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parse.cpp
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parse.cpp
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <string>
#include <cmath>
#include <cstdlib>
#include "options.h"
#include "helper.h"
#include "stats.h"
#include "nlist.h"
void getOutputFilename(CArgs & a)
{
////////////////////////////////////////
// Insert commands from a file
if (a.find("--script"))
{
string f = a.value("--script");
a.fromScript(f);
}
if (a.find("--rerun"))
{
string f = a.value("--rerun");
a.fromPriorLog(f);
}
////////////////////////////////////////////////////
// Start processing commands
if (a.find("--out"))
{
par::output_file_name = a.value("--out");
}
if (a.find("--gplink"))
{
if ( par::cli )
error("Cannot specify --gplink and --interactive");
par::silent = true;
par::gplink = true;
}
if (a.find("--silent"))
{
if ( par::cli )
error("Cannot specify --silent and --interactive");
par::silent = true;
}
if (a.find("--interactive"))
{
if ( a.find("--script") )
error("Cannot specify --script and --interactive");
par::cli = true;
}
}
void setOptions(CArgs & a)
{
/////////////////////////////////////
// Web-based functions
if (a.find("--noweb")) par::web_check = false;
if (a.find("--lookup"))
{
par::lookup = true;
par::lookup_single_snp = true;
par::lookup_snp = a.value("--lookup");
}
if (a.find("--lookup-list"))
{
par::lookup = true;
par::lookup_to_file = true;
par::lookup_single_snp = false;
par::lookup_snp = a.value("--lookup-list");
}
if (a.find("--lookup-save"))
par::lookup_to_file = true;
if (a.find("--lookup-gene"))
{
par::lookup = true;
par::lookup_to_file = true;
par::lookup_gene = true;
par::lookup_gene_name = a.value("--lookup-gene");
}
if (a.find("--lookup-gene-list"))
{
par::lookup = true;
par::lookup_to_file = true;
par::lookup_multiple_genes = true;
par::lookup_gene = true;
par::lookup_gene_name = a.value("--lookup-gene-list");
}
if (a.find("--lookup-gene-kb"))
{
par::lookup_gene_kb_window = a.value_int("--lookup-gene-kb");
}
if (a.find("--lookup-kb"))
{
par::lookup_snp_kb_window = a.value_int("--lookup-kb");
}
if (a.find("--lookup2"))
{
par::lookup2 = true;
par::lookup2_cmd = a.value("--lookup2");
}
if (a.find("--lookup-gene2"))
{
par::lookup2 = true;
par::lookup_gene = true;
par::lookup2_cmd = a.value("--lookup-gene2");
}
if (a.find("--id-dict"))
{
par::idhelp = true;
par::idhelp_dictionary = a.value("--id-dict");
if ( a.find("--id-auto-alias") )
par::idhelp_auto_alias = true;
// Just print each exact line matching field=value
if ( a.find("--id-dump") )
{
par::idhelp_dump_from_dict = true;
par::idhelp_dump_from_dict_cmd = a.value("--id-dump");
}
// Default is to dump whole table
if ( a.find("--id-table"))
{
par::idhelp_subset = "dump_subtable";
par::idhelp_subset_string = a.value("--id-table");
}
if ( a.find("--id-lookup"))
{
par::idhelp_lookup = true;
par::idhelp_lookup_string = a.value("--id-lookup");
}
if ( a.find("--id-replace"))
{
par::idhelp_replace = true;
vector<string> s = a.value("--id-replace",3);
par::idhelp_replace_string = s[0] + "," + "," + s[1] + "," + s[2];
}
if ( a.find("--id-match"))
{
if ( a.find("--id-replace"))
error("You cannot ID match and ID replace together");
par::idhelp_match = true;
par::idhelp_match_string = a.varValue("--id-match");
}
if (a.find("--id-delimit"))
{
par::idhelp_output_delimit = a.value("--id-delimit");
if ( par::idhelp_output_delimit == "tab" )
