collr2: QCDH

# TODO: Add comment
# 
# Author: kaiyin
###############################################################################


#' A wrapper for plink
#' 
#' A wrapper for plink. All the parameters of this function is documented in \code{\link{getPlinkParam}}.
#' 
#' @import stringr
#' @export
#' @seealso \code{\link{getPlinkParam}}
#' 
plinkr = function(
	D=NULL,
	K=NULL,
	a1_allele=NULL,
	a2_allele=NULL,
	adjust=NULL,
	all=NULL,
	all_pheno=NULL,
	allele1234=NULL,
	alleleACGT=NULL,
	allele_count=NULL,
	allow_extra_chr=NULL,
	allow_no_sex=NULL,
	alt_group=NULL,
	alt_snp=NULL,
	annotate=NULL,
	annotate_snp_field=NULL,
	aperm=NULL,
	assoc=NULL,
	attrib=NULL,
	attrib_indiv=NULL,
	autosome=NULL,
	autosome_num=NULL,
	autosome_xy=NULL,
	bcf=NULL,
	bd=NULL,
	bed=NULL,
	beta=NULL,
	bfile=NULL,
	bgen=NULL,
	biallelic_only=NULL,
	bim=NULL,
	blocks=NULL,
	blocks_inform_frac=NULL,
	blocks_max_kb=NULL,
	blocks_min_maf=NULL,
	blocks_recomb_highci=NULL,
	blocks_strong_highci=NULL,
	blocks_strong_lowci=NULL,
	bmerge=NULL,
	border=NULL,
	bp_space=NULL,
	case_only=NULL,
	cc=NULL,
	cell=NULL,
	cfile=NULL,
	chap=NULL,
	check_sex=NULL,
	chr=NULL,
	chr_set=NULL,
	ci=NULL,
	clump=NULL,
	clump_allow_overlap=NULL,
	clump_annotate=NULL,
	clump_best=NULL,
	clump_field=NULL,
	clump_index_first=NULL,
	clump_kb=NULL,
	clump_p1=NULL,
	clump_p2=NULL,
	clump_r2=NULL,
	clump_range=NULL,
	clump_range_border=NULL,
	clump_replicate=NULL,
	clump_snp_field=NULL,
	clump_verbose=NULL,
	cluster=NULL,
	cluster_missing=NULL,
	cm_map=NULL,
	cnv_blue=NULL,
	cnv_border=NULL,
	cnv_brown=NULL,
	cnv_check_no_overlap=NULL,
	cnv_count=NULL,
	cnv_del=NULL,
	cnv_disrupt=NULL,
	cnv_drop_no_segment=NULL,
	cnv_dup=NULL,
	cnv_enrichment_test=NULL,
	cnv_exclude=NULL,
	cnv_exclude_off_by_1=NULL,
	cnv_freq_excldue_above=NULL,
	cnv_freq_excldue_below=NULL,
	cnv_freq_excldue_exact=NULL,
	cnv_freq_exclude_above=NULL,
	cnv_freq_exclude_below=NULL,
	cnv_freq_exclude_exact=NULL,
	cnv_freq_incldue_exact=NULL,
	cnv_freq_include_exact=NULL,
	cnv_freq_method2=NULL,
	cnv_freq_overlap=NULL,
	cnv_green=NULL,
	cnv_indiv_perm=NULL,
	cnv_intersect=NULL,
	cnv_kb=NULL,
	cnv_list=NULL,
	cnv_make_map=NULL,
	cnv_max_kb=NULL,
	cnv_max_score=NULL,
	cnv_max_sites=NULL,
	cnv_overlap=NULL,
	cnv_red=NULL,
	cnv_region_overlap=NULL,
	cnv_report_regions=NULL,
	cnv_score=NULL,
	cnv_seglist=NULL,
	cnv_sites=NULL,
	cnv_subset=NULL,
	cnv_test=NULL,
	cnv_test_1sided=NULL,
	cnv_test_2sided=NULL,
	cnv_test_region=NULL,
	cnv_test_window=NULL,
	cnv_track=NULL,
	cnv_union_overlap=NULL,
	cnv_unique=NULL,
	cnv_verbose_report_regions=NULL,
	cnv_write=NULL,
	cnv_write_freq=NULL,
	complement_sets=NULL,
	compound_genotypes=NULL,
	compress=NULL,
	condition=NULL,
	condition_list=NULL,
	consensus_match=NULL,
	const_fid=NULL,
	control=NULL,
	counts=NULL,
