// File: /workspace/github_cpp_makefile_star2_O1/auton1[P]viterbi/parameters.cpp
// Function: parameters::parameters(int, char**)
parameters::parameters(int argc, char *argv[])
{
	if (isatty(STDERR_FILENO))
		stream_err = false;
	else
		stream_err = true;

	string tmp;
	for (int i=0; i<argc; i++)
	{
		tmp = argv[i];
		this->argv.push_back(tmp);
	}

	BED_exclude = false;
	BED_file = "";
	contigs_file = "";
	end_pos = numeric_limits<int>::max();
	exclude_positions_file = "";
	exclude_positions_overlap_file = "";
	indv_exclude_file = "";
	indv_keep_file = "";
	invert_mask = false;
	keep_only_indels = false;
	min_mac = -1;
	min_maf = -1.0;
	mask_file = "";
	max_alleles = numeric_limits<int>::max();
	max_genotype_depth = numeric_limits<int>::max();
	max_mac = numeric_limits<int>::max();
	max_maf = numeric_limits<double>::max();
	max_mean_depth = numeric_limits<double>::max();
	max_missing_call_count = numeric_limits<int>::max();
	max_non_ref_ac = numeric_limits<int>::max();
	max_non_ref_af = numeric_limits<double>::max();
	max_N_indv = -1;
	min_alleles = -1;
	min_genotype_depth = -1;
	min_genotype_quality = -1.0;
	min_HWE_pvalue = -1.0;
	min_interSNP_distance = -1;
	min_kept_mask_value = 0;
	min_mean_depth = -1.0;
	min_quality = -1.0;
	min_r2 = -1.0;
	min_site_call_rate = 0;
	min_non_ref_ac = -1;
	min_non_ref_af = -1.0;
	num_outputs = 0;
	output_prefix = "out";
	phased_only = false;
	positions_file = "";
	positions_overlap_file = "";
	remove_all_filtered_genotypes = false;
	remove_all_filtered_sites = false;
	remove_indels = false;
	snps_to_exclude_file = "";
	snps_to_keep_file = "";
	start_pos = -1;
	stream_in = false;
	stream_out = false;
	temp_dir = "/tmp/";

	Ne = 10000;
	recomb_rate = 1.0;	// cM/Mb
	map_filename = "";
	p_error = 0.0;
	max_threads = 64;

	time_t start;
	time(&start);
	seed = start;
	generator.seed(seed);

	run_viterbi = true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x118, %rsp            # imm = 0x118
movq %rdx, 0xe8(%rsp)
movl %esi, %r15d
movq %rdi, %rbx
leaq 0x18(%rdi), %rax
movq %rax, 0xd8(%rsp)
movq %rax, 0x8(%rdi)
xorl %r12d, %r12d
movq %r12, 0x10(%rdi)
movb %r12b, 0x18(%rdi)
leaq 0x30(%rdi), %rax
movl %r12d, 0x30(%rdi)
movq %r12, 0x38(%rdi)
movq %rax, 0x40(%rdi)
movq %rax, 0x48(%rdi)
movq %r12, 0x50(%rdi)
leaq 0x60(%rdi), %rax
movl %r12d, 0x60(%rdi)
movq %r12, 0x68(%rdi)
movq %rax, 0x70(%rdi)
movq %rax, 0x78(%rdi)
movq %r12, 0x80(%rdi)
leaq 0x98(%rdi), %rax
movq %rax, 0xd0(%rsp)
movq %rax, 0x88(%rdi)
movq %r12, 0x90(%rdi)
