// File: 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:
subq $0x158, %rsp            # imm = 0x158
movq %rdi, 0x150(%rsp)
movl %esi, 0x14c(%rsp)
movq %rdx, 0x140(%rsp)
movq 0x150(%rsp), %rdi
movq %rdi, 0xf8(%rsp)
addq $0x8, %rdi
movq %rdi, 0x10(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x28, %rdi
movq %rdi, 0x18(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x58, %rdi
movq %rdi, 0x20(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x88, %rdi
movq %rdi, 0x28(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0xb0, %rdi
movq %rdi, 0x30(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0xd0, %rdi
movq %rdi, 0x38(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0xf0, %rdi
movq %rdi, 0x40(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x120, %rdi            # imm = 0x120
movq %rdi, 0x48(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x140, %rdi            # imm = 0x140
movq %rdi, 0x50(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x160, %rdi            # imm = 0x160
movq %rdi, 0x58(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x190, %rdi            # imm = 0x190
movq %rdi, 0x60(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x1c0, %rdi            # imm = 0x1C0
movq %rdi, 0x68(%rsp)
callq 0x10260
movq 0xf8(%rsp), %rdi
addq $0x1e8, %rdi            # imm = 0x1E8
movq %rdi, 0x70(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x290, %rdi            # imm = 0x290
movq %rdi, 0x78(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x2b8, %rdi            # imm = 0x2B8
movq %rdi, 0x80(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x2d8, %rdi            # imm = 0x2D8
movq %rdi, 0x88(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x300, %rdi            # imm = 0x300
movq %rdi, 0x90(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x330, %rdi            # imm = 0x330
movq %rdi, 0x98(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x360, %rdi            # imm = 0x360
movq %rdi, 0xa0(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x390, %rdi            # imm = 0x390
movq %rdi, 0xa8(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x3c0, %rdi            # imm = 0x3C0
movq %rdi, 0xb0(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x3e0, %rdi            # imm = 0x3E0
movq %rdi, 0xb8(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x400, %rdi            # imm = 0x400
movq %rdi, 0xc0(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x438, %rdi            # imm = 0x438
movq %rdi, 0xc8(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x458, %rdi            # imm = 0x458
movq %rdi, 0xd0(%rsp)
callq 0x10260
movq 0xf8(%rsp), %rdi
addq $0x470, %rdi            # imm = 0x470
movq %rdi, 0xd8(%rsp)
callq 0x1b250
movq 0xf8(%rsp), %rdi
addq $0x498, %rdi            # imm = 0x498
movq %rdi, 0xe0(%rsp)
callq 0x1b250
movq 0xf8(%rsp), %rdi
addq $0x4c0, %rdi            # imm = 0x4C0
movq %rdi, 0xe8(%rsp)
callq 0x5ec60
movq 0xf8(%rsp), %rdi
addq $0x4f8, %rdi            # imm = 0x4F8
