_reg >= 0; i_reg--)
	{
		t_sorting_info* cur_reg_sorting_info = new t_sorting_info();
		if(current_cumulative_start > regions->at(i_reg)->start)
		{
			current_cumulative_start = regions->at(i_reg)->start;	
		}

		cur_reg_sorting_info->cumulative_sorted_start = current_cumulative_start;

		regions->at(i_reg)->sort_info = cur_reg_sorting_info;
	} // i_reg loop.

	// Set the cumulative end: Cumulative end from the beginning of the list.
	int current_cumulative_end = 0;
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		//t_sorting_info* cur_reg_sorting_info = new t_sorting_info();
		t_sorting_info* cur_reg_sorting_info = regions->at(i_reg)->sort_info;
		if(current_cumulative_end < regions->at(i_reg)->end)
		{
			current_cumulative_end = regions->at(i_reg)->end;	
		}

		cur_reg_sorting_info->cumulative_sorted_end = current_cumulative_end;
	} // i_reg loop.
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rdx
movq %rdi, %rbx
movq (%rdi), %rdi
movq 0x8(%rbx), %rsi
cmpq %rdi, %rsi
je 0x124ab
testq %rdx, %rdx
je 0x123e1
callq 0x17bcf
movq (%rbx), %rdi
movq 0x8(%rbx), %rsi
movq -0x8(%rsi), %rax
movl 0xc(%rax), %ebp
subq %rdi, %rsi
shrq $0x3, %rsi
movl %esi, %r13d
decq %r13
pushq $0x8
popq %r14
testl %r13d, %r13d
js 0x12455
movq %r14, %rdi
callq 0x2170
movq %rax, %r15
andq $0x0, (%rax)
movl %r13d, %r12d
andl $0x7fffffff, %r12d      # imm = 0x7FFFFFFF
movq %rbx, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpl 0xc(%rax), %ebp
jle 0x1243b
movq %rbx, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movl %ebp, (%r15)
movq %rbx, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movq %r15, 0x38(%rax)
decq %r13
jmp 0x123f9
xorl %r14d, %r14d
xorl %ebp, %ebp
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r14
jge 0x124ab
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x38(%rax), %r15
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpl 0x20(%rax), %ebp
jge 0x124a2
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %ebp
movl %ebp, 0x4(%r15)
incq %r14
jmp 0x1245a
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: extend_BED(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, int, bool, bool)
void extend_BED(vector<t_annot_region*>* regions, int l_extend, bool extend_3p, bool extend_5p)
{	
	for(int i = 0; i < (int)regions->size(); i++)
	{
		int l_2_extend = (l_extend>0)?(l_extend):(regions->at(i)->end-regions->at(i)->start);

		if(regions->at(i)->strand == '+')
		{
			if(extend_5p)
			{
				regions->at(i)->start = (regions->at(i)->start > l_2_extend)?(regions->at(i)->start - l_2_extend):(1);
			}
			
			if(extend_3p)
			{
				regions->at(i)->end = (regions->at(i)->end + l_2_extend);
			}
		} // strand check for pos. strand.
		else
		{
			if(extend_3p)
			{
				regions->at(i)->start = (regions->at(i)->start > l_2_extend)?(regions->at(i)->start - l_2_extend):(1);
			}
			
			if(extend_5p)
			{
				regions->at(i)->end = (regions->at(i)->end + l_2_extend);
			}
		} // strand check for neg. strand.
	} // i loop.
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %ecx, %ebx
movl %edx, %ebp
movl %esi, %r13d
movq %rdi, %r15
xorl %r12d, %r12d
movl %ecx, 0x4(%rsp)
movq 0x8(%r15), %rax
subq (%r15), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x12632
movl %r13d, %r14d
testl %r13d, %r13d
jg 0x1255e
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r14d
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
subl 0xc(%rax), %r14d
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpb $0x2b, 0x8(%rax)
jne 0x125bd
testb %bl, %bl
je 0x125b6
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
pushq $0x1
popq %rbx
cmpl %r14d, 0xc(%rax)
jle 0x125a1
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebx
subl %r14d, %ebx
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl %ebx, 0xc(%rax)
movl 0x4(%rsp), %ebx
testb %bpl, %bpl
jne 0x12606
jmp 0x1262a
testb %bpl, %bpl
je 0x12602
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
pushq $0x1
popq %rbx
cmpl %r14d, 0xc(%rax)
jle 0x125ed
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebx
subl %r14d, %ebx
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl %ebx, 0xc(%rax)
movl 0x4(%rsp), %ebx
testb %bl, %bl
je 0x1262a
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
addl 0x20(%rax), %r14d
movq %r15, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl %r14d, 0x20(%rax)
incq %r12
jmp 0x1251c
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: locate_posn_region_per_region_starts(int, std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, int, int)
int locate_posn_region_per_region_starts(int start_posn, vector<t_annot_region*>* region_list, int i, int j)
{
	int i_mid = (i + j) / 2;

	if(i_mid == i ||
		i_mid == j)
	{
		//return(i);
		while(i_mid > 0 && region_list->at(i_mid)->start >= start_posn)
		{
			i_mid--;
		}