par::idhelp_output_delimit = "\t";
if ( par::idhelp_output_delimit == "bar" )
par::idhelp_output_delimit = "|";
if ( par::idhelp_output_delimit == "semi-colon" )
par::idhelp_output_delimit = ";";
if ( par::idhelp_output_delimit == "comma" )
par::idhelp_output_delimit = ",";
if ( par::idhelp_output_delimit == "space" )
par::idhelp_output_delimit = " ";
}
if ( a.find("--id-alias"))
par::idhelp_list_aliases = true;
if ( par::idhelp_match && par::idhelp_replace )
error("Cannot specify --id-replace and --id-match together");
if ( par::idhelp_replace && par::idhelp_lookup )
error("Cannot specify --id-replace and --id-lookup together");
if ( par::idhelp_replace && par::idhelp_subset )
error("Cannot specify --id-replace and --id-table together");
if ( par::idhelp_match && par::idhelp_lookup )
error("Cannot specify --id-match and --id-lookup together");
}
if ( a.find("--id-match") && !a.find("--id-dict") )
{
par::idhelp = true;
par::idhelp_match = true;
par::idhelp_no_dict = true;
par::idhelp_match_string = a.varValue("--id-match");
}
if (a.find("--R"))
{
par::run_R_script = true;
par::R_script = a.value("--R");
}
if (a.find("--R-port"))
par::R_port = a.value_int("--R-port");
if (a.find("--R-debug"))
par::run_R_write_script = true;
if (a.find("--R-chisq"))
par::run_R_chisq = true;
if (a.find("--R-z"))
par::run_R_z = true;
if (a.find("--R-nsnps"))
par::run_R_nsnps = a.value_int("--R-nsnps");
if (a.find("--seed"))
par::random_seed = a.value_lui("--seed");
////////////////////////////////////////
// A data-generation option?
bool makedata = false;
if (a.find("--recode"))
{
makedata = true;
par::recode = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode12"))
{
makedata = true;
par::recode_12 = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recodeHV"))
{
makedata = true;
par::recode_HV = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-lgen"))
{
makedata = true;
par::recode_long = true;
if (a.find("--with-reference"))
par::recode_long_ref = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-rlist"))
{
makedata = true;
par::recode_mutlist = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-whap"))
{
makedata = true;
par::recode_whap = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-fastphase"))
{
makedata = true;
par::recode_fastphase = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-structure"))
{
makedata = true;
par::recode_structure = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-bimbam"))
{
makedata = true;
par::recode_bimbam = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recodeAD"))
{
makedata = true;
par::recode_AD = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recodeA"))
{
makedata = true;
par::recode_AD = true;
par::recode_AD_Aonly = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
if (a.find("--recode-allele"))
{
if ( ! par::recode_AD )
error("You need to specify --recodeA or --recodeAD also");
par::recode_allele_coding = true;
par::recode_allele_coding_file = a.value("--recode-allele");
}
if (a.find("--make-bed"))
{
makedata = true;
par::write_bitfile = true;
// and unless otherwise specified, set GENO = 1 and MAF = 0
if (!a.find("--maf")) par::min_af = 0.0;
if (!a.find("--geno")) par::MAX_GENO_MISSING = 1;
if (!a.find("--mind")) par::MAX_IND_MISSING = 1;
}
//////////////////////////////////////////////
// Modifiers of main data generation commands
if (a.find("--alleleACGT") || a.find("--allele-ACGT")) par::recode_ACGT = true;