	covar=NULL,
	covar_name=NULL,
	covar_number=NULL,
	cow=NULL,
	d=NULL,
	data=NULL,
	debug=NULL,
	decompress=NULL,
	dfam=NULL,
	distance=NULL,
	distance_exp=NULL,
	distance_matrix=NULL,
	dog=NULL,
	dominant=NULL,
	dosage=NULL,
	double_id=NULL,
	dprime=NULL,
	dummy=NULL,
	dummy_coding=NULL,
	each_versus_others=NULL,
	each_vs_others=NULL,
	epistasis=NULL,
	epistasis_summary_merge=NULL,
	exclude=NULL,
	exclude_before_extract=NULL,
	exclude_snp=NULL,
	exclude_snps=NULL,
	extract=NULL,
	fam=NULL,
	family=NULL,
	fast_epistasis=NULL,
	fid=NULL,
	file=NULL,
	fill_missing_a2=NULL,
	filter=NULL,
	filter_cases=NULL,
	filter_controls=NULL,
	filter_females=NULL,
	filter_founders=NULL,
	filter_males=NULL,
	filter_nonfounders=NULL,
	fisher=NULL,
	flip=NULL,
	flip_scan=NULL,
	flip_scan_threshold=NULL,
	flip_scan_verbose=NULL,
	flip_scan_window=NULL,
	flip_scan_window_kb=NULL,
	flip_subset=NULL,
	freq=NULL,
	freqx=NULL,
	from=NULL,
	from_bp=NULL,
	from_kb=NULL,
	from_mb=NULL,
	frqx=NULL,
	fst=NULL,
	gap=NULL,
	gates=NULL,
	gc=NULL,
	gen=NULL,
	gene=NULL,
	gene_all=NULL,
	gene_list=NULL,
	gene_list_border=NULL,
	gene_report=NULL,
	gene_report_empty=NULL,
	gene_report_snp_field=NULL,
	gene_subset=NULL,
	genedrop=NULL,
	genepi=NULL,
	geno=NULL,
	genome=NULL,
	genome_full=NULL,
	genome_lists=NULL,
	genome_minimal=NULL,
	genotypic=NULL,
	gfile=NULL,
	gplink=NULL,
	grm=NULL,
	grm_bin=NULL,
	grm_gz=NULL,
	group_avg=NULL,
	groupdist=NULL,
	gxe=NULL,
	hap...=NULL,
	hap=NULL,
	hap_assoc=NULL,
	hap_freq=NULL,
	hap_impute=NULL,
	hap_max_phase=NULL,
	hap_min_phase_prob=NULL,
	hap_miss=NULL,
	hap_phase=NULL,
	hap_phase_wide=NULL,
	hap_pp=NULL,
	hap_snps=NULL,
	hap_tdt=NULL,
	hap_window=NULL,
	hard_call_threshold=NULL,
	hardy2=NULL,
	hardy=NULL,
	help=NULL,
	het=NULL,
	hethom=NULL,
	hide_covar=NULL,
	homog=NULL,
	homozyg=NULL,
	homozyg_density=NULL,
	homozyg_gap=NULL,
	homozyg_group=NULL,
	homozyg_het=NULL,
	homozyg_include_missing=NULL,
	homozyg_kb=NULL,
	homozyg_match=NULL,
	homozyg_snp=NULL,
	homozyg_verbose=NULL,
	homozyg_window_het=NULL,
	homozyg_window_kb=NULL,
	homozyg_window_missing=NULL,
	homozyg_window_snp=NULL,
	homozyg_window_threshold=NULL,
	horse=NULL,
	hwe=NULL,
	hwe_all=NULL,
	ibc=NULL,
	ibm=NULL,
	ibs_matrix=NULL,
	ibs_test=NULL,
	id_delim=NULL,
	id_dict=NULL,
	id_match=NULL,
	iid=NULL,
	impossible=NULL,
	impute_sex=NULL,
	ind_major=NULL,
	indep=NULL,
	indep_pairphase=NULL,
	indep_pairwise=NULL,
	independent_effect=NULL,
	indiv_sort=NULL,
	inter_chr=NULL,
	interaction=NULL,
	je_cellmin=NULL,
	keep=NULL,
	keep_allele_order=NULL,
	keep_autoconv=NULL,
	keep_before_remove=NULL,
	keep_cluster_names=NULL,
	keep_clusters=NULL,
	keep_fam=NULL,
	lambda=NULL,
	lasso=NULL,
	lasso_select_covars=NULL,
	ld=NULL,
	ld_snp=NULL,
	ld_snp_list=NULL,
	ld_snps=NULL,
	ld_window=NULL,
