// File: /workspace/github_cpp_makefile_star2_O2/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 $0xf8, %rsp
movq %rdi, %rbx
leaq 0x18(%rdi), %rax
movq %rax, 0x8(%rdi)
andq $0x0, 0x10(%rdi)
xorl %r13d, %r13d
movb %r13b, 0x18(%rdi)
leaq 0x30(%rdi), %rax
andl $0x0, 0x30(%rdi)
andq $0x0, 0x38(%rdi)
movq %rax, 0x40(%rdi)
movq %rax, 0x48(%rdi)
andq $0x0, 0x50(%rdi)
andl $0x0, 0x60(%rdi)
andq $0x0, 0x68(%rdi)
leaq 0x60(%rdi), %rax
movq %rax, 0x70(%rdi)
movq %rax, 0x78(%rdi)
andq $0x0, 0x80(%rdi)
leaq 0x98(%rdi), %rax
movq %rax, 0x88(%rdi)
andq $0x0, 0x90(%rdi)
movb %r13b, 0x98(%rdi)
leaq 0xc0(%rdi), %rax
movq %rax, 0xb0(%rdi)
andq $0x0, 0xb8(%rdi)
movb %r13b, 0xc0(%rdi)
leaq 0xe0(%rdi), %rax
movq %rax, 0xd0(%rdi)
andq $0x0, 0xd8(%rdi)
movb %r13b, 0xe0(%rdi)
andl $0x0, 0xf8(%rdi)
andq $0x0, 0x100(%rdi)
leaq 0xf8(%rdi), %rax
movq %rax, 0x108(%rdi)
movq %rax, 0x110(%rdi)
andq $0x0, 0x118(%rdi)
leaq 0x130(%rdi), %rax
movq %rax, 0x120(%rdi)
andq $0x0, 0x128(%rdi)
movb %r13b, 0x130(%rdi)
leaq 0x150(%rdi), %rax
movq %rax, 0x140(%rdi)
andq $0x0, 0x148(%rdi)
movb %r13b, 0x150(%rdi)
leaq 0x168(%rdi), %rax
andl $0x0, 0x168(%rdi)
andq $0x0, 0x170(%rdi)
movq %rax, 0x178(%rdi)
movq %rax, 0x180(%rdi)
andq $0x0, 0x188(%rdi)
andl $0x0, 0x198(%rdi)
andq $0x0, 0x1a0(%rdi)
leaq 0x198(%rdi), %rax
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, 0x1e8(%rdi)
andq $0x0, 0x1f0(%rdi)
movb %r13b, 0x1f8(%rdi)
leaq 0x2a0(%rdi), %rax
movq %rax, 0x290(%rdi)
andq $0x0, 0x298(%rdi)
movb %r13b, 0x2a0(%rdi)
leaq 0x2c8(%rdi), %rax
movq %rax, 0x2b8(%rdi)
andq $0x0, 0x2c0(%rdi)
movb %r13b, 0x2c8(%rdi)
leaq 0x2e8(%rdi), %rax
movq %rax, 0x2d8(%rdi)
andq $0x0, 0x2e0(%rdi)
movb %r13b, 0x2e8(%rdi)
leaq 0x308(%rdi), %rax
andl $0x0, 0x308(%rdi)
andq $0x0, 0x310(%rdi)
movq %rax, 0x318(%rdi)
movq %rax, 0x320(%rdi)
andq $0x0, 0x328(%rdi)
leaq 0x338(%rdi), %rax
andl $0x0, 0x338(%rdi)
andq $0x0, 0x340(%rdi)
movq %rax, 0x348(%rdi)
movq %rax, 0x350(%rdi)
andq $0x0, 0x358(%rdi)
leaq 0x368(%rdi), %rax
andl $0x0, 0x368(%rdi)
andq $0x0, 0x370(%rdi)
movq %rax, 0x378(%rdi)
movq %rax, 0x380(%rdi)
andq $0x0, 0x388(%rdi)
andl $0x0, 0x398(%rdi)