if (a.find("--allele1234") || a.find("--allele-1234")) par::recode_1234 = true;
if (a.find("--reference-allele"))
{
par::set_reference_allele = true;
par::set_reference_allele_file = a.value("--reference-allele");
par::make_minor_allele = false;
}
if (a.find("--transpose"))
{
if ( ! ( a.find("--recode") || a.find("--recode12") ) )
error("--transpose requires --recode or --recode12");
par::recode_transpose = true;
}
if (a.find("--tab"))
{
if ( ! makedata )
error("You can only specify --tab with a --recode* option");
par::recode_delimit = "\t";
}
////////////////////////////////////////////////////
// Convenience functions and obligatory missingness
// Zero out genotypes for a particular SNP / cluster
if ( a.find("--zero-cluster") )
{
if ( ! a.find("--within") )
error("You must specify --within with --zero-cluster");
par::zero_cluster = true;
par::zero_cluster_filename = a.value("--zero-cluster");
checkFileExists(par::zero_cluster_filename);
}
// Perform genotyping rate calculations, but allow for
// obligatory missingness
if ( a.find("--oblig-missing") )
{
if ( ! a.find("--oblig-clusters") )
error("You must specify --oblig-clusters with --oblig-missing");
par::oblig_missing = true;
par::oblig_missing_filename = a.value("--oblig-missing");
checkFileExists(par::oblig_missing_filename);
}
if ( a.find("--oblig-clusters") )
{
if ( ! a.find("--oblig-missing") )
error("You must specify --oblig-missing with --oblig-clusters");
par::oblig_clusters_filename = a.value("--oblig-clusters");
checkFileExists(par::oblig_clusters_filename );
}
// Multiple category phenotype
if ( a.find("--loop-assoc") )
{
if ( a.find("--within") )
error("You cannot specify --within with --loop-assoc");
par::all_pheno = true;
par::assoc_test = true;
par::loop_over = true;
par::include_cluster_from_file = true;
par::include_cluster_filename = a.value("--loop-assoc");
checkFileExists(par::include_cluster_filename);
}
////////////////////////////////////////
// TODO list
if (a.find("--todo"))
{
cout << "TODO list\n"
<< " * Make --min/--max thresholds apply w/ read-segment\n"
<< " * Odds ratio for DFAM\n"
<< " * Check Hotelling's T2 imputation of missing genotypes\n"
<< " * Add improved familial phasing to haplotype tests\n"
<< " * Add OR and CI to haplotype tests\n"
<< " * Add CMH and/or permutation to haplotype tests\n"
<< " \n";
exit(0);
}
///////////////////////////////////////
// Output options
if (a.find("--flag")) par::flag = true;
if (a.find("--verbose")) par::verbose = true;
if (a.find("--pedigree")) par::dumpped = true;
if (a.find("--tucc")) par::tucc = true;
if (a.find("--debug")) par::debug = true;
///////////////////////////////////////
// IBD analyses, output options
if (a.find("--multi")) par::multi_output = true;
if (a.find("--gmulti")) par::gmulti_output = true;
if (a.find("--summarise-ibd")) par::summary_ibd_output = true;
if (a.find("--genome") ||
a.find("--Z-genome") ||
a.find("--genome-minimal") )
{
// By default, include everybody
if (!a.find("--min"))
{
par::MIN_PIHAT = 0;
par::pihat_filter = false;
}
par::genome_output = true;
if (a.find("--Z-genome"))
par::compress_genome = true;
if (a.find("--genome-minimal"))
par::genome_output_minimal = true;
else if (a.find("--genome-full"))
par::genome_output_full = true;
}
if (a.find("--rel-check"))
par::genome_only_check_rels = true;
if (a.find("--impossible"))
{
if (!a.find("--genome"))