		return(i_mid);
	}

	if(region_list->at(i_mid)->start == start_posn)
	{
		while(i_mid > 0 && region_list->at(i_mid)->start >= start_posn)
		{
			i_mid--;
		}

		return(i_mid);
	}
	else if(region_list->at(i_mid)->start > start_posn)
	{
		return(locate_posn_region_per_region_starts(start_posn, region_list, i, i_mid));
	}
	else if(region_list->at(i_mid)->start < start_posn)
	{
		return(locate_posn_region_per_region_starts(start_posn, region_list, i_mid, j));
	}
	else
	{
		fprintf(stderr, "Current indices are (%d, %d), searching for %d @ %s(%d)\n", region_list->at(i)->start, region_list->at(j)->start,
			start_posn, __FILE__, __LINE__);
		exit(0);
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %ecx, %r15d
movl %edx, %r12d
movq %rsi, %r14
movl %edi, %ebx
movl %r12d, %r13d
movl %r15d, %r12d
movl %r12d, %r15d
leal (%r15,%r13), %eax
cltd
pushq $0x2
popq %rcx
idivl %ecx
movl %eax, %ebp
cmpl %r13d, %eax
je 0x12ec2
cmpl %r15d, %ebp
je 0x12ec2
movslq %ebp, %r12
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpl %ebx, 0xc(%rax)
je 0x12ef0
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpl %ebx, 0xc(%rax)
jg 0x12e0a
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpl %ebx, 0xc(%rax)
jl 0x12e04
movq 0x2216e(%rip), %rax     # 0x34fe0
movq (%rax), %r12
movslq %r13d, %rsi
movq %r14, %rdi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movslq %r15d, %rsi
movq %r14, %rdi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ecx
movl $0xbca, (%rsp)          # imm = 0xBCA
leaq 0x14fc3(%rip), %rsi     # 0x27e68
leaq 0x14b37(%rip), %r9      # 0x279e3
movq %r12, %rdi
movl %ebp, %edx
movl %ebx, %r8d
xorl %eax, %eax
callq 0x2240
xorl %edi, %edi
callq 0x21d0
movl %ebp, %r15d
movl %ebp, %r12d
sarl $0x1f, %r12d
andl %ebp, %r12d
incl %ebp
testl %r15d, %r15d
jle 0x12f1e
movq %r14, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
decq %r15
decl %ebp
cmpl %ebx, 0xc(%rax)
jge 0x12ed1
jmp 0x12f21
movl %ebp, %r15d
movl %ebp, %r12d
sarl $0x1f, %r12d
andl %ebp, %r12d
incl %ebp
testl %r15d, %r15d
jle 0x12f1e
movq %r14, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
decq %r15
decl %ebp
cmpl %ebx, 0xc(%rax)
jge 0x12eff
jmp 0x12f21
movl %r12d, %ebp
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: delete_restructured_annot_regions(t_sorted_annot_region_lists*)
void delete_restructured_annot_regions(t_sorted_annot_region_lists* restructured_region_lists)
{
	for(int i_chr = 0; i_chr < (int)restructured_region_lists->chr_ids->size(); i_chr++)
	{
		delete [] restructured_region_lists->chr_ids->at(i_chr);
		delete restructured_region_lists->neg_strand_regions_per_chrom[i_chr];
		delete restructured_region_lists->pos_strand_regions_per_chrom[i_chr];
		delete restructured_region_lists->regions_per_chrom[i_chr];
	} // i_chr loop.

	delete [] restructured_region_lists->neg_strand_regions_per_chrom;
	delete [] restructured_region_lists->pos_strand_regions_per_chrom;
	delete [] restructured_region_lists->regions_per_chrom;
	delete restructured_region_lists->chr_ids;

	delete restructured_region_lists;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
xorl %r14d, %r14d
pushq $0x18
popq %r15
movq 0x18(%rbx), %rdi
movq 0x8(%rdi), %rax
subq (%rdi), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r14
jge 0x12fd6
movq %r14, %rsi
callq 0x7342
movq (%rax), %rdi
testq %rdi, %rdi
je 0x12f6f
callq 0x2210
movq 0x10(%rbx), %rax
movq (%rax,%r14,8), %r12
testq %r12, %r12
je 0x12f84
movq %r12, %rdi
callq 0x832c
movq %r12, %rdi
movq %r15, %rsi
callq 0x2180
movq 0x8(%rbx), %rax
movq (%rax,%r14,8), %r12
testq %r12, %r12
je 0x12fa4
movq %r12, %rdi
callq 0x832c
movq %r12, %rdi
movq %r15, %rsi
callq 0x2180
movq (%rbx), %rax
movq (%rax,%r14,8), %r12
testq %r12, %r12
je 0x12fc3
movq %r12, %rdi
callq 0x832c
movq %r12, %rdi
movq %r15, %rsi
callq 0x2180
incq %r14
jmp 0x12f44
movq 0x10(%rbx), %rdi
testq %rdi, %rdi
je 0x12fe4
callq 0x2210
movq 0x8(%rbx), %rdi
testq %rdi, %rdi
je 0x12ff2
callq 0x2210
movq (%rbx), %rdi
testq %rdi, %rdi
je 0x12fff
callq 0x2210
movq 0x18(%rbx), %r14
testq %r14, %r14
je 0x13010
movq %r14, %rdi
callq 0x7cb8
pushq $0x18
popq %rsi
movq %r14, %rdi
callq 0x2180
pushq $0x20
popq %rsi
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x2180
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: duplicate_region(t_annot_region*)
t_annot_region* duplicate_region(t_annot_region* region_2_dup)
{
	t_annot_region* dup_region = new t_annot_region();