movq %rdx, %r14
andq $0x0, 0x3a0(%rdi)
movl %esi, %r15d
leaq 0x398(%rdi), %rax
movq %rax, 0x3a8(%rdi)
movq %rax, 0x3b0(%rdi)
andq $0x0, 0x3b8(%rdi)
leaq 0x3d0(%rdi), %rax
movq %rax, 0x3c0(%rdi)
andq $0x0, 0x3c8(%rdi)
leaq 0x8(%rdi), %rax
movq %rax, 0x70(%rsp)
leaq 0x88(%rdi), %rax
movq %rax, 0x68(%rsp)
movb %r13b, 0x3d0(%rdi)
leaq 0x3f0(%rdi), %rax
movq %rax, 0x3e0(%rdi)
andq $0x0, 0x3e8(%rdi)
movb %r13b, 0x3f0(%rdi)
andl $0x0, 0x408(%rdi)
leaq 0xb0(%rdi), %rax
movq %rax, 0x60(%rsp)
andq $0x0, 0x410(%rdi)
leaq 0xd0(%rdi), %rax
movq %rax, 0x58(%rsp)
leaq 0x408(%rdi), %rax
movq %rax, 0x418(%rdi)
movq %rax, 0x420(%rdi)
andq $0x0, 0x428(%rdi)
leaq 0x448(%rdi), %rax
movq %rax, 0x438(%rdi)
andq $0x0, 0x440(%rdi)
movb %r13b, 0x448(%rdi)
andq $0x0, 0x480(%rdi)
leaq 0x120(%rdi), %rax
movq %rax, 0x50(%rsp)
andl $0x0, 0x488(%rdi)
leaq 0x140(%rdi), %rax
movq %rax, 0x48(%rsp)
andq $0x0, 0x4a8(%rdi)
leaq 0x1e8(%rdi), %rax
movq %rax, 0x40(%rsp)
andl $0x0, 0x4b0(%rdi)
leaq 0x290(%rdi), %rax
movq %rax, 0x38(%rsp)
andq $0x0, 0x4b8(%rdi)
leaq 0x2b8(%rdi), %rax
movq %rax, 0x30(%rsp)
andl $0x0, 0x4c8(%rdi)
leaq 0x2d8(%rdi), %rax
movq %rax, 0x28(%rsp)
andq $0x0, 0x4d0(%rdi)
movups %xmm0, 0x468(%rdi)
andl $0x0, 0x478(%rdi)
movups %xmm0, 0x458(%rdi)
andl $0x0, 0x4a0(%rdi)
leaq 0x4c8(%rdi), %rax
movups %xmm0, 0x490(%rdi)
movq %rax, 0x4d8(%rdi)
movq %rax, 0x4e0(%rdi)
andq $0x0, 0x4e8(%rdi)
leaq 0x508(%rdi), %rax
movq %rax, 0x4f8(%rdi)
andq $0x0, 0x500(%rdi)
leaq 0x3c0(%rdi), %rax
movq %rax, 0x20(%rsp)
movb %r13b, 0x508(%rdi)
movq $0x1, 0x530(%rdi)
movups %xmm0, 0x538(%rdi)
andq $0x0, 0x548(%rdi)
leaq 0x3e0(%rdi), %rax
movq %rax, 0x18(%rsp)
leaq 0x438(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x458(%rdi), %rax
movq %rax, 0xc8(%rsp)
leaq 0x4f8(%rdi), %rax
movq %rax, 0x8(%rsp)
leaq 0x538(%rdi), %rbp
pushq $0x2
popq %rdi
callq 0x57f0
testl %eax, %eax
sete 0x434(%rbx)
leaq 0xe8(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb %r13b, (%rax)
testl %r15d, %r15d
cmovlel %r13d, %r15d
leaq 0xd8(%rsp), %r12
cmpq %r13, %r15
je 0x27492
movq (%r14,%r13,8), %rsi
movq %r12, %rdi
callq 0x58b0
movq %rbp, %rdi
movq %r12, %rsi
callq 0xfda2