movq %rdi, 0xf0(%rsp)
callq 0x67e0
movq 0xf8(%rsp), %rdi
addq $0x530, %rdi            # imm = 0x530
callq 0x70a20
jmp 0x67455
movq 0xf8(%rsp), %rdi
addq $0x538, %rdi            # imm = 0x538
movq %rdi, 0x8(%rsp)
callq 0x10260
movl $0x2, %edi
callq 0x69d0
cmpl $0x0, %eax
je 0x674a7
movq 0xf8(%rsp), %rax
movb $0x0, 0x434(%rax)
jmp 0x674b6
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x138(%rsp)
movl %eax, 0x134(%rsp)
jmp 0x67925
movq 0xf8(%rsp), %rax
movb $0x1, 0x434(%rax)
leaq 0x110(%rsp), %rdi
callq 0x67e0
movl $0x0, 0x10c(%rsp)
movl 0x10c(%rsp), %eax
cmpl 0x14c(%rsp), %eax
jge 0x67568
movq 0x140(%rsp), %rax
movslq 0x10c(%rsp), %rcx
movq (%rax,%rcx,8), %rsi
leaq 0x110(%rsp), %rdi
callq 0x67b0
jmp 0x67505
movq 0xf8(%rsp), %rdi
addq $0x538, %rdi            # imm = 0x538
leaq 0x110(%rsp), %rsi
callq 0x2a190
jmp 0x67523
jmp 0x67525
movl 0x10c(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x10c(%rsp)
jmp 0x674ce
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x138(%rsp)
movl %eax, 0x134(%rsp)
leaq 0x110(%rsp), %rdi
callq 0x6b50
movq 0x8(%rsp), %rdi
callq 0x10cc0
jmp 0x67925
movq 0xf8(%rsp), %rdi
movb $0x0, 0x1(%rdi)
addq $0x8, %rdi
leaq 0xe7aa(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x67586
movq 0xf8(%rsp), %rdi
addq $0x88, %rdi
leaq 0xe78d(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x675a3
callq 0x10bd0
movq 0xf8(%rsp), %rdi
movl %eax, 0xa8(%rdi)
addq $0xb0, %rdi
leaq 0xe765(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x675cb
movq 0xf8(%rsp), %rdi
addq $0xd0, %rdi
leaq 0xe748(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x675e8
movq 0xf8(%rsp), %rdi
addq $0x120, %rdi            # imm = 0x120
leaq 0xe72b(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x67605
movq 0xf8(%rsp), %rdi
addq $0x140, %rdi            # imm = 0x140
leaq 0xe70e(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x67622
movq 0xf8(%rsp), %rdi
movb $0x0, 0x1d8(%rdi)
movb $0x0, 0x1d9(%rdi)
movl $0xffffffff, 0x1dc(%rdi) # imm = 0xFFFFFFFF
movabsq $-0x4010000000000000, %rax # imm = 0xBFF0000000000000
movq %rax, 0x1e0(%rdi)
addq $0x1e8, %rdi            # imm = 0x1E8
leaq 0xe6c8(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x67668
callq 0x10bd0
movl %eax, %ecx
movq 0xf8(%rsp), %rax
movl %ecx, 0x208(%rax)
callq 0x10bd0
movl %eax, %ecx
movq 0xf8(%rsp), %rax
movl %ecx, 0x20c(%rax)
callq 0x10bd0
movl %eax, %ecx
movq 0xf8(%rsp), %rax
movl %ecx, 0x210(%rax)
callq 0xf250
movq 0xf8(%rsp), %rax
movsd %xmm0, 0x218(%rax)
callq 0xf250
movq 0xf8(%rsp), %rax
movsd %xmm0, 0x220(%rax)
callq 0x10bd0
movl %eax, %ecx
movq 0xf8(%rsp), %rax
movl %ecx, 0x228(%rax)
callq 0x10bd0
movl %eax, %ecx
movq 0xf8(%rsp), %rax
movl %ecx, 0x22c(%rax)
callq 0xf250
movq 0xf8(%rsp), %rdi
movsd %xmm0, 0x230(%rdi)
movl $0xffffffff, 0x238(%rdi) # imm = 0xFFFFFFFF
movl $0xffffffff, 0x23c(%rdi) # imm = 0xFFFFFFFF
movl $0xffffffff, 0x240(%rdi) # imm = 0xFFFFFFFF
movabsq $-0x4010000000000000, %rax # imm = 0xBFF0000000000000
movq %rax, 0x248(%rdi)
movq %rax, 0x250(%rdi)