error("Can only specify --impossible with --genome");
par::show_impossible_IBD = false;
}
if (a.find("--nudge"))
{
if (!a.find("--genome"))
error("Can only specify --nudge with --genome");
if (a.find("--impossible"))
error("Cannot specify --impossible and --nudge together");
par::nudge = true;
}
if (a.find("--unbounded"))
{
par::bound = false;
par::MIN_PIHAT = -1;
par::MAX_PIHAT = 1;
}
if (a.find("--genome-lists"))
{
if ( ! ( a.find("--genome") || a.find("--segment") ) )
error("Must specify --genome or --segment with --genome-lists");
par::genome_2sets = true;
vector<string> s = a.value("--genome-lists",2);
par::genome_setlist1 = s[0];
par::genome_setlist2 = s[1];
}
if (a.find("--segment-within"))
{
if ( !a.find("--within"))
error("You need to specify a --within {clusterfile}");
par::IBD_within = true;
}
if (a.find("--genome-test"))
{
par::genome_test = true;
par::genome_test_threshold = a.value_double("--genome-test");
par::plink = true;
par::permute = true;
par::adaptive_perm = false;
par::replicates = 100000;
}
if (a.find("--ibs-test"))
{
par::ibs_test = true;
par::permute = true;
par::adaptive_perm = false;
par::replicates = 100000;
}
if (a.find("--ibs-test2"))
{
par::ibs_test = true;
par::ibs_test_method2 = true;
par::permute = true;
par::adaptive_perm = false;
par::replicates = 100000;
}
if (a.find("--segment-match-snp"))
par::genome_test_min_snp = a.value_int("--segment-match-snp");
///////////////////////////////////////////
// WGAS main options: summary stats and QC
if (a.find("--missing")) { par::report_missing = true; }
if (a.find("--mendel")) { par::MENDEL_report = true; }
if (a.find("--hardy")) par::HWD_report = true;
if (a.find("--hardy2")) par::HWD_report = par::HWD_standard = true;
if (a.find("--het")) par::inbreeding = true;
if (a.find("--Fst") || a.find("--fst"))
{
if ( ! a.find("--within") )
error("Need to specify --within with --Fst");
par::calcFst = true;
}
if (a.find("--check-sex"))
par::check_sex = true;
if (a.find("--impute-sex"))
par::check_sex = par::impute_sex = true;
if (a.find("--test-missing")) { par::test_missing = true; }
if (a.find("--test-mishap")) { par::mishap_test = true; }
if (a.find("--mishap-window"))
{
par::mishap_test = true;
par::mishap_window = a.value_int("--mishap-window");
}
if (a.find("--score"))
{
par::score_risk = true;
par::score_risk_file = a.value("--score");
if (a.find("--score-no-mean-imputation"))
par::score_impute_expected = false;
if (a.find("--score-ranges"))
{
par::score_risk_ranges = true;
par::score_risk_ranges_file = a.value("--score-ranges");
}
if (a.find("--score-ranges-min"))
par::score_risk_ranges_min = a.value_int("--score-ranges-min");
if (a.find("--score-ranges-border"))
par::make_set_border = a.value_int("--score-ranges-border") * 1000;
if (a.find("--q-score-file"))
{
if ( ! a.find("--q-score-range") )
error("Must specify --q-score-range with --q-score-file");
par::score_risk_on_qrange = true;
par::score_qrange_file = a.value("--q-score-range");
par::score_qfile = a.value("--q-score-file");
}
if ( a.find("--score-test") )
{
par::score_test = true;
}
if ( a.find("--set") || a.find("--make-set") )
par::profile_sets = true;
}
////////////////////////////////////////////////////////////////
// Proxy association methods
if (a.find("--proxy-assoc"))
{
par::proxy_assoc = true;
par::proxy_CC = true;
par::proxy_assoc_snp = a.value("--proxy-assoc");
if ( par::proxy_assoc_snp == "all" || par::proxy_assoc_snp == "ALL" )