	ld_window_kb=NULL,
	ld_window_r2=NULL,
	ld_xchr=NULL,
	lfile=NULL,
	liability=NULL,
	linear=NULL,
	list=NULL,
	list_23_indels=NULL,
	list_all=NULL,
	logistic=NULL,
	lookup...=NULL,
	lookup=NULL,
	lookup_gene=NULL,
	lookup_list=NULL,
	loop_assoc=NULL,
	maf=NULL,
	maf_succ=NULL,
	make_bed=NULL,
	make_founders=NULL,
	make_grm=NULL,
	make_grm_bin=NULL,
	make_grm_gz=NULL,
	make_just_bim=NULL,
	make_just_fam=NULL,
	make_perm_pheno=NULL,
	make_pheno=NULL,
	make_rel=NULL,
	make_set=NULL,
	make_set_border=NULL,
	make_set_collapse_group=NULL,
	make_set_complement_all=NULL,
	make_set_complement_group=NULL,
	map=NULL,
	mat=NULL,
	match=NULL,
	match_type=NULL,
	matrix=NULL,
	max=NULL,
	max_maf=NULL,
	mc=NULL,
	mcc=NULL,
	mcovar=NULL,
	mds_cluster=NULL,
	mds_plot=NULL,
	me=NULL,
	me_exclude_one=NULL,
	memory=NULL,
	mendel=NULL,
	mendel_duos=NULL,
	mendel_multigen=NULL,
	merge=NULL,
	merge_equal_pos=NULL,
	merge_list=NULL,
	merge_mode=NULL,
	merge_x=NULL,
	meta_analysis=NULL,
	meta_analysis_..._field=NULL,
	mfilter=NULL,
	mh=NULL,
	mhf=NULL,
	min=NULL,
	mind=NULL,
	mishap_window=NULL,
	missing=NULL,
	missing_code=NULL,
	missing_genotype=NULL,
	missing_phenotype=NULL,
	missing_var_code=NULL,
	mlma=NULL,
	mlma_loco=NULL,
	mlma_no_adj_covar=NULL,
	model=NULL,
	model_dom=NULL,
	model_gen=NULL,
	model_rec=NULL,
	model_trend=NULL,
	mouse=NULL,
	mperm=NULL,
	mperm_save=NULL,
	mperm_save_all=NULL,
	mpheno=NULL,
	must_have_sex=NULL,
	mwithin=NULL,
	neighbour=NULL,
	no_fid=NULL,
	no_parents=NULL,
	no_pheno=NULL,
	no_sex=NULL,
	no_snp=NULL,
	no_x_sex=NULL,
	nonfounders=NULL,
	nop=NULL,
	not_chr=NULL,
	nudge=NULL,
	null_group=NULL,
	null_snp=NULL,
	oblig_cluster=NULL,
	oblig_clusters=NULL,
	oblig_missing=NULL,
	out=NULL,
	output_chr=NULL,
	output_missing_genotype=NULL,
	output_missing_phenotype=NULL,
	oxford_pheno_name=NULL,
	parallel=NULL,
	parameters=NULL,
	parentdt1=NULL,
	parentdt2=NULL,
	pat=NULL,
	pca=NULL,
	pca_cluster_names=NULL,
	pca_clusters=NULL,
	ped=NULL,
	pedigree=NULL,
	perm=NULL,
	perm_batch_size=NULL,
	perm_count=NULL,
	pfilter=NULL,
	pheno=NULL,
	pheno_merge=NULL,
	pheno_name=NULL,
	pick1=NULL,
	plist=NULL,
	poo=NULL,
	pool_size=NULL,
	ppc=NULL,
	ppc_gap=NULL,
	proxy_...=NULL,
	proxy_assoc=NULL,
	proxy_b_kb=NULL,
	proxy_b_maxsnp=NULL,
	proxy_b_r2=NULL,
	proxy_b_threshold=NULL,
	proxy_b_window=NULL,
	proxy_dosage=NULL,
	proxy_drop=NULL,
	proxy_flanking=NULL,
	proxy_geno=NULL,
	proxy_genotypic_concordance=NULL,
	proxy_glm=NULL,
	proxy_impute=NULL,
	proxy_impute_threshold=NULL,
	proxy_kb=NULL,
	proxy_list=NULL,
	proxy_maf=NULL,
	proxy_maxsnp=NULL,
	proxy_mhf=NULL,
	proxy_r2=NULL,
	proxy_r2_no_filter=NULL,
	proxy_replace=NULL,
	proxy_show_proxies=NULL,
	proxy_sub_maxsnp=NULL,
	proxy_sub_r2=NULL,
	proxy_tdt=NULL,
	proxy_verbose=NULL,
	proxy_window=NULL,
	prune=NULL,
