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cnvnator.cpp
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cnvnator.cpp
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// C/C++ includes
#include <iostream>
#include <fstream>
#include <string>
#ifdef USE_YEPPP
#include <yepMath.h>
#include <yepLibrary.h>
#endif
using namespace std;
// Application includes
#include "AliParser.hh"
#include "HisMaker.hh"
#include "EXOnator.hh"
#include "IO.hh"
#include "Visualizer.hh"
int main(int argc,char *argv[])
{
string usage = "\nCNVnator ";
#ifdef CNVNATOR_VERSION
usage += CNVNATOR_VERSION;
#else
usage += "v???";
#endif
usage += "\n\nUsage:\n";
usage += argv[0];
usage += " -root out.root [-genome name] [-chrom 1 2 ...] -tree file1.bam ... [-lite]\n";
usage += argv[0];
usage += " -root out.root [-genome name] [-chrom 1 2 ...] -merge file1.root ...\n";
usage += argv[0];
usage += " -root file.root [-genome name] [-chrom 1 2 ...] -vcf [file.vcf.gz | file.vcf] [-rmchr] [-addchr]\n";
usage += argv[0];
usage += " -root file.root [-genome name] [-chrom 1 2 ...] -idvar [file.vcf.gz | file.vcf] [-rmchr] [-addchr]\n";
usage += argv[0];
usage += " -root file.root [-genome name] [-chrom 1 2 ...] -mask strict.mask.file.fa.gz [-rmchr] [-addchr]\n";
usage += argv[0];
usage += " -root file.root [-genome name] [-chrom 1 2 ...] [-d dir | -fasta file.fa.gz] -his bin_size\n";
usage += argv[0];
usage += " -root file.root [-genome name] [-chrom 1 2 ...] -baf bin_size [-hap] [-useid] [-nomask]\n";
usage += argv[0];
usage += " -root file.root [-chrom 1 2 ...] -stat bin_size\n";
usage += argv[0];
usage += " -root file.root -eval bin_size\n";
usage += argv[0];
usage += " -root file.root [-chrom 1 2 ...] -partition bin_size [-ngc]\n";
// usage += argv[0];
//usage += " -root file.root [-chrom 1 2 ...] -spartition bin_size [-gc]\n";
usage += argv[0];
usage += " -root file.root [-chrom 1 2 ...] -call bin_size [-ngc]\n";
usage += argv[0];
usage += " -root file.root -genotype bin_size [-ngc]\n";
usage += argv[0];
usage += " -root file.root -view bin_size [-ngc]\n";
usage += argv[0];
usage += " -pe file1.bam ... -qual val(20) -over val(0.8) [-f file]\n";
usage += argv[0];
usage += "-root file.root [-chrom 1 2 ...] -cptrees newfile.root\n";
usage += argv[0];
usage += "-root file.root -ls\n";
usage += "\n";
usage += "Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19, mm9, hg38, GRCh38\n";
if (argc < 2) {
cerr<<"Not enough parameters."<<endl;
cerr<<usage<<endl;
return 0;
}
#ifdef USE_YEPPP
YepStatus yepStatus = yepLibrary_Init();
if (yepStatus != YepStatusOk) {
cerr<<"Yeppp library initialization failed with status "<<yepStatus<<"."<<endl;
return 1;
}
#endif
static const int OPT_TREE = 0x00001;
static const int OPT_MERGE = 0x00002;
static const int OPT_HIS = 0x00004;
static const int OPT_HISMERGE = 0x00008;
static const int OPT_STAT = 0x00010;
static const int OPT_PARTITION = 0x00020;
static const int OPT_EPARTITION = 0x00040;
static const int OPT_CALL = 0x00080;
static const int OPT_VIEW = 0x00100;
static const int OPT_VIEWER = 0x00101;
static const int OPT_GENOTYPE = 0x00200;
static const int OPT_EVAL = 0x00400;
static const int OPT_PE = 0x00800;
static const int OPT_PANEL = 0x01000;
static const int OPT_FIT = 0x02000;
static const int OPT_SPARTITION = 0x04000;
static const int OPT_PARTITION2D = 0x08000;
static const int OPT_HIS_NEW = 0x10000;
static const int OPT_AGGREGATE = 0x20000;
static const int OPT_VCF = 0x50001;
static const int OPT_IDVAR = 0x50002;
static const int OPT_MASK = 0x50003;
static const int OPT_BAF = 0x50004;
static const int OPT_CALLBAF = 0x50005;
static const int OPT_CPTREES = 0x60001;
static const int OPT_LS = 0x60002;