	if(region_2_dup->chrom != NULL)
	{
		dup_region->chrom = new char[strlen(region_2_dup->chrom) + 2];
		strcpy(dup_region->chrom, region_2_dup->chrom);
	}
	else
	{
		dup_region->chrom = NULL;
	}

	if(region_2_dup->name != NULL)
	{
		dup_region->name = new char[strlen(region_2_dup->name) + 2];
		strcpy(dup_region->name, region_2_dup->name);
	}
	else
	{
		dup_region->name = NULL;
	}

	dup_region->start = region_2_dup->start;
	dup_region->end = region_2_dup->end;
	dup_region->strand = region_2_dup->strand;
	dup_region->n_exons = dup_region->n_exons;
	dup_region->score = dup_region->score;
	dup_region->thick_start = dup_region->thick_start;
	dup_region->thick_end = dup_region->thick_end;

	dup_region->intervals = NULL;

	return(dup_region);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
pushq $0x50
popq %rdi
callq 0x2170
movq %rax, %r14
xorps %xmm0, %xmm0
movaps %xmm0, (%rax)
movaps %xmm0, 0x10(%rax)
movaps %xmm0, 0x20(%rax)
movaps %xmm0, 0x30(%rax)
movaps %xmm0, 0x40(%rax)
movq (%rbx), %r15
testq %r15, %r15
je 0x13507
movq %r15, %rdi
callq 0x20d0
leaq 0x2(%rax), %rdi
callq 0x2040
movq %rax, %r12
movq %rax, %rdi
movq %r15, %rsi
callq 0x2140
jmp 0x1350a
xorl %r12d, %r12d
movq %r12, (%r14)
movq 0x18(%rbx), %r15
testq %r15, %r15
je 0x13537
movq %r15, %rdi
callq 0x20d0
leaq 0x2(%rax), %rdi
callq 0x2040
movq %rax, %r12
movq %rax, %rdi
movq %r15, %rsi
callq 0x2140
jmp 0x1353a
xorl %r12d, %r12d
movq %r12, 0x18(%r14)
movl 0xc(%rbx), %eax
movl %eax, 0xc(%r14)
movl 0x20(%rbx), %eax
movl %eax, 0x20(%r14)
movb 0x8(%rbx), %al
movb %al, 0x8(%r14)
andq $0x0, 0x30(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_chr_ids(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
vector<char*>* get_chr_ids(vector<t_annot_region*>* annot_regions)
{
	//printf("/*Determining*/ the chromosome list from region list.\n");
	vector<char*>* chr_ids = new vector<char*>();

	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		bool is_new_id = true;

		// Check if the the current chromosome id is included in the list of chromosome ids already collected, otherwise add it.
		for(int i_chr = 0; 
			is_new_id && i_chr < (int)chr_ids->size(); 
			i_chr++)
		{
			if(strcmp(chr_ids->at(i_chr), annot_regions->at(i_reg)->chrom) == 0)
			{
				is_new_id = false;
			}
		} // i_chr loop

		if(is_new_id)
		{
			char* new_id = new char[strlen(annot_regions->at(i_reg)->chrom) + 2];
			strcpy(new_id, annot_regions->at(i_reg)->chrom);
			chr_ids->push_back(new_id); // Add the new id.
		}
	} // i_reg loop.

	//printf("Determined %d chromosomes from region list.\n", chr_ids->size());
	return(chr_ids);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r14
andq $0x0, 0x10(%rax)
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
xorl %r15d, %r15d
movq %rsp, %r12
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x13883
movb $0x1, %al
xorl %r13d, %r13d
testb $0x1, %al
je 0x1387b
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r13
jge 0x13831
movq %r14, %rdi
movq %r13, %rsi
callq 0x7342
movq (%rax), %rbp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rsi
movq %rbp, %rdi
callq 0x2230
testl %eax, %eax
setne %al
incq %r13
jmp 0x137e6
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rdi
callq 0x20d0
leaq 0x2(%rax), %rdi
callq 0x2040
movq %rax, %r13
movq %rax, (%rsp)
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rsi
movq %r13, %rdi
callq 0x2140
movq %r14, %rdi
movq %r12, %rsi
callq 0xecb8
incq %r15
jmp 0x137cb
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: check_line_skip(char*)
bool check_line_skip(char* cur_line)
{
	// Skip empty lines.
	if(strlen(cur_line) == 0)
	{
		return(true);
	}