incq %r13
jmp 0x27471
movb $0x0, 0x1(%rbx)
leaq 0x799a(%rip), %rsi      # 0x2ee37
movq 0x70(%rsp), %rdi
callq 0x58b0
leaq 0x7989(%rip), %rsi      # 0x2ee37
movq 0x68(%rsp), %rdi
callq 0x58b0
movl $0x7fffffff, 0xa8(%rbx) # imm = 0x7FFFFFFF
leaq 0x796e(%rip), %rsi      # 0x2ee37
movq 0x60(%rsp), %rdi
callq 0x58b0
leaq 0x795d(%rip), %rsi      # 0x2ee37
movq 0x58(%rsp), %rdi
callq 0x58b0
leaq 0x794c(%rip), %rsi      # 0x2ee37
movq 0x50(%rsp), %rdi
callq 0x58b0
leaq 0x793b(%rip), %rsi      # 0x2ee37
movq 0x48(%rsp), %rdi
callq 0x58b0
andw $0x0, 0x1d8(%rbx)
orl $-0x1, 0x1dc(%rbx)
movabsq $-0x4010000000000000, %r14 # imm = 0xBFF0000000000000
movq %r14, 0x1e0(%rbx)
leaq 0x790a(%rip), %rsi      # 0x2ee37
movq 0x40(%rsp), %rdi
callq 0x58b0
movabsq $0x7fffffff7fffffff, %rax # imm = 0x7FFFFFFF7FFFFFFF
movq %rax, 0x208(%rbx)
movl $0x7fffffff, 0x210(%rbx) # imm = 0x7FFFFFFF
movaps 0x7b17(%rip), %xmm0     # 0x2f070
movups %xmm0, 0x218(%rbx)
movq %rax, 0x228(%rbx)
movabsq $0x7fefffffffffffff, %rax # imm = 0x7FEFFFFFFFFFFFFF
movq %rax, 0x230(%rbx)
orq $-0x1, 0x238(%rbx)
orl $-0x1, 0x240(%rbx)
movaps 0x7af2(%rip), %xmm0     # 0x2f080
movups %xmm0, 0x248(%rbx)
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movq %rax, 0x258(%rbx)
movq %r14, 0x260(%rbx)
movsd 0x69d0(%rip), %xmm1     # 0x2df80
movups %xmm1, 0x280(%rbx)
orl $-0x1, 0x268(%rbx)
movups %xmm0, 0x270(%rbx)
andl $0x0, 0x2b0(%rbx)
leaq 0x7ce3(%rip), %rsi      # 0x2f2b6
movq 0x38(%rsp), %rdi
callq 0x58b0
movb $0x0, 0x2b4(%rbx)
leaq 0x784c(%rip), %rsi      # 0x2ee37
movq 0x30(%rsp), %rdi
callq 0x58b0
leaq 0x783b(%rip), %rsi      # 0x2ee37
movq 0x28(%rsp), %rdi
callq 0x58b0
andw $0x0, 0x2f8(%rbx)
movb $0x0, 0x2fa(%rbx)
leaq 0x781b(%rip), %rsi      # 0x2ee37
movq 0x20(%rsp), %rdi
callq 0x58b0
leaq 0x780a(%rip), %rsi      # 0x2ee37
movq 0x18(%rsp), %rdi
callq 0x58b0
orl $-0x1, 0x430(%rbx)
xorl %eax, %eax
movb %al, (%rbx)
movb %al, 0x435(%rbx)
leaq 0x7a41(%rip), %rsi      # 0x2f090
movq 0x10(%rsp), %rdi
callq 0x58b0
movabsq $0x40c3880000000000, %rax # imm = 0x40C3880000000000
movq %rax, 0x4f0(%rbx)
movabsq $0x3ff0000000000000, %rax # imm = 0x3FF0000000000000