// tree, merge, his, stat, partition, spartition, call, view, genotype
int max_opts = 10000, n_opts = 0, opts[max_opts], bins[max_opts], gbin = 0;
for (int i = 0;i < n_opts;i++) bins[i] = 0;
bool useGCcorr = true,useATcorr = false;
bool lite = false,relaxCalling = false;
string out_root_file(""),call_file(""),group_name(""),fastafile("");
string chroms[1000],data_files[100000],root_files[100000] = {""},dir = ".";
int n_chroms = 0,n_files = 0,n_root_files = 0,range = 128, qual = 20;
double over = 0.8;
double deltaAF = 0.25;
Genome *genome = NULL;
// vcf, idvar, mask option -rmchr -addchr
bool rmchr=false,addchr=false;
// baf option -hap -useid -nomask
bool useHaplotype=false,useid=false,usemask=true;
string signal="";
string signal2="";
int index = 1;
while (index < argc) {
string option = argv[index++];
if (option == "-tree" || option == "-merge" || option == "-pe" || option == "-vcf" || option == "-idvar" || option == "-mask" || option == "-cptrees") {
if (option == "-tree") opts[n_opts++] = OPT_TREE;
if (option == "-merge") opts[n_opts++] = OPT_MERGE;
if (option == "-pe") opts[n_opts++] = OPT_PE;
if (option == "-vcf") opts[n_opts++] = OPT_VCF;
if (option == "-idvar") opts[n_opts++] = OPT_IDVAR;
if (option == "-mask") opts[n_opts++] = OPT_MASK;
if (option == "-cptrees") opts[n_opts++] = OPT_CPTREES;
while (index < argc && argv[index][0] != '-')
if (strlen(argv[index++]) > 0) data_files[n_files++] = argv[index - 1];
} else if (option == "-his" || option == "-his_new" ||
option == "-hismerge" ||
option == "-stat" || option == "-eval" ||
option == "-partition" || option == "-partition2D" ||
option == "-epartition" || option == "-spartition" ||
option == "-call" || option == "-view" || option == "-viewer" ||
option == "-genotype" || option == "-aggregate" ||
option == "-baf" || option == "-callbaf") {
int bs = 0;
if (index < argc && argv[index][0] != '-') {
TString tmp = argv[index++];
if (!tmp.IsDigit()) {
cerr<<"Bin size must be integer for option '"<<option<<"'."<<endl;
cerr<<usage<<endl;
return 0;
}
bs = tmp.Atoi();
}
if (option == "-his") opts[n_opts] = OPT_HIS;
if (option == "-hismerge") opts[n_opts] = OPT_HISMERGE;
if (option == "-stat") opts[n_opts] = OPT_STAT;
if (option == "-partition") opts[n_opts] = OPT_PARTITION;
if (option == "-partition2D") opts[n_opts] = OPT_PARTITION2D;
if (option == "-epartition") opts[n_opts] = OPT_EPARTITION;
if (option == "-spartition") opts[n_opts] = OPT_SPARTITION;
if (option == "-call") opts[n_opts] = OPT_CALL;
if (option == "-callbaf") opts[n_opts] = OPT_CALLBAF;
if (option == "-view") opts[n_opts] = OPT_VIEW;
if (option == "-viewer") opts[n_opts] = OPT_VIEWER;
if (option == "-genotype") opts[n_opts] = OPT_GENOTYPE;
if (option == "-his_new") opts[n_opts] = OPT_HIS_NEW;
if (option == "-eval") opts[n_opts] = OPT_EVAL;
if (option == "-aggregate") opts[n_opts] = OPT_AGGREGATE;
if (option == "-baf") opts[n_opts] = OPT_BAF;
bins[n_opts++] = bs;
} else if (option == "-ls") {
opts[n_opts++] = OPT_LS;
} else if (option == "-panel") {
opts[n_opts++] = OPT_PANEL;
} else if (option == "-fit") {
opts[n_opts++] = OPT_FIT;
if (index < argc && argv[index][0] != '-') group_name = argv[index++];
else {
cout<<"Please provide name of a sample group."<<endl;
return 0;
}
} else if (option == "-outroot") {
if (index < argc && argv[index][0] != '-') out_root_file = argv[index++];
else {
cout<<"Please provide new root-file name."<<endl;
return 0;
}
} else if (option == "-root") {
while (index < argc && argv[index][0] != '-')
if (strlen(argv[index++]) > 0)
root_files[n_root_files++] = argv[index - 1];
if (n_root_files == 0) {
cerr<<"Please provide root-file name."<<endl;
cerr<<usage<<endl;