	q_score_file=NULL,
	q_score_range=NULL,
	qfam...=NULL,
	qmatch=NULL,
	qq_plot=NULL,
	qt=NULL,
	qt_means=NULL,
	qual_geno_...=NULL,
	qual_geno_max_threshold=NULL,
	qual_geno_scores=NULL,
	qual_geno_threshold=NULL,
	qual_max_threshold=NULL,
	qual_scores=NULL,
	qual_threshold=NULL,
	r2=NULL,
	r=NULL,
	range=NULL,
	rank=NULL,
	read_dists=NULL,
	read_freq=NULL,
	read_genome=NULL,
	read_genome_list=NULL,
	read_genome_minimal=NULL,
	recessive=NULL,
	recode12=NULL,
	recode=NULL,
	recodeA=NULL,
	recodeAD=NULL,
	recodeHV=NULL,
	recode_allele=NULL,
	recode_beagle=NULL,
	recode_bimbam=NULL,
	recode_fastphase=NULL,
	recode_lgen=NULL,
	recode_rlist=NULL,
	recode_structure=NULL,
	recode_vcf=NULL,
	recode_whap=NULL,
	reference=NULL,
	reference_allele=NULL,
	regress_distance=NULL,
	regress_pcs=NULL,
	regress_rel=NULL,
	rel_check=NULL,
	rel_cutoff=NULL,
	remove=NULL,
	remove_cluster_names=NULL,
	remove_clusters=NULL,
	remove_fam=NULL,
	rerun=NULL,
	rice=NULL,
	sample=NULL,
	score=NULL,
	score_no_mean_imputation=NULL,
	script=NULL,
	seed=NULL,
	set=NULL,
	set_by_all=NULL,
	set_collapse_all=NULL,
	set_hh_missing=NULL,
	set_max=NULL,
	set_me_missing=NULL,
	set_missing_nonsnp_ids=NULL,
	set_missing_snp_ids=NULL,
	set_missing_var_ids=NULL,
	set_names=NULL,
	set_p=NULL,
	set_r2=NULL,
	set_r2_phase=NULL,
	set_table=NULL,
	set_test=NULL,
	sex=NULL,
	sheep=NULL,
	show_tags=NULL,
	silent=NULL,
	simulate=NULL,
	simulate_haps=NULL,
	simulate_label=NULL,
	simulate_missing=NULL,
	simulate_n=NULL,
	simulate_ncases=NULL,
	simulate_ncontrols=NULL,
	simulate_prevalence=NULL,
	simulate_qt=NULL,
	simulate_tags=NULL,
	snp=NULL,
	snps=NULL,
	snps_only=NULL,
	specific_haplotype=NULL,
	split_x=NULL,
	standard_beta=NULL,
	subset=NULL,
	swap_parents=NULL,
	swap_sibs=NULL,
	swap_unrel=NULL,
	tab=NULL,
	tag_kb=NULL,
	tag_mode2=NULL,
	tag_r2=NULL,
	tail_pheno=NULL,
	tdt=NULL,
	test_all=NULL,
	test_mishap=NULL,
	test_missing=NULL,
	test_snp=NULL,
	tests=NULL,
	tfam=NULL,
	tfile=NULL,
	thin=NULL,
	thin_count=NULL,
	threads=NULL,
	to=NULL,
	to_bp=NULL,
	to_kb=NULL,
	to_mb=NULL,
	tped=NULL,
	transpose=NULL,
	trend=NULL,
	tucc=NULL,
	twolocus=NULL,
	unbounded=NULL,
	unrelated_heritability=NULL,
	update_alleles=NULL,
	update_chr=NULL,
	update_cm=NULL,
	update_ids=NULL,
	update_map=NULL,
	update_name=NULL,
	update_parents=NULL,
	update_sex=NULL,
	vcf=NULL,
	vcf_filter=NULL,
	vcf_half_call=NULL,
	vcf_idspace_to=NULL,
	vcf_min_qual=NULL,
	vegas=NULL,
	version=NULL,
	vif=NULL,
	whap=NULL,
	window=NULL,
	with_freqs=NULL,
	with_phenotype=NULL,
	with_reference=NULL,
	within=NULL,
	write_cluster=NULL,
	write_covar=NULL,
	write_dosage=NULL,
	write_set=NULL,
	write_set_r2=NULL,
	write_snplist=NULL,
	xchr_model=NULL,
	zero_cluster=NULL,
	zero_cms=NULL,
	one = NULL,
	twothreefile = NULL,
	stdout="",
	stderr="",
	wait=TRUE
	