par::proxy_all = true;
if ( a.find("--proxy-glm") )
par::proxy_glm = true;
}
if (a.find("--proxy-drop"))
{
if ( a.find("--proxy-impute"))
error("Cannot have --proxy-drop and --proxy-impute (already implied)");
par::proxy_leave_out = true;
}
if (a.find("--proxy-exclude"))
{
par::proxy_exclude = true;
par::proxy_exclude_from_file = false;
par::proxy_exclude_list = a.value("--proxy-exclude");
}
else if (a.find("--proxy-exclude-list"))
{
par::proxy_exclude = true;
par::proxy_exclude_from_file = true;
par::proxy_exclude_list = a.value("--proxy-exclude-list");
}
if (a.find("--proxy-include-reference"))
par::proxy_include_reference = true;
if (a.find("--proxy-impute"))
{
par::proxy_assoc = true;
par::proxy_impute = true;
par::proxy_assoc_snp = a.value("--proxy-impute");
if ( par::proxy_assoc_snp == "all" || par::proxy_assoc_snp == "ALL" )
par::proxy_all = true;
if ( a.find("--proxy-dosage") )
par::proxy_record_dosage = true;
if ( a.find("--proxy-replace") )
par::proxy_impute_replace = true;
// if ( a.find("--proxy-preserve") )
// par::proxy_impute_preserve_genotyped = true;
if ( a.find("--proxy-genotypic-concordance") )
par::proxy_impute_genotypic_concordance = true;
}
if (a.find("--proxy-error")) par::proxy_error = true;
if (a.find("--proxy-impute-threshold"))
par::proxy_impute_threshold = a.value_double("--proxy-impute-threshold");
if (a.find("--proxy-tdt"))
{
if (a.find("--hap-tdt"))
error("Cannot specify --proxy-tdt and --hap together");
par::proxy_assoc = true;
par::proxy_TDT = true;
par::proxy_assoc_snp = a.value("--proxy-tdt");
if ( par::proxy_assoc_snp == "all" || par::proxy_assoc_snp == "ALL" )
par::proxy_all = true;
}
if ( par::proxy_assoc )
{
// Reset default missing rate per individual
// per haplotype (more relevant if the window
// size is small (i.e. to goal is not to discard
// too many / any individuals, but rely on E-M
// phasing to reconstruct missing genotypes. Normally
// the default value here is 0.5; it can be modified as
// --hap-miss option is below this one
par::hap_missing_geno = 0.9;
}
if (a.find("--proxy-verbose"))
par::proxy_full_report = true;
if (a.find("--proxy-flanking"))
{
if ( par::proxy_all )
error("Cannt specify --proxy-flanking with >1 reference SNP");
par::proxy_list = true;
par::proxy_list_file = a.value("--proxy-flanking");
}
if (a.find("--proxy-list"))
{
if ( a.find("--proxy-flanking"))
error("Cannt specify --proxy-flanking with >1 reference SNP");
par::proxy_all_list = true;
par::proxy_all_list_file = a.value("--proxy-list");
}
if (a.find("--proxy-sub-r2"))
par::proxy_r2 = a.value_double("--proxy-sub-r2");
if (a.find("--proxy-maf"))
par::proxy_maf = a.value_double("--proxy-maf");
if (a.find("--proxy-geno"))
par::proxy_geno = a.value_double("--proxy-geno");
if (a.find("--proxy-mhf"))
par::proxy_mhf = a.value_double("--proxy-mhf");
if (a.find("--proxy-sub-maxsnp"))
par::proxy_maxhap = a.value_int("--proxy-sub-maxsnp");
if (a.find("--proxy-no-r2-filter"))
par::proxy_r2_filter = false;
if (a.find("--proxy-show-proxies"))
par::proxy_list_proxies = true;
if (a.find("--proxy-r2-reference-only"))
par::proxy_reference_only = true;
//////////////////////////////////////
// Frequency dependent proxy filters
// Plans A and B
if (a.find("--proxy-r2"))
{
par::proxy_r2_filter = true;
vector<string> s = a.value("--proxy-r2",3);
par::proxy_r2_filter_A_planA = getDouble(s[0], "--proxy-r2");
