// File: /workspace/github_cpp_makefile_star2_O2/gersteinlab[P]MUSIC/src/ms_annot_region_tools.cpp
// Function: restructure_annot_regions(std::vector<t_annot_region*, std::allocator<t_annot_region*>>*)
t_sorted_annot_region_lists* restructure_annot_regions(vector<t_annot_region*>* regions)
{
	// This is the list of regions per chromosome.
	vector<char*>* chr_ids = get_chr_ids(regions);
	t_sorted_annot_region_lists* region_lists = new t_sorted_annot_region_lists();

	// The chromosome id list is built up dynamically in the region list loop.
	//region_lists->chr_ids = new vector<char*>();
	region_lists->chr_ids = chr_ids;
	region_lists->neg_strand_regions_per_chrom = new vector<t_annot_region*>*[(int)chr_ids->size() + 2];
	region_lists->pos_strand_regions_per_chrom = new vector<t_annot_region*>*[(int)chr_ids->size() + 2];
	region_lists->regions_per_chrom = new vector<t_annot_region*>*[(int)chr_ids->size() + 2];

	for(int i_chr = 0; i_chr < (int)chr_ids->size(); i_chr++)
	{
		region_lists->pos_strand_regions_per_chrom[i_chr] = new vector<t_annot_region*>();
		region_lists->neg_strand_regions_per_chrom[i_chr] = new vector<t_annot_region*>();
		region_lists->regions_per_chrom[i_chr] = new vector<t_annot_region*>();
	} // i_chr loop.

	// Go over all the regions and separate them into appropriate list.
	for(int i_reg = 0; i_reg < (int)regions->size(); i_reg++)
	{
		int i_chr = t_string::get_i_str(chr_ids, regions->at(i_reg)->chrom);

		if(i_chr < (int)chr_ids->size())
		{
			region_lists->regions_per_chrom[i_chr]->push_back(regions->at(i_reg));

			if(regions->at(i_reg)->strand == '+')
			{
				region_lists->pos_strand_regions_per_chrom[i_chr]->push_back(regions->at(i_reg));
			}
			else if(regions->at(i_reg)->strand == '-')
			{
				region_lists->neg_strand_regions_per_chrom[i_chr]->push_back(regions->at(i_reg));
			}
			else
			{
				printf("Unknown strand char %c @ %s(%d).\n", regions->at(i_reg)->strand, __FILE__, __LINE__);
				exit(0);
			}
		}
	} // i_reg loop.

	// Sort the regions per chromosome and all the regions.
	for(int i_chr = 0; i_chr < (int)chr_ids->size(); i_chr++)
	{
		sort(region_lists->pos_strand_regions_per_chrom[i_chr]->begin(), region_lists->pos_strand_regions_per_chrom[i_chr]->end(), sort_regions);
		sort(region_lists->neg_strand_regions_per_chrom[i_chr]->begin(), region_lists->neg_strand_regions_per_chrom[i_chr]->end(), sort_regions);
		sort(region_lists->regions_per_chrom[i_chr]->begin(), region_lists->regions_per_chrom[i_chr]->end(), sort_regions);
	} // i_chr loop.

	// Finally sort the regions.
	return(region_lists);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdi, %rbp
callq 0x137a1
movq %rax, %rbx
pushq $0x20
popq %rdi
callq 0x2170
movq %rax, %r12
movq %rbx, 0x18(%rax)
movq 0x8(%rbx), %r15
subq (%rbx), %r15
movq %r15, %rax
shlq $0x1d, %rax
movabsq $0x200000000, %rcx      # imm = 0x200000000
addq %rax, %rcx
movq %rcx, %rax
sarq $0x1d, %rax
testq %rcx, %rcx
pushq $-0x1
popq %r14
cmovnsq %rax, %r14
movq %r14, %rdi
callq 0x2040
movq %rax, (%rsp)
movq %rax, 0x10(%r12)
movq %r14, %rdi
callq 0x2040
movq %rax, 0x8(%rsp)
movq %rax, 0x8(%r12)
movq %r14, %rdi
callq 0x2040
movq %rax, %r13
movq %r12, 0x10(%rsp)
movq %rax, (%r12)
shrq $0x3, %r15
movslq %r15d, %r15
xorl %r12d, %r12d
pushq $0x18
popq %r14
cmpq %r15, %r12
jge 0x12c8c
movq %r14, %rdi
callq 0x2170
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
movq 0x8(%rsp), %rcx
movq %rax, (%rcx,%r12,8)
movq %r14, %rdi
callq 0x2170
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
andq $0x0, 0x10(%rax)
movq (%rsp), %rcx
movq %rax, (%rcx,%r12,8)
movq %r14, %rdi
callq 0x2170
andq $0x0, 0x10(%rax)
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
movq %rax, (%r13,%r12,8)
incq %r12
jmp 0x12c33
xorl %r14d, %r14d
movq 0x8(%rbp), %rax
subq (%rbp), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r14
jge 0x12d43
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x21152
movq 0x8(%rbx), %rcx
subq (%rbx), %rcx
shrq $0x3, %rcx
cmpl %ecx, %eax
jge 0x12d3b
movslq %eax, %r12
movq (%r13,%r12,8), %r15
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpb $0x2b, 0x8(%rax)
movq 0x8(%rsp), %rax
je 0x12d21
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
cmpb $0x2d, 0x8(%rax)
movq (%rsp), %rax
jne 0x12dbb
movq (%rax,%r12,8), %r15
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq %r15, %rdi
movq %rax, %rsi
callq 0x7448
incq %r14
jmp 0x12c8f
xorl %r15d, %r15d
leaq 0x74a(%rip), %r14       # 0x13497
movq 0x8(%rbx), %rax
subq (%rbx), %rax
shrq $0x3, %rax
cltq
cmpq %rax, %r15
jge 0x12da7
movq 0x8(%rsp), %rax
movq (%rax,%r15,8), %rax
movq (%rax), %rdi
movq 0x8(%rax), %rsi
movq %r14, %rdx
callq 0x17bcf
movq (%rsp), %rax
movq (%rax,%r15,8), %rax
movq (%rax), %rdi
movq 0x8(%rax), %rsi
movq %r14, %rdx
callq 0x17bcf
movq (%r13,%r15,8), %rax
movq (%rax), %rdi
movq 0x8(%rax), %rsi
movq %r14, %rdx
callq 0x17bcf
incq %r15
jmp 0x12d4d
movq 0x10(%rsp), %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rbp, %rdi
movq %r14, %rsi
callq 0x7404
movq (%rax), %rax
movsbl 0x8(%rax), %esi
leaq 0x14bed(%rip), %rdi     # 0x279c1
leaq 0x14c08(%rip), %rdx     # 0x279e3
movl $0x241, %ecx            # imm = 0x241
xorl %eax, %eax
callq 0x2050
xorl %edi, %edi
callq 0x21d0