	// Check comment.
	if(cur_line[0] == '#')
	{
		return(true);
	}
	
	// Check track info line.
	char* first_word = new char[strlen(cur_line) + 2];
	strcpy(first_word, cur_line);
	sscanf(cur_line, "%s", first_word);

	if(strcmp(first_word, "track") == 0)
	{
		delete [] first_word;
		return(true);
	}

	delete [] first_word;

	return(false);
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdi, %rbx
callq 0x20d0
movb $0x1, %bpl
testq %rax, %rax
je 0x13f03
cmpb $0x23, (%rbx)
je 0x13f03
addq $0x2, %rax
movq %rax, %rdi
callq 0x2040
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x2140
leaq 0x13665(%rip), %rsi     # 0x2753e
movq %rbx, %rdi
movq %r14, %rdx
xorl %eax, %eax
callq 0x2150
leaq 0x13eab(%rip), %rsi     # 0x27d98
movq %r14, %rdi
callq 0x2230
testl %eax, %eax
sete %bpl
movq %r14, %rdi
callq 0x2210
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: validate_region_coords(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
bool validate_region_coords(vector<t_annot_region*>* regions)
{
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		if(regions->at(i_reg)->start > regions->at(i_reg)->end)
		{
			fprintf(stderr, "%s:%d-%d is not valid.\n", regions->at(i_reg)->chrom, regions->at(i_reg)->start, regions->at(i_reg)->end);
			return(false);
		}
	} // i_reg loop.

	return(true);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %r14
pushq $-0x1
popq %rbx
movq 0x8(%r14), %rax
subq (%r14), %rax
incq %rbx
shrq $0x3, %rax
movslq %eax, %r13
cmpq %r13, %rbx
jge 0x14371
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7404
movq (%rax), %rax
cmpl 0x20(%rax), %ebp
jle 0x142e3
movq 0x20cbc(%rip), %rax     # 0x34fe0
movq (%rax), %r15
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %r12
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r8d
leaq 0x13b66(%rip), %rsi     # 0x27ec8
movq %r15, %rdi
movq %r12, %rdx
movl %ebp, %ecx
xorl %eax, %eax
callq 0x2240
cmpq %r13, %rbx
setge %al
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: dump_BED_w_p_values(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, char*)
void dump_BED_w_p_values(vector<t_annot_region*>* regions, char* op_fp)
{
	FILE* f_op = open_f(op_fp, "w");

	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		t_significance_info* sig_info = (t_significance_info*)(regions->at(i_reg)->significance_info);
		fprintf(f_op, "%s\t%d\t%d\t.\t%lf\t%c\n", regions->at(i_reg)->chrom, regions->at(i_reg)->start, regions->at(i_reg)->end, sig_info->log_p_val / log(10.0), regions->at(i_reg)->strand);
	} // i_reg loop.

	fclose(f_op);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rsi, %rax
movq %rdi, %rbx
leaq 0x106dd(%rip), %rsi     # 0x24aa8
movq %rax, %rdi
callq 0x2027c
movq %rax, 0x8(%rsp)
xorl %r15d, %r15d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x14486
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x40(%rax), %r14
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %r13
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r12d
movsd (%r14), %xmm0
divsd 0x1258c(%rip), %xmm0    # 0x269d0
movsd %xmm0, 0x10(%rsp)
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movsbl 0x8(%rax), %r9d
movq 0x8(%rsp), %rdi
leaq 0x136c3(%rip), %rsi     # 0x27b2c
movq %r13, %rdx
movl %ebp, %ecx
movl %r12d, %r8d
movsd 0x10(%rsp), %xmm0
movb $0x1, %al
callq 0x2240
incq %r15
jmp 0x143db
movq 0x8(%rsp), %rdi
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x2160
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: dump_BED_w_q_values(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, char*)
void dump_BED_w_q_values(vector<t_annot_region*>* regions, char* op_fp)
{
	FILE* f_op = open_f(op_fp, "w");

	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		t_significance_info* sig_info = (t_significance_info*)(regions->at(i_reg)->significance_info);
		fprintf(f_op, "%s\t%d\t%d\t.\t%lf\t%c\n", regions->at(i_reg)->chrom, regions->at(i_reg)->start, regions->at(i_reg)->end, sig_info->log_q_val, regions->at(i_reg)->strand);
	} // i_reg loop.

	fclose(f_op);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rsi, %rax
movq %rdi, %rbx
leaq 0x105ef(%rip), %rsi     # 0x24aa8
movq %rax, %rdi
callq 0x2027c
movq %rax, 0x8(%rsp)
xorl %r15d, %r15d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x1456d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x40(%rax), %r14
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %r13
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r12d
movsd 0x8(%r14), %xmm0
movsd %xmm0, 0x10(%rsp)
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movsbl 0x8(%rax), %r9d
movq 0x8(%rsp), %rdi
leaq 0x135dc(%rip), %rsi     # 0x27b2c
movq %r13, %rdx
movl %ebp, %ecx
movl %r12d, %r8d
movsd 0x10(%rsp), %xmm0
movb $0x1, %al
callq 0x2240
incq %r15
jmp 0x144c9
movq 0x8(%rsp), %rdi
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x2160
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: load_BED_w_p_values(char*)
vector<t_annot_region*>* load_BED_w_p_values(char* regions_bed_fp)
{
	// Load the BED file with scores.
	vector<t_annot_region*>* regions = new vector<t_annot_region*>();
	FILE* f_reg = open_f(regions_bed_fp, "r");
	while(1)
	{
		char* cur_line = getline(f_reg);
		if(cur_line == NULL)
		{
			break;
		}

		char chrom[1000];
		int start;
		int end;
		double log_p_val = 0;