movb %r12b, 0x98(%rdi)
leaq 0xc0(%rdi), %rax
movq %rax, 0xc8(%rsp)
movq %rax, 0xb0(%rdi)
movq %r12, 0xb8(%rdi)
movb %r12b, 0xc0(%rdi)
leaq 0xe0(%rdi), %rax
movq %rax, 0xc0(%rsp)
movq %rax, 0xd0(%rdi)
movq %r12, 0xd8(%rdi)
movb %r12b, 0xe0(%rdi)
leaq 0xf8(%rdi), %rax
movl %r12d, 0xf8(%rdi)
movq %r12, 0x100(%rdi)
movq %rax, 0x108(%rdi)
movq %rax, 0x110(%rdi)
movq %r12, 0x118(%rdi)
leaq 0x130(%rdi), %rax
movq %rax, 0xb8(%rsp)
movq %rax, 0x120(%rdi)
movq %r12, 0x128(%rdi)
movb %r12b, 0x130(%rdi)
leaq 0x150(%rdi), %rax
movq %rax, 0xb0(%rsp)
movq %rax, 0x140(%rdi)
movq %r12, 0x148(%rdi)
movb %r12b, 0x150(%rdi)
leaq 0x168(%rdi), %rax
movl %r12d, 0x168(%rdi)
movq %r12, 0x170(%rdi)
movq %rax, 0x178(%rdi)
movq %rax, 0x180(%rdi)
movq %r12, 0x188(%rdi)
leaq 0x198(%rdi), %rax
movl %r12d, 0x198(%rdi)
movq %r12, 0x1a0(%rdi)
movq %rax, 0x1a8(%rdi)
movq %rax, 0x1b0(%rdi)
leaq 0x1f8(%rdi), %rax
xorps %xmm0, %xmm0
movups %xmm0, 0x1c8(%rdi)
movups %xmm0, 0x1b8(%rdi)
movq %rax, 0xa8(%rsp)
movq %rax, 0x1e8(%rdi)
movq %r12, 0x1f0(%rdi)
movb %r12b, 0x1f8(%rdi)
leaq 0x2a0(%rdi), %rax
movq %rax, 0xa0(%rsp)
movq %rax, 0x290(%rdi)
movq %r12, 0x298(%rdi)
movb %r12b, 0x2a0(%rdi)
leaq 0x2c8(%rdi), %rax
movq %rax, 0x98(%rsp)
movq %rax, 0x2b8(%rdi)
movq %r12, 0x2c0(%rdi)
movb %r12b, 0x2c8(%rdi)
leaq 0x2e8(%rdi), %rax
movq %rax, 0x90(%rsp)
movq %rax, 0x2d8(%rdi)
movq %r12, 0x2e0(%rdi)
movb %r12b, 0x2e8(%rdi)
leaq 0x308(%rdi), %rax
movl %r12d, 0x308(%rdi)
movq %r12, 0x310(%rdi)
movq %rax, 0x318(%rdi)
movq %rax, 0x320(%rdi)
movq %r12, 0x328(%rdi)
leaq 0x338(%rdi), %rax
movl %r12d, 0x338(%rdi)
movq %r12, 0x340(%rdi)
movq %rax, 0x348(%rdi)
movq %rax, 0x350(%rdi)
movq %r12, 0x358(%rdi)
leaq 0x368(%rdi), %rax
movl %r12d, 0x368(%rdi)
movq %r12, 0x370(%rdi)
movq %rax, 0x378(%rdi)
movq %rax, 0x380(%rdi)
movq %r12, 0x388(%rdi)
leaq 0x398(%rdi), %rax
movl %r12d, 0x398(%rdi)
movq %r12, 0x3a0(%rdi)
movq %rax, 0x3a8(%rdi)
movq %rax, 0x3b0(%rdi)
movq %r12, 0x3b8(%rdi)
leaq 0x3d0(%rdi), %rax
movq %rax, 0x88(%rsp)
movq %rax, 0x3c0(%rdi)
movq %r12, 0x3c8(%rdi)
movb %r12b, 0x3d0(%rdi)
leaq 0x3f0(%rdi), %rax
movq %rax, 0x80(%rsp)
movq %rax, 0x3e0(%rdi)
movq %r12, 0x3e8(%rdi)
movb %r12b, 0x3f0(%rdi)
movl %r12d, 0x408(%rdi)
movq %r12, 0x410(%rdi)
leaq 0x408(%rdi), %rax
movq %rax, 0x418(%rdi)
movq %rax, 0x420(%rdi)
movq %r12, 0x428(%rdi)
leaq 0x448(%rdi), %rax
movq %rax, 0x78(%rsp)
movq %rax, 0x438(%rdi)
movq %r12, 0x440(%rdi)
movb %r12b, 0x448(%rdi)
movq %r12, 0x480(%rdi)
movl %r12d, 0x488(%rdi)
movq %r12, 0x4a8(%rdi)