par::proxy_r2_filter_B_planA = getDouble(s[1], "--proxy-r2");
par::proxy_r2_filter_C_planA = getDouble(s[2], "--proxy-r2");
}
if (a.find("--proxy-maxsnp"))
par::proxy_snp_filter_planA = a.value_int("--proxy-maxsnp");
if (a.find("--proxy-window"))
par::proxy_window_planA = a.value_int("--proxy-window");
if (a.find("--proxy-kb"))
par::proxy_kb_planA = a.value_double("--proxy-kb");
// And plan B
if (a.find("--proxy-b-threshold"))
par::proxy_planB_threshold = a.value_double("--proxy-b-threshold");
if (a.find("--proxy-b-r2"))
{
par::proxy_r2_filter = true;
vector<string> s = a.value("--proxy-b-r2",3);
par::proxy_r2_filter_A_planB = getDouble(s[0], "--proxy-b-r2");
par::proxy_r2_filter_B_planB = getDouble(s[1], "--proxy-b-r2");
par::proxy_r2_filter_C_planB = getDouble(s[2], "--proxy-b-r2");
}
if (a.find("--proxy-b-maxsnp"))
par::proxy_snp_filter_planB = a.value_int("--proxy-b-maxsnp");
if (a.find("--proxy-b-window"))
par::proxy_window_planB = a.value_int("--proxy-b-window");
if (a.find("--proxy-b-kb"))
par::proxy_kb_planB = a.value_double("--proxy-b-kb");
////////////////////////////////////////
// Segmental options
// --segment-match-snp
// --homozyg
// --homozyg-window-kb
// --homozyg-window-snp
// --homozyg-window-het
// --homozyg-window-missing
// --homozyg-snp
// --homozyg-kb
// --homozyg-density
// --homozyg-gap
// --homozyg-group
// --homozyg-match
// --homozyg-het
// --homozyg-verbose
// --segment
// --segment-gap
// --segment-length
// --segment-thresholds
// --segment-minimal
// --segment-group
// --segment-spanning
// --segment-from
// --segment-to
// --segment-force
// --segment-match
// --segment-verbose
// --pool-size
// Read segments back in
// --read-segment
// --read-segment-minimal
//////////////////////////
// CNV/other segment types
if (a.find("--cnv-list"))
{
par::cnv_list = true;
par::cnv_listname = a.value("--cnv-list");
}
if (a.find("--cfile"))
{
if ( a.find("--cnv-list"))
error("Cannot specify --cfile and --cnv-list together");
if ( a.find("--fam"))
error("Cannot specify --cfile and --fam together");
if ( a.find("--map"))
error("Cannot specify --cfile and --map together");
par::cnv_list = true;
par::fileroot = a.value("--cfile");
par::cnv_listname = par::fileroot + ".cnv";
par::famfile = par::fileroot + ".fam";
par::mapfile = par::fileroot + ".cnv.map";
}
if ( par::cnv_list )
{
// Remove any missing individuals
if (!a.find("--cnv-missing-phenotypes"))
par::ignore_phenotypes = false;
if (a.find("--cnv-make-map"))
par::cnv_makemap = true;
if (a.find("--cnv-write"))
{
par::cnv_writelist = true;
if (a.find("--with-phenotype"))
par::dump_covar_with_phenotype = true;
}
if ( a.find("--cnv-disrupt" ) )
{
if (a.find("--cnv-overlap") || a.find("--cnv-union-overlap") || a.find("--cnv-region-overlap"))
error("Cannot specify --cnv-overlap and --cnv-disrupt together");
par::cnv_disrupt = true;
}
if (a.find("--cnv-intersect"))
{
if ( a.find("--cnv-exclude") ||
a.find("--cnv-count") )
error("Cannot specify --cnv-count/intersect/exclude/disrupt together");
par::cnv_intersect = true;
par::cnv_intersect_file = a.value("--cnv-intersect");
}
if (a.find("--cnv-subset"))
{
if ( ! ( a.find("--cnv-exclude") ||
a.find("--cnv-count") ||
a.find("--cnv-intersect")) )
error("Must use --cnv-intersect/exclude/count with --cnv-subset");
par::cnv_intersect_subset = true;
par::cnv_intersect_subset_file = a.value("--cnv-subset");
}
if (a.find("--cnv-check-no-overlap"))
par::cnv_check_overlap = true;