		if(sscanf(cur_line, "%s %d %d %*s %lf", chrom, &start, &end, &log_p_val) != 4)
		{
			fprintf(stderr, "Could not parse %s", cur_line);
			exit(0);
		}

		t_significance_info* cur_reg_sig_info = new t_significance_info();
		cur_reg_sig_info->log_p_val = log_p_val;
		cur_reg_sig_info->log_q_val = 0.0;

		t_annot_region* cur_reg = get_empty_region();
		cur_reg->chrom = t_string::copy_me_str(chrom);
		cur_reg->start = start;
		cur_reg->end = end;
		cur_reg->strand = '+';
		cur_reg->significance_info = cur_reg_sig_info;

		regions->push_back(cur_reg);
	} // reg file reading loop.
	fclose(f_reg);

	return(regions);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x408, %rsp            # imm = 0x408
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %rbx
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
leaq 0x12752(%rip), %rsi     # 0x26d08
movq %r14, %rdi
callq 0x2027c
movq %rax, %r14
leaq 0x20(%rsp), %r12
pushq $0x10
popq %r13
leaq 0x8(%rsp), %rbp
movq %r14, %rdi
callq 0x2017f
testq %rax, %rax
je 0x14670
movq %rax, %r15
andq $0x0, 0x18(%rsp)
movq %rax, %rdi
leaq 0x1354c(%rip), %rsi     # 0x27b3f
movq %r12, %rdx
leaq 0x14(%rsp), %rcx
leaq 0x10(%rsp), %r8
leaq 0x18(%rsp), %r9
xorl %eax, %eax
callq 0x2150
cmpl $0x4, %eax
jne 0x1468d
movq %r13, %rdi
callq 0x2170
movq %rax, %r15
movsd 0x18(%rsp), %xmm0
movsd %xmm0, (%rax)
andq $0x0, 0x8(%rax)
callq 0x11e71
movq %rax, 0x8(%rsp)
movq %r12, %rdi
callq 0x21062
movq 0x8(%rsp), %rcx
movq %rax, (%rcx)
movl 0x14(%rsp), %eax
movq 0x8(%rsp), %rcx
movl %eax, 0xc(%rcx)
movl 0x10(%rsp), %eax
movl %eax, 0x20(%rcx)
movb $0x2b, 0x8(%rcx)
movq %r15, 0x40(%rcx)
movq %rbx, %rdi
movq %rbp, %rsi
callq 0x7448
jmp 0x145cf
movq %r14, %rdi
callq 0x2160
movq %rbx, %rax
addq $0x408, %rsp            # imm = 0x408
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2094c(%rip), %rax     # 0x34fe0
movq (%rax), %rdi
leaq 0x134b2(%rip), %rsi     # 0x27b50
movq %r15, %rdx
xorl %eax, %eax
callq 0x2240
xorl %edi, %edi
callq 0x21d0
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_benjamini_hochberg_corrected_p_values(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
void get_benjamini_hochberg_corrected_p_values(vector<t_annot_region*>* regions)
{
	sort(regions->begin(), regions->end(), sort_regions_per_increasing_p_value);

	// Do BH corrections.
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		double cur_region_rank = (double)i_reg + 1;

		t_significance_info* cur_reg_sig_info = regions->at(i_reg)->significance_info;
		cur_reg_sig_info->log_q_val = (cur_reg_sig_info->log_p_val + log((double)regions->size() / (double)cur_region_rank));
	} // i_reg loop.

	// Sort with respect to q-values.
	sort(regions->begin(), regions->end(), sort_regions_per_increasing_q_value);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdi, %rbx
movq (%rdi), %rdi
movq 0x8(%rbx), %rsi
leaq -0x343(%rip), %rdx      # 0x14386
callq 0x17bcf
xorl %esi, %esi
movq (%rbx), %rdi
movq 0x8(%rbx), %rax
movq %rax, %rcx
subq %rdi, %rcx
shrq $0x3, %rcx
movslq %ecx, %rcx
cmpq %rcx, %rsi
jge 0x1475b
leaq 0x1(%rsi), %r14
cvtsi2sd %r14d, %xmm0
movsd %xmm0, 0x8(%rsp)
movq %rbx, %rdi
callq 0x7404
movq (%rax), %rax
movq 0x40(%rax), %r15
movsd (%r15), %xmm0
movsd %xmm0, (%rsp)
movq 0x8(%rbx), %rax
subq (%rbx), %rax
sarq $0x3, %rax
movq %rax, %xmm1
punpckldq 0x131a7(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x131af(%rip), %xmm1    # 0x278e0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
divsd 0x8(%rsp), %xmm0
callq 0x2120
addsd (%rsp), %xmm0
movsd %xmm0, 0x8(%r15)
movq %r14, %rsi
jmp 0x146d0
leaq -0x3c8(%rip), %rdx      # 0x1439a
movq %rax, %rsi
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
jmp 0x17bcf
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_all_intervals_per_composite_intervals(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
vector<t_annot_region*>* get_all_intervals_per_composite_intervals(vector<t_annot_region*>* composite_intervals)
{
	vector<t_annot_region*>* all_intervals = new vector<t_annot_region*>();
	for(int i_reg = 0; i_reg < (int)composite_intervals->size(); i_reg++)
	{
		vector<t_annot_region*>* cur_intervals = composite_intervals->at(i_reg)->intervals;

		for(int i_int = 0; i_int < (int)cur_intervals->size(); i_int++)
		{
			all_intervals->push_back(cur_intervals->at(i_int));
		} // i_int loop.
	} // i_reg loop.

