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/*Copyright (C) 2015 Olivier Delaneau, Halit Ongen, Emmanouil T. Dermitzakis
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.*/
#include "mode_cis/cis_data.h"
#include "mode_trans/trans_data.h"
#include "mode_match/match_data.h"
#include "mode_fenrich/fenrich_data.h"
#include "mode_correct/correct_data.h"
#include "mode_rtc/rtc_data.h"
#include "mode_pca/pca_data.h"
#include "mode_genrich/genrich_data.h"
#include "mode_extract/extract_data.h"
#include "mode_ase/ase_data.h"
#include "mode_quan/quan_data.h"
#include "mode_union/union_data.h"
#include "mode_bamstat/bamstat_data.h"
#include "mode_fdensity/fdensity_data.h"
void printModes(){
vrb.ctitle("Usage:");
vrb.print(" QTLtools [mode] [options]");
vrb.print(" eg: QTLtools cis --help");
vrb.ctitle("Available modes:");
vrb.print(" bamstat Calculate basic QC metrics for BAM/SAM");
vrb.print(" mbv Match BAM to VCF ");
vrb.print(" pca Calculate principal components for a BED/VCF/BCF file");
vrb.print(" correct Covariate correction of a BED file");
vrb.print(" cis cis QTL analysis");
vrb.print(" trans trans QTL analysis");
vrb.print(" fenrich Functional enrichment for QTLs");
vrb.print(" fdensity Functional density around QTLs");
vrb.print(" genrich GWAS enrichment for QTLs");
vrb.print(" rtc Regulatory Trait Concordance analysis");
vrb.print(" rtc-union Find the union of QTLs");
vrb.print(" extract Data extraction mode");
vrb.print(" quan Quantification mode");
vrb.print(" ase Measure allelic imbalance at every het genotype");
}
int main(int argc, char ** argv) {
//1. Start timing
timer running_timer;
//2. Open LOG file if necessary
bool match_mode = false;
for (int a = 1 ; a < argc - 1 ; a ++) {
if ((strcmp(argv[a], "--log") == 0) && !vrb.open_log(string(argv[a+1]))) vrb.error("Impossible to open log file!");
if (strcmp(argv[a], "--silent") == 0) vrb.set_silent();
if (strcmp(argv[a], "mbv") == 0) match_mode = true;
}
//3. Print header on screen
vrb.ctitle("QTLtools");
vrb.bullet("Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS");
vrb.bullet("Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch");
vrb.bullet("Webpage : https://qtltools.github.io/qtltools/");
vrb.bullet("Version : " + string(QTLTOOLS_VERSION));
vrb.bullet("Date : " + running_timer.date());
if (!match_mode) vrb.bullet("Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1101/068635");
else vrb.bullet("Citation: MBV; a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay data sets");
//4. Switch mode
vector < string > args;
if (argc < 2){
printModes();
exit(EXIT_SUCCESS);
}
for (int a = 2 ; a < argc ; a ++) args.push_back(string(argv[a]));
//5.1. CIS mode
if (strcmp(argv[1], "cis") == 0) cis_main(args);
//5.2. TRANS mode
else if (strcmp(argv[1], "trans") == 0) trans_main(args);
//5.3. MATCH mode
else if (strcmp(argv[1], "mbv") == 0) match_main(args);
//5.4. FENRICH mode
else if (strcmp(argv[1], "fenrich") == 0) fenrich_main(args);
//5.5. GENRICH mode
else if (strcmp(argv[1], "genrich") == 0) genrich_main(args);
//5.6. CORRECT mode
else if (strcmp(argv[1], "correct") == 0) correct_main(args);
//5.7. RTC mode
else if (strcmp(argv[1], "rtc") == 0) rtc_main(args);
//5.8. PCA mode
else if (strcmp(argv[1], "pca") == 0) pca_main(args);
//5.9. EXTRACT mode
else if (strcmp(argv[1], "extract") == 0) extract_main(args);
//5.10. RTC-UNION mode
else if (strcmp(argv[1], "rtc-union") == 0) union_main(args);
//5.11. QUANTIFICATION mode
else if (strcmp(argv[1], "quan") == 0) quan_main(args);
//5.12. ASE mode
else if (strcmp(argv[1], "ase") == 0) ase_main(args);
//5.13. BAMSTAT mode
else if (strcmp(argv[1], "bamstat") == 0) bamstat_main(args);
//5.14. FDENSITY mode
else if (strcmp(argv[1], "fdensity") == 0) fdensity_main(args);
//5.15. UNRECOGNIZED mode
else if (strcmp(argv[1], "--help") == 0) {
printModes();
exit(EXIT_SUCCESS);
} else {
printModes();
vrb.error("Unrecognized QTLtools mode!");
}
//5. Terminate
vrb.title("Running time: " + stb.str(running_timer.abs_time()) + " seconds");
vrb.close_log();
}
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