movq %rax, 0x518(%rbx)
leaq 0x77b5(%rip), %rsi      # 0x2ee37
movq 0x8(%rsp), %rdi
callq 0x58b0
andq $0x0, 0x520(%rbx)
movl $0x40, 0x528(%rbx)
leaq 0xd0(%rsp), %r14
movq %r14, %rdi
callq 0x5430
movq (%r14), %rax
movl %eax, 0x2fc(%rbx)
cltq
movl $0x7fffffff, %ecx       # imm = 0x7FFFFFFF
xorl %edx, %edx
divq %rcx
cmpq $0x1, %rdx
adcq $0x0, %rdx
movq %rdx, 0x530(%rbx)
movb $0x1, 0x52c(%rbx)
leaq 0xd8(%rsp), %rdi
callq 0x5908
addq $0xf8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x276fa
movq %rax, %r13
leaq 0x498(%rbx), %r15
leaq 0x470(%rbx), %r14
leaq 0x1c0(%rbx), %rax
movq %rax, 0xb0(%rsp)
leaq 0x4c0(%rbx), %r12
leaq 0x400(%rbx), %rax
movq %rax, 0x78(%rsp)
leaq 0x390(%rbx), %rax
movq %rax, 0x80(%rsp)
leaq 0x360(%rbx), %rax
movq %rax, 0x88(%rsp)
leaq 0x330(%rbx), %rax
movq %rax, 0x90(%rsp)
leaq 0x300(%rbx), %rax
movq %rax, 0x98(%rsp)
leaq 0x190(%rbx), %rax
movq %rax, 0xa0(%rsp)
leaq 0x160(%rbx), %rax
movq %rax, 0xa8(%rsp)
leaq 0xf0(%rbx), %rax
movq %rax, 0xb8(%rsp)
leaq 0x58(%rbx), %rax
movq %rax, 0xc0(%rsp)
addq $0x28, %rbx
leaq 0xd8(%rsp), %rdi
callq 0x5908
movq %rbp, %rdi
callq 0x9f1c
movq 0x8(%rsp), %rdi
callq 0x5908
movq %r12, %rdi
callq 0xa0b6
movq %r15, %rdi
callq 0xa0a6
movq %r14, %rdi
callq 0xa0a6
movq 0xc8(%rsp), %rdi
callq 0x9f1c
movq 0x10(%rsp), %rdi
callq 0x5908
movq 0x78(%rsp), %rdi
callq 0xa0b6
movq 0x18(%rsp), %rdi
callq 0x5908
movq 0x20(%rsp), %rdi
callq 0x5908
movq 0x80(%rsp), %rdi
callq 0xa0b6
movq 0x88(%rsp), %rdi
callq 0xa0b6
movq 0x90(%rsp), %rdi
callq 0xa0b6
movq 0x98(%rsp), %rdi
callq 0xa0b6
movq 0x28(%rsp), %rdi
callq 0x5908
movq 0x30(%rsp), %rdi
callq 0x5908
movq 0x38(%rsp), %rdi
callq 0x5908
movq 0x40(%rsp), %rdi
callq 0x5908
movq 0xb0(%rsp), %rdi
callq 0x9f1c
movq 0xa0(%rsp), %rdi
callq 0xa0b6
movq 0xa8(%rsp), %rdi
callq 0xa0b6
movq 0x48(%rsp), %rdi
callq 0x5908
movq 0x50(%rsp), %rdi
callq 0x5908
movq 0xb8(%rsp), %rdi
callq 0xa0b6
movq 0x58(%rsp), %rdi
callq 0x5908
movq 0x60(%rsp), %rdi
callq 0x5908
movq 0x68(%rsp), %rdi
callq 0x5908
movq 0xc0(%rsp), %rdi
callq 0xa0b6
movq %rbx, %rdi
callq 0xa0b6
movq 0x70(%rsp), %rdi
callq 0x5908
movq %r13, %rdi
callq 0x5800
nop