movl %r12d, 0x4b0(%rdi)
movq %r12, 0x4b8(%rdi)
movl %r12d, 0x4c8(%rdi)
movq %r12, 0x4d0(%rdi)
movl %r12d, 0x478(%rdi)
movups %xmm0, 0x468(%rdi)
movups %xmm0, 0x458(%rdi)
movups %xmm0, 0x490(%rdi)
movl %r12d, 0x4a0(%rdi)
leaq 0x4c8(%rdi), %rax
movq %rax, 0x4d8(%rdi)
movq %rax, 0x4e0(%rdi)
movq %r12, 0x4e8(%rdi)
leaq 0x508(%rdi), %rax
movq %rax, 0xe0(%rsp)
movq %rax, 0x4f8(%rdi)
movq %r12, 0x500(%rdi)
movb %r12b, 0x508(%rdi)
movq $0x1, 0x530(%rdi)
movups %xmm0, 0x538(%rdi)
movq %r12, 0x548(%rdi)
leaq 0x8(%rdi), %rax
movq %rax, 0x60(%rsp)
leaq 0x88(%rdi), %rax
movq %rax, 0x58(%rsp)
leaq 0xb0(%rdi), %rax
movq %rax, 0x50(%rsp)
leaq 0xd0(%rdi), %rax
movq %rax, 0x48(%rsp)
leaq 0x120(%rdi), %rax
movq %rax, 0x40(%rsp)
leaq 0x140(%rdi), %rax
movq %rax, 0x38(%rsp)
leaq 0x1e8(%rdi), %rax
movq %rax, 0x30(%rsp)
leaq 0x290(%rdi), %rax
movq %rax, 0x28(%rsp)
leaq 0x2b8(%rdi), %rax
movq %rax, 0x20(%rsp)
leaq 0x2d8(%rdi), %rax
movq %rax, 0x18(%rsp)
leaq 0x3c0(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x3e0(%rdi), %rax
movq %rax, 0x8(%rsp)
leaq 0x438(%rdi), %rax
movq %rax, (%rsp)
leaq 0x4f8(%rdi), %rax
movq %rax, 0x68(%rsp)
leaq 0x538(%rdi), %rax
movq %rax, 0x70(%rsp)
movl $0x2, %edi
callq 0x57c0
testl %eax, %eax
sete 0x434(%rbx)
leaq 0x100(%rsp), %rax
movq %rax, -0x10(%rax)
movq %r12, -0x8(%rax)
movb %r12b, (%rax)
testl %r15d, %r15d
jle 0x2faca
movl %r15d, %ebp
xorl %r14d, %r14d
leaq 0xf0(%rsp), %r15
movq 0xe8(%rsp), %rax
movq (%rax,%r14,8), %r12
movq 0xf8(%rsp), %r13
movq %r12, %rdi
callq 0x5180
movq %r15, %rdi
xorl %esi, %esi
movq %r13, %rdx
movq %r12, %rcx
movq %rax, %r8
callq 0x5690
movq 0x70(%rsp), %rdi
movq %r15, %rsi
callq 0x13080
incq %r14
cmpq %r14, %rbp
jne 0x2fa86
movb $0x0, 0x1(%rbx)
movq 0x10(%rbx), %rdx
leaq 0xb426(%rip), %rcx      # 0x3aeff
movq 0x60(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0x90(%rbx), %rdx
leaq 0xb409(%rip), %rcx      # 0x3aeff
movq 0x58(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movl $0x7fffffff, 0xa8(%rbx) # imm = 0x7FFFFFFF
movq 0xb8(%rbx), %rdx
leaq 0xb3e2(%rip), %rcx      # 0x3aeff
movq 0x50(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0xd8(%rbx), %rdx
leaq 0xb3c5(%rip), %rcx      # 0x3aeff
movq 0x48(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0x128(%rbx), %rdx
leaq 0xb3a8(%rip), %rcx      # 0x3aeff
movq 0x40(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0x148(%rbx), %rdx
leaq 0xb38b(%rip), %rcx      # 0x3aeff
movq 0x38(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movw $0x0, 0x1d8(%rbx)