	return(all_intervals);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %rbx
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r14
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r15d, %r15d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x14b5f
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x30(%rax), %r12
xorl %r13d, %r13d
movq 0x8(%r12), %rax
subq (%r12), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r13
jge 0x14b5a
movq %r12, %rdi
movq %r13, %rsi
callq 0x7404
movq %r14, %rdi
movq %rax, %rsi
callq 0x7448
incq %r13
jmp 0x14b2b
incq %r15
jmp 0x14b04
movq %r14, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: coverage(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
double coverage(vector<t_annot_region*>* annot_regions)
{
	double covrg = 0.0;

	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		if(annot_regions->at(i_reg) != NULL)
		{
			if(annot_regions->at(i_reg)->end < annot_regions->at(i_reg)->start)
			{
				//printf("Region %d has its start index larger than its end index: %d, %d\n", i_reg, 
				//	annot_regions->at(i_reg)->start,
				//	annot_regions->at(i_reg)->end);
			}
			else
			{
				covrg += annot_regions->at(i_reg)->end - annot_regions->at(i_reg)->start + 1;
			}
		}
	} // i_reg loop.

	return(covrg);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
xorpd %xmm0, %xmm0
movsd %xmm0, (%rsp)
xorl %r14d, %r14d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r14
jge 0x1505b
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
cmpq $0x0, (%rax)
je 0x15053
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %ebp
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpl 0xc(%rax), %ebp
jl 0x15053
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r15d
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %eax
negl %eax
addl %r15d, %eax
incl %eax
cvtsi2sd %eax, %xmm0
movsd (%rsp), %xmm1
addsd %xmm0, %xmm1
movsd %xmm1, (%rsp)
incq %r14
jmp 0x14fd0
movsd (%rsp), %xmm0
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: nuc_overlap(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
double nuc_overlap(vector<t_annot_region*>* annot_regions1, 
					vector<t_annot_region*>* annot_regions2)
{
	// Compute the coverage of overlap divided by the coverage of all regions.
	vector<t_annot_region*>* overlapping_regions = intersect_annot_regions(annot_regions1, annot_regions2, false);

	int overlap_cvg = (int)(coverage(overlapping_regions));
	int total_cvg = (int)(coverage(annot_regions1) + coverage(annot_regions2));

	if(total_cvg == 0)
	{
		return 0.0;
	}

	return((double)(2 * overlap_cvg) / total_cvg);
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x18, %rsp
movq %rsi, %rbx
movq %rdi, %r14
xorl %edx, %edx
callq 0x150d3
movq %rax, %rdi
callq 0x14fba
movsd %xmm0, 0x8(%rsp)
movq %r14, %rdi
callq 0x14fba
movsd %xmm0, 0x10(%rsp)
movq %rbx, %rdi
callq 0x14fba
addsd 0x10(%rsp), %xmm0
cvttsd2si %xmm0, %eax
testl %eax, %eax
je 0x150c7
cvttsd2si 0x8(%rsp), %ecx
addl %ecx, %ecx
cvtsi2sd %ecx, %xmm0
cvtsi2sd %eax, %xmm1
divsd %xmm1, %xmm0
jmp 0x150cb
xorpd %xmm0, %xmm0
addq $0x18, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: inter_region_distances(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
vector<int>* inter_region_distances(vector<t_annot_region*>* annot_regions)
{
	vector<char*>* chr_ids = get_chr_ids(annot_regions);

	vector<int>* inter_reg_dists = new vector<int>();

	for(int i_chr = 0; i_chr < (int)chr_ids->size(); i_chr++)
	{
		vector<t_annot_region*>* cur_chr_regs = get_regions_per_chromosome(annot_regions,
																			chr_ids->at(i_chr));

		// Dump the distances between consecutive regions.
		for(int i_reg = 0; (i_reg + 1) < (int)cur_chr_regs->size(); i_reg++)
		{
			signed int cur_dist = cur_chr_regs->at(i_reg+1)->start - cur_chr_regs->at(i_reg)->end;
		
			if(cur_dist < 0)
			{
				printf("Negative distance: <%d-%d> and <%d-%d>\n", 
					cur_chr_regs->at(i_reg)->start,
					cur_chr_regs->at(i_reg)->end,
					cur_chr_regs->at(i_reg+1)->start,
					cur_chr_regs->at(i_reg+1)->end);
			}

			inter_reg_dists->push_back(cur_dist);
		} // i_reg loop.

		cur_chr_regs->clear();
		delete(cur_chr_regs);
	} // i_chr loop.