) {
	paramList = mget(names(formals()),sys.frame(sys.nframe()))
	# Should I wait for the process to finish?
	wait = paramList$wait
	paramList$wait = NULL

	# stdout and stderr settings, default is to the R console
	stdout = paramList$stdout
	paramList$stdout = NULL
	stderr = paramList$stderr
	paramList$stderr = NULL
	
	paramVector = unlist(paramList)
	paramVector = paramVector[!is.null(paramVector)]
	paramVector = str_trim(paramVector)
	
	
	paramName = names(paramVector)
	names(paramVector) = NULL
	paramName = gsub("_", "-", paramName)
	paramName = paste("--", paramName, sep="")
	
	
	if("--one" %in% paramName) {
		idx = which(paramName == "--one")
		paramName[idx] = "--1"
	}
	if("--twothreefile" %in% paramName) {
		idx = which(paramName == "--twothreefile")
		paramName[idx] = "--23file"
	}


	
	nParam = length(paramName)
	idxOdd = seq(1, nParam * 2, 2)
	idxEven = seq(2, nParam * 2, 2)
	paramNameWithValue = character(nParam * 2)
	paramNameWithValue[idxOdd] = paramName
	paramNameWithValue[idxEven] = paramVector
	
	ret = system2('plink', paramNameWithValue, wait=wait, stdout=stdout, stderr=stderr)
    if(ret != 0) {
        stop("PLINK failed.")
    }
}