movl $0xffffffff, 0x258(%rdi) # imm = 0xFFFFFFFF
movl $0x0, 0x25c(%rdi)
movq %rax, 0x260(%rdi)
movq %rax, 0x278(%rdi)
movq %rax, 0x280(%rdi)
movq $0x0, 0x288(%rdi)
movl $0xffffffff, 0x268(%rdi) # imm = 0xFFFFFFFF
movq %rax, 0x270(%rdi)
movl $0x0, 0x2b0(%rdi)
addq $0x290, %rdi            # imm = 0x290
leaq 0xe9e3(%rip), %rsi      # 0x76186
callq 0x67b0
jmp 0x677aa
movq 0xf8(%rsp), %rdi
movb $0x0, 0x2b4(%rdi)
addq $0x2b8, %rdi            # imm = 0x2B8
leaq 0xe562(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x677ce
movq 0xf8(%rsp), %rdi
addq $0x2d8, %rdi            # imm = 0x2D8
leaq 0xe545(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x677eb
movq 0xf8(%rsp), %rdi
movb $0x0, 0x2f8(%rdi)
movb $0x0, 0x2f9(%rdi)
movb $0x0, 0x2fa(%rdi)
addq $0x3c0, %rdi            # imm = 0x3C0
leaq 0xe513(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x6781d
movq 0xf8(%rsp), %rdi
addq $0x3e0, %rdi            # imm = 0x3E0
leaq 0xe4f6(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x6783a
movq 0xf8(%rsp), %rdi
movl $0xffffffff, 0x430(%rdi) # imm = 0xFFFFFFFF
movb $0x0, (%rdi)
movb $0x0, 0x435(%rdi)
addq $0x438, %rdi            # imm = 0x438
leaq 0xe6fc(%rip), %rsi      # 0x75f60
callq 0x67b0
jmp 0x6786b
movq 0xf8(%rsp), %rdi
movabsq $0x40c3880000000000, %rax # imm = 0x40C3880000000000
movq %rax, 0x4f0(%rdi)
movabsq $0x3ff0000000000000, %rax # imm = 0x3FF0000000000000
movq %rax, 0x518(%rdi)
addq $0x4f8, %rdi            # imm = 0x4F8
leaq 0xe486(%rip), %rsi      # 0x75d29
callq 0x67b0
jmp 0x678aa
movq 0xf8(%rsp), %rax
movq $0x0, 0x520(%rax)
movl $0x40, 0x528(%rax)
leaq 0x100(%rsp), %rdi
callq 0x64d0
movq 0xf8(%rsp), %rax
movl 0x100(%rsp), %ecx
movl %ecx, 0x2fc(%rax)
movq %rax, %rdi
addq $0x530, %rdi            # imm = 0x530
movslq 0x2fc(%rax), %rsi
callq 0x70a40
jmp 0x67901
movq 0xf8(%rsp), %rax
movb $0x1, 0x52c(%rax)
leaq 0x110(%rsp), %rdi
callq 0x6b50
addq $0x158, %rsp            # imm = 0x158
retq
movq 0xf0(%rsp), %rdi
callq 0x6b50
movq 0xe8(%rsp), %rdi
callq 0x112f0
movq 0xe0(%rsp), %rdi
callq 0x11300
movq 0xd8(%rsp), %rdi
callq 0x11300
movq 0xd0(%rsp), %rdi
callq 0x10cc0
movq 0xc8(%rsp), %rdi
callq 0x6b50
movq 0xc0(%rsp), %rdi
callq 0x112f0
movq 0xb8(%rsp), %rdi
callq 0x6b50
movq 0xb0(%rsp), %rdi
callq 0x6b50
movq 0xa8(%rsp), %rdi
callq 0x112f0
movq 0xa0(%rsp), %rdi
callq 0x112f0
movq 0x98(%rsp), %rdi
callq 0x112f0
movq 0x90(%rsp), %rdi
callq 0x112f0
movq 0x88(%rsp), %rdi
callq 0x6b50
movq 0x80(%rsp), %rdi
callq 0x6b50
movq 0x78(%rsp), %rdi
callq 0x6b50
movq 0x70(%rsp), %rdi
callq 0x6b50
movq 0x68(%rsp), %rdi
callq 0x10cc0
movq 0x60(%rsp), %rdi
callq 0x112f0
movq 0x58(%rsp), %rdi
callq 0x112f0
movq 0x50(%rsp), %rdi
callq 0x6b50
movq 0x48(%rsp), %rdi
callq 0x6b50
movq 0x40(%rsp), %rdi
callq 0x112f0
movq 0x38(%rsp), %rdi
callq 0x6b50
movq 0x30(%rsp), %rdi
callq 0x6b50
movq 0x28(%rsp), %rdi
callq 0x6b50
movq 0x20(%rsp), %rdi
callq 0x112f0
movq 0x18(%rsp), %rdi
callq 0x112f0
movq 0x10(%rsp), %rdi
callq 0x6b50
movq 0x138(%rsp), %rdi
callq 0x69e0
nopw %cs:(%rax,%rax)