	return(inter_reg_dists);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, 0x10(%rsp)
callq 0x137a1
movq %rax, %rbx
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r12
xorps %xmm0, %xmm0
andq $0x0, 0x10(%rax)
movups %xmm0, (%rax)
leaq 0x4(%rsp), %r13
xorl %esi, %esi
movq %rbx, 0x8(%rsp)
movq %rax, 0x20(%rsp)
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %rsi
jge 0x15b1f
movq %rbx, %rdi
movq %rsi, 0x18(%rsp)
callq 0x7342
movq (%rax), %rsi
movq 0x10(%rsp), %rdi
callq 0x15b31
movq %rax, %rbx
xorl %r15d, %r15d
leaq 0x1(%r15), %r14
movq (%rbx), %rax
movq 0x8(%rbx), %rcx
movq %rcx, %rdx
subq %rax, %rdx
shrq $0x3, %rdx
movslq %edx, %rdx
cmpq %rdx, %r14
jge 0x15af1
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
subl 0x20(%rax), %ebp
movl %ebp, 0x4(%rsp)
jns 0x15ade
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movq %r13, %r12
movl 0xc(%rax), %r13d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r15d
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0xc(%rax), %ebp
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %r8d
leaq 0x122a9(%rip), %rdi     # 0x27d70
movl %r13d, %esi
movq %r12, %r13
movq 0x20(%rsp), %r12
movl %r15d, %edx
movl %ebp, %ecx
xorl %eax, %eax
callq 0x2050
movq %r12, %rdi
movq %r13, %rsi
callq 0x73a8
movq %r14, %r15
jmp 0x15a2d
cmpq %rax, %rcx
je 0x15afa
movq %rax, 0x8(%rbx)
movq %rbx, %rdi
callq 0x832c
movq %rbx, %rdi
pushq $0x18
popq %rsi
callq 0x2180
movq 0x18(%rsp), %rsi
incq %rsi
movq 0x8(%rsp), %rbx
jmp 0x159f7
movq %r12, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_regions_per_chromosome(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, char*)
vector<t_annot_region*>* get_regions_per_chromosome(vector<t_annot_region*>* annot_regions,
													char* chr_id)
{
	vector<t_annot_region*>* chr_regions = new vector<t_annot_region*>();

	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		//bool new_id = false;

		// Check if the the current chromosome id is included in the list of chromosome ids already collected, otherwise add it.
		if(strcmp(annot_regions->at(i_reg)->chrom, chr_id) == 0)
		{
			// Add the current region to the chromosome regions.
			chr_regions->push_back(annot_regions->at(i_reg));
		}
	} // i_reg loop.

	return(chr_regions);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r15
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r12d, %r12d
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x15ba2
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rdi
movq %rbx, %rsi
callq 0x2230
testl %eax, %eax
jne 0x15b9d
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r12
jmp 0x15b58
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: exclude_annot_regions(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, bool)
vector<t_annot_region*>* exclude_annot_regions(vector<t_annot_region*>* annot_regions1,
													vector<t_annot_region*>* annot_regions2, 
													bool strand_specific)
{
	if(strand_specific)
	{
		vector<t_annot_region*>* excluded_regions = new vector<t_annot_region*>();

		vector<t_annot_region*>* reg1_pos_regs = get_regions_per_strand(annot_regions1, '+');
		vector<t_annot_region*>* reg1_neg_regs = get_regions_per_strand(annot_regions1, '-');

		vector<t_annot_region*>* reg2_pos_regs = get_regions_per_strand(annot_regions2, '+');
		vector<t_annot_region*>* reg2_neg_regs = get_regions_per_strand(annot_regions2, '-');

		// Do strand specific exclusion.
		vector<t_annot_region*>* reg1_min_reg2_pos = exclude_annot_regions(reg1_pos_regs, reg2_pos_regs);
		vector<t_annot_region*>* reg1_min_reg2_neg = exclude_annot_regions(reg1_neg_regs, reg2_neg_regs);

		// Add the excluded regions.
		excluded_regions->insert(excluded_regions->end(), reg1_min_reg2_pos->begin(), reg1_min_reg2_pos->end());
		excluded_regions->insert(excluded_regions->end(), reg1_min_reg2_neg->begin(), reg1_min_reg2_neg->end());

		return(excluded_regions);
	}
	else
	{
		vector<t_annot_region*>* excluded_regions = exclude_annot_regions(annot_regions1, annot_regions2);
		return(excluded_regions);
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %r15
testl %edx, %edx
je 0x160ef
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %rbx
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
pushq $0x2b
popq %rbp
movq %r15, %rdi
movl %ebp, %esi
callq 0x16108
movq %rax, %r12
pushq $0x2d
popq %r13
movq %r15, %rdi
movl %r13d, %esi
callq 0x16108
movq %rax, %r15
movq %r14, %rdi
movl %ebp, %esi
callq 0x16108
movq %rax, %rbp
movq %r14, %rdi
movl %r13d, %esi
callq 0x16108
movq %rax, %r14
movq %r12, %rdi
movq %rbp, %rsi
callq 0x1617d
movq %rax, %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0x1617d
movq %rax, %r14
movq (%r12), %rdx
movq 0x8(%r12), %rcx
movq %rbx, %rdi
xorl %esi, %esi
callq 0x73e4
movq 0x8(%rbx), %rsi
movq (%r14), %rdx
movq 0x8(%r14), %rcx
movq %rbx, %rdi
callq 0x73e4
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %r15, %rdi
movq %r14, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x1617d
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_regions_per_strand(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, char)
vector<t_annot_region*>* get_regions_per_strand(vector<t_annot_region*>* annot_regions,
													char strand)
{
	vector<t_annot_region*>* chr_regions = new vector<t_annot_region*>();