movl $0xffffffff, 0x1dc(%rbx) # imm = 0xFFFFFFFF
movabsq $-0x4010000000000000, %r14 # imm = 0xBFF0000000000000
movq %r14, 0x1e0(%rbx)
movq 0x1f0(%rbx), %rdx
leaq 0xb34a(%rip), %rcx      # 0x3aeff
movq 0x30(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movabsq $0x7fffffff7fffffff, %rax # imm = 0x7FFFFFFF7FFFFFFF
movq %rax, 0x208(%rbx)
movl $0x7fffffff, 0x210(%rbx) # imm = 0x7FFFFFFF
movaps 0xb55a(%rip), %xmm0     # 0x3b140
movups %xmm0, 0x218(%rbx)
movq %rax, 0x228(%rbx)
movabsq $0x7fefffffffffffff, %rax # imm = 0x7FEFFFFFFFFFFFFF
movq %rax, 0x230(%rbx)
movq $-0x1, 0x238(%rbx)
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movl %eax, 0x240(%rbx)
movaps 0xb52e(%rip), %xmm0     # 0x3b150
movups %xmm0, 0x248(%rbx)
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
movq %rcx, 0x258(%rbx)
movq %r14, 0x260(%rbx)
movsd 0xa41c(%rip), %xmm1     # 0x3a060
movups %xmm1, 0x280(%rbx)
movl %eax, 0x268(%rbx)
movups %xmm0, 0x270(%rbx)
movl $0x0, 0x2b0(%rbx)
movq 0x298(%rbx), %rdx
leaq 0xb716(%rip), %rcx      # 0x3b386
movl $0x3, %r8d
movq 0x28(%rsp), %rdi
xorl %esi, %esi
callq 0x5690
movb $0x0, 0x2b4(%rbx)
movq 0x2c0(%rbx), %rdx
leaq 0xb268(%rip), %rcx      # 0x3aeff
movq 0x20(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0x2e0(%rbx), %rdx
leaq 0xb24b(%rip), %rcx      # 0x3aeff
movq 0x18(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movw $0x0, 0x2f8(%rbx)
movb $0x0, 0x2fa(%rbx)
movq 0x3c8(%rbx), %rdx
leaq 0xb21e(%rip), %rcx      # 0x3aeff
movq 0x10(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq 0x3e8(%rbx), %rdx
leaq 0xb201(%rip), %rcx      # 0x3aeff
movq 0x8(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movl $0xffffffff, 0x430(%rbx) # imm = 0xFFFFFFFF
xorl %eax, %eax
movb %al, (%rbx)
movb %al, 0x435(%rbx)
movq 0x440(%rbx), %rdx
leaq 0xb431(%rip), %rcx      # 0x3b160
movl $0x5, %r8d
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x5690
movabsq $0x40c3880000000000, %rax # imm = 0x40C3880000000000
movq %rax, 0x4f0(%rbx)
movabsq $0x3ff0000000000000, %rax # imm = 0x3FF0000000000000
movq %rax, 0x518(%rbx)
movq 0x500(%rbx), %rdx
leaq 0xb18f(%rip), %rcx      # 0x3aeff
movq 0x68(%rsp), %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x5690
movq $0x0, 0x520(%rbx)
movl $0x40, 0x528(%rbx)
leaq 0x110(%rsp), %r14
movq %r14, %rdi
callq 0x5400
movq (%r14), %rax
movl %eax, 0x2fc(%rbx)
movslq %eax, %rcx
movabsq $0x200000005, %rdx      # imm = 0x200000005
movq %rcx, %rax
mulq %rdx
movq %rcx, %rax
subq %rdx, %rax
shrq %rax
addq %rdx, %rax
shrq $0x1e, %rax
movq %rax, %rdx
shlq $0x1f, %rdx
subq %rdx, %rax
leaq (%rcx,%rax), %rdx
cmpq $0x1, %rdx
adcq %rcx, %rax
movq %rax, 0x530(%rbx)
movb $0x1, 0x52c(%rbx)
movq 0xf0(%rsp), %rdi
leaq 0x100(%rsp), %rax
cmpq %rax, %rdi
je 0x2fe0d
callq 0x5410
addq $0x118, %rsp            # imm = 0x118
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x2fe21
movq %rax, %rbp
movq 0xf0(%rsp), %rdi
leaq 0x100(%rsp), %rax
cmpq %rax, %rdi
je 0x2fe3e
callq 0x5410
leaq 0x498(%rbx), %r14
leaq 0x4c0(%rbx), %r15
movq 0x70(%rsp), %rdi
callq 0xc4f0
movq 0x68(%rsp), %rax
movq (%rax), %rdi
cmpq 0xe0(%rsp), %rdi
je 0x2fe6d
callq 0x5410
movq %r15, %rdi
callq 0xc74a
movq %r14, %rdi
callq 0xc7b2
leaq 0x470(%rbx), %rdi
callq 0xc7b2
leaq 0x400(%rbx), %r14
leaq 0x458(%rbx), %rdi
callq 0xc4f0
movq (%rsp), %rax
movq (%rax), %rdi
cmpq 0x78(%rsp), %rdi
je 0x2feaf
callq 0x5410
movq %r14, %rdi
callq 0xc74a
movq 0x8(%rsp), %rax
movq (%rax), %rdi
cmpq 0x80(%rsp), %rdi
je 0x2fece
callq 0x5410
leaq 0x300(%rbx), %r14
leaq 0x330(%rbx), %r15
leaq 0x360(%rbx), %r12
leaq 0x390(%rbx), %r13
movq 0x10(%rsp), %rax
movq (%rax), %rdi
cmpq 0x88(%rsp), %rdi
je 0x2ff01
callq 0x5410
movq %r13, %rdi
callq 0xc74a
movq %r12, %rdi
callq 0xc74a
movq %r15, %rdi
callq 0xc74a
movq %r14, %rdi
callq 0xc74a
movq 0x18(%rsp), %rax
movq (%rax), %rdi
cmpq 0x90(%rsp), %rdi
je 0x2ff38
callq 0x5410
movq 0x20(%rsp), %rax
movq (%rax), %rdi
cmpq 0x98(%rsp), %rdi
je 0x2ff4f
callq 0x5410
movq 0x28(%rsp), %rax
movq (%rax), %rdi
cmpq 0xa0(%rsp), %rdi
je 0x2ff66
callq 0x5410
leaq 0x160(%rbx), %r14
leaq 0x190(%rbx), %r15
leaq 0x1c0(%rbx), %r12
movq 0x30(%rsp), %rax
movq (%rax), %rdi
cmpq 0xa8(%rsp), %rdi
je 0x2ff92
callq 0x5410
movq %r12, %rdi
callq 0xc4f0
movq %r15, %rdi
callq 0xc74a
movq %r14, %rdi
callq 0xc74a
movq 0x38(%rsp), %rax
movq (%rax), %rdi
cmpq 0xb0(%rsp), %rdi
je 0x2ffc1
callq 0x5410
leaq 0xf0(%rbx), %r14
movq 0x40(%rsp), %rax
movq (%rax), %rdi
cmpq 0xb8(%rsp), %rdi
je 0x2ffdf
callq 0x5410
movq %r14, %rdi
callq 0xc74a
movq 0x48(%rsp), %rax
movq (%rax), %rdi
cmpq 0xc0(%rsp), %rdi
je 0x2fffe
callq 0x5410
movq 0x50(%rsp), %rax
movq (%rax), %rdi
cmpq 0xc8(%rsp), %rdi
je 0x30015
callq 0x5410
leaq 0x28(%rbx), %r14
addq $0x58, %rbx
movq 0x58(%rsp), %rax
movq (%rax), %rdi
cmpq 0xd0(%rsp), %rdi
je 0x30034
callq 0x5410
movq %rbx, %rdi
callq 0xc74a
movq %r14, %rdi
callq 0xc74a
movq 0x60(%rsp), %rax
movq (%rax), %rdi
cmpq 0xd8(%rsp), %rdi
je 0x3005b
callq 0x5410
movq %rbp, %rdi
callq 0x57d0
jmp 0x30065
movq %rax, %rdi
callq 0xc7a6
nop