return 0;
}
} else if (option == "-outroot") {
if (index < argc && argv[index][0] != '-') out_root_file = argv[index++];
else {
cout<<"Please provide new root-file name."<<endl;
return 0;
}
} else if (option == "-chrom") {
while (index < argc && argv[index][0] != '-')
chroms[n_chroms++] = argv[index++];
if (n_chroms == 0) {
cerr<<"Provide chromosome names."<<endl;
cerr<<usage<<endl;
return 0;
}
} else if (option == "-ngc") {
useGCcorr = false;
} else if (option == "-at") {
useATcorr = true;
} else if (option == "-genome") {
if (index < argc) genome = Genome::get(argv[index++]);
} else if (option == "-d") {
if (index < argc && argv[index][0] != '-')
dir = argv[index++];
else cerr<<"No directory is given."<<endl;
} else if (option == "-fasta") {
if (index < argc && argv[index][0] != '-')
fastafile = argv[index++];
else cerr<<"Fasta file is not given."<<endl;
}else if (option == "-qual") {
if (index >= argc || argv[index][0] == '-') {
cerr<<"No quality value is provided."<<endl;
cerr<<usage<<endl;
return 0;
}
TString tmp = argv[index++];
if (!tmp.IsDigit()) {
cerr<<"Quality value must be integer."<<endl;
cerr<<usage<<endl;
return 0;
}
qual = tmp.Atoi();
} else if (option == "-over") {
if (index >= argc || argv[index][0] == '-') {
cerr<<"No fraction of overlap is provided."<<endl;
cerr<<usage<<endl;
return 0;
}
TString tmp = argv[index++];
if (!tmp.IsFloat()) {
cerr<<"Fraction of overlap must be number."<<endl;
cerr<<usage<<endl;
return 0;
}
over = tmp.Atof();
} else if (option == "-f") {
if (index >= argc || argv[index][0] == '-') {
cerr<<"No file name is provided."<<endl;
cerr<<usage<<endl;
return 0;
}
call_file = argv[index++];
} else if (option == "-lite") {
lite = true;
} else if (option == "-rmchr") {
rmchr=true;
} else if (option == "-addchr") {
addchr=true;
} else if (option == "-useid") {
useid=true;
} else if (option == "-nomask") {
usemask=false;
} else if (option == "-hap") {
useHaplotype=true;
} else if (option == "-range") {
range = atoi(argv[index++]);
} else if (option == "-signal") {
while((index < argc) && argv[index][0] != '-') {
if(signal!="") signal+=" ";
signal += argv[index++];
}
} else if (option == "-signal2") {
while((index < argc) && argv[index][0] != '-') {
if(signal2!="") signal2+=" ";
signal2 += argv[index++];
}
} else if (option == "-relax") {
relaxCalling = true;
} else if (option == "-deltaAF") {
if (index >= argc || argv[index][0] == '-') {
cerr<<"No delta value is provided."<<endl;
cerr<<usage<<endl;
return 0;
}
TString tmp = argv[index++];
if (!tmp.IsFloat()) {
cerr<<"Quality value must be real number."<<endl;
cerr<<usage<<endl;
return 0;
}
deltaAF = tmp.Atof();
} else if (option[0] == '-') {
cerr<<"Unknown option '"<<option<<"'.\n"<<endl;
}
}
if (out_root_file.length() <= 0) out_root_file = root_files[0];
if (out_root_file.length() <= 0)
cerr<<"WARNING: no name of root-file provided."<<endl;
for (int o = 0;o < n_opts;o++) {
int option = opts[o];
int bin = bins[o]; if (bin <= 0) bin = gbin;
if (option == OPT_TREE) { // tree
HisMaker maker(out_root_file,genome);
maker.setDataDir(dir);
maker.produceTrees(chroms,n_chroms,data_files,n_files,lite);
}
if (option == OPT_VCF) { // vcf
HisMaker maker(out_root_file,genome);
maker.setDataDir(dir);
maker.addVcf(chroms,n_chroms,data_files,n_files,rmchr,addchr);
}
if (option == OPT_IDVAR) { // idvar
HisMaker maker(out_root_file,genome);
maker.setDataDir(dir);
maker.IdVar(chroms,n_chroms,data_files,n_files,rmchr,addchr);
}
if (option == OPT_MASK) { // mask
HisMaker maker(out_root_file,genome);
maker.setDataDir(dir);
maker.MaskVar(chroms,n_chroms,data_files,n_files,rmchr,addchr);
}
if (option == OPT_CPTREES) { // cptrees
IO io(out_root_file);
if(n_files==1) io.cptrees(data_files[0],chroms,n_chroms);
else cerr << "Provide one new root file name!" << endl;
}
if (option == OPT_MERGE) { // merge
HisMaker maker(out_root_file,genome);
maker.mergeTrees(chroms,n_chroms,data_files,n_files);
}
if (option == OPT_HIS ||
option == OPT_HISMERGE) { // his
HisMaker maker(out_root_file,bin,useGCcorr,genome);
if(fastafile!="") {
maker.setFastaFile(fastafile);
maker.produceHistogramsFa(chroms,n_chroms,root_files,n_root_files,false);
if (option == OPT_HISMERGE) maker.produceHistogramsFa(chroms,n_chroms,root_files,n_root_files,true);
} else {
maker.setDataDir(dir);
maker.produceHistograms(chroms,n_chroms,root_files,n_root_files,false);
if (option == OPT_HISMERGE) maker.produceHistograms(chroms,n_chroms,root_files,n_root_files,true);
}
}
if (option == OPT_BAF) { // baf
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.setDataDir(dir);
maker.produceBAF(chroms,n_chroms,useGCcorr,useHaplotype,useid,usemask);
}
if (option == OPT_STAT) { // stat
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.stat(chroms,n_chroms,useATcorr);
}
if (option == OPT_PARTITION) { // partition
unsigned int flag=(usemask?FLAG_USEMASK:0)|(useid?FLAG_USEID:0)|(useHaplotype?FLAG_USEHAP:0)|(useGCcorr?FLAG_GC_CORR:0);
HisMaker maker(out_root_file,bin,useGCcorr,genome);
if(signal=="") maker.partition(chroms,n_chroms,false,useATcorr,useGCcorr,false,range);
else maker.partitionSignal(bin,signal,flag,chroms,n_chroms,false,false,range);
}
if (option == OPT_PARTITION2D) { // partition
unsigned int flag=(usemask?FLAG_USEMASK:0)|(useid?FLAG_USEID:0)|(useHaplotype?FLAG_USEHAP:0)|(useGCcorr?FLAG_GC_CORR:0);
HisMaker maker(out_root_file,bin,useGCcorr,genome);
// maker.partition2D(chroms,n_chroms,false,useATcorr,useGCcorr,false,range);
if(signal!="" && signal2!="") maker.partitionSignal2D(bin,signal,signal2,flag,chroms,n_chroms,range);
else maker.partitionSignal2D(bin,"RD","SNP i1",flag,chroms,n_chroms,range);
}
if (option == OPT_EPARTITION) { // exome partition
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.partition(chroms,n_chroms,false,useATcorr,useGCcorr,true,range);
}
if (option == OPT_CALL) { // call
unsigned int flag=(usemask?FLAG_USEMASK:0)|(useid?FLAG_USEID:0)|(useHaplotype?FLAG_USEHAP:0)|(useGCcorr?FLAG_GC_CORR:0);
HisMaker maker(out_root_file,bin,useGCcorr,genome);
if(signal=="") maker.callSVs(chroms,n_chroms,useATcorr,useGCcorr,deltaAF);
else maker.callSVsSignal(bin,signal,flag,chroms,n_chroms,deltaAF);
}
if (option == OPT_CALLBAF) { // callbaf
unsigned int flag=(usemask?FLAG_USEMASK:0)|(useid?FLAG_USEID:0)|(useHaplotype?FLAG_USEHAP:0)|(useGCcorr?FLAG_GC_CORR:0);
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.callBAF(chroms,n_chroms,useGCcorr,useHaplotype,useid,usemask);
}
if (option == OPT_VIEW) { // view
HisMaker maker(out_root_file,bin,useGCcorr,genome);
TApplication theApp("App",0,0);
maker.view(root_files,n_root_files,useATcorr,useGCcorr);
theApp.Run();
}
if (option == OPT_VIEWER) { // viewer
unsigned int flags=(usemask?FLAG_USEMASK:0)|(useid?FLAG_USEID:0)|(useHaplotype?FLAG_USEHAP:0)|(useGCcorr?FLAG_GC_CORR:0);
Visualizer vis(root_files,n_root_files,bin,flags);
TApplication theApp("App",0,0);
vis.prompt();
theApp.Run();
}
if (option == OPT_GENOTYPE) { // genotype
HisMaker maker(out_root_file,bin,useGCcorr,genome);
TApplication theApp("App",0,0);
maker.genotype(root_files,n_root_files,useATcorr,useGCcorr);
theApp.Run();
}
if (option == OPT_EVAL) { // eval
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.eval(root_files,n_root_files,useATcorr,useGCcorr);
}
if (option == OPT_PE) { // pe
HisMaker maker("null",genome);
if (call_file.length() > 0)
maker.pe_for_file(call