	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		//bool new_id = false;

		// Check if the the current chromosome id is included in the list of chromosome ids already collected, otherwise add it.
		if(annot_regions->at(i_reg)->strand == strand)
		{
			// Add the current region to the chromosome regions.
			chr_regions->push_back(annot_regions->at(i_reg));
		}
	} // i_reg loop.

	return(chr_regions);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movl %esi, %ebx
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r15
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r12d, %r12d
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x1616e
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpb %bl, 0x8(%rax)
jne 0x16169
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r12
jmp 0x1612e
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: delete_annot_regions(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
void delete_annot_regions(vector<t_annot_region*>* region_list)
{
	for(int i_reg = 0; i_reg < (int)region_list->size(); i_reg++)
	{
		if(region_list->at(i_reg) != NULL)
		{
			delete [] region_list->at(i_reg)->chrom;

			if(region_list->at(i_reg)->name != NULL)
			{
				delete [] region_list->at(i_reg)->name;
			}

			delete(region_list->at(i_reg));
		}
	} // i_reg loop.

	region_list->clear();
	delete(region_list);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
xorl %r14d, %r14d
pushq $0x50
popq %r15
movq (%rbx), %rax
movq 0x8(%rbx), %rcx
movq %rcx, %rdx
subq %rax, %rdx
shrq $0x3, %rdx
movslq %edx, %rdx
cmpq %rdx, %r14
jge 0x1664b
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
cmpq $0x0, (%rax)
je 0x16643
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rdi
testq %rdi, %rdi
je 0x165fc
callq 0x2210
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpq $0x0, 0x18(%rax)
je 0x1662d
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x18(%rax), %rdi
testq %rdi, %rdi
je 0x1662d
callq 0x2210
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rdi
movq %r15, %rsi
callq 0x2180
incq %r14
jmp 0x165b7
cmpq %rax, %rcx
je 0x16654
movq %rax, 0x8(%rbx)
movq %rbx, %rdi
callq 0x832c
pushq $0x18
popq %rsi
movq %rbx, %rdi
popq %rbx
popq %r14
popq %r15
jmp 0x2180
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: delete_intersect_info(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
void delete_intersect_info(vector<t_annot_region*>* regions)
{
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		if(regions->at(i_reg)->data != NULL)
		{
			t_intersect_info* intersect_info = (t_intersect_info*)(regions->at(i_reg)->data);
			delete intersect_info;
		}
	} // i_reg loop.
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
xorl %r14d, %r14d
pushq $0x18
popq %r15
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r14
jge 0x167f9
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpq $0x0, 0x48(%rax)
je 0x167f4
movq %rbx, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movq 0x48(%rax), %rdi
movq %r15, %rsi
callq 0x2180
incq %r14
jmp 0x167b3
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_regions_per_end_max(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, int)
vector<t_annot_region*>* get_regions_per_end_max(vector<t_annot_region*>* annot_regions, int end_max)
{
	vector<t_annot_region*>* end_max_regs = new vector<t_annot_region*>();
	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		if(annot_regions->at(i_reg)->end < end_max)
		{
			end_max_regs->push_back(annot_regions->at(i_reg));
		}
	} // i_reg loop.

	return(end_max_regs);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movl %esi, %ebx
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r15
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r12d, %r12d
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x16865
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
cmpl %ebx, 0x20(%rax)
jge 0x16860
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r12
jmp 0x16825
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_regions_per_min_run(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, int)
vector<t_annot_region*>* get_regions_per_min_run(vector<t_annot_region*>* annot_regions, int l_min_run)
{
	vector<t_annot_region*>* min_run_regs = new vector<t_annot_region*>();
	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		if(annot_regions->at(i_reg)->end - annot_regions->at(i_reg)->start > l_min_run)
		{
			min_run_regs->push_back(annot_regions->at(i_reg));
		}
	} // i_reg loop.

	return(min_run_regs);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %esi, %ebx
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r15
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r12d, %r12d
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x168ed
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %ebp
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
subl 0xc(%rax), %ebp
cmpl %ebx, %ebp
jle 0x168e8
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r12
jmp 0x1689a
movq %r15, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: get_regions_per_max_run(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*, int)
vector<t_annot_region*>* get_regions_per_max_run(vector<t_annot_region*>* annot_regions, int l_max_run)
{
	vector<t_annot_region*>* min_run_regs = new vector<t_annot_region*>();
	for(int i_reg = 0; i_reg < (int)annot_regions->size(); i_reg++)
	{
		if(annot_regions->at(i_reg)->end - annot_regions->at(i_reg)->start < l_max_run)
		{
			min_run_regs->push_back(annot_regions->at(i_reg));
		}
	} // i_reg loop.

	return(min_run_regs);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %esi, %ebx
movq %rdi, %r14
pushq $0x18
popq %rdi
callq 0x2170
movq %rax, %r15
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
xorl %r12d, %r12d
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r12
jge 0x16972
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
movl 0x20(%rax), %ebp
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq (%rax), %rax
subl 0xc(%rax), %ebp
cmpl %ebx, %ebp
jge 0x1696d
movq %r14, %rdi
movq %r12, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r12
jmp 0x1691f
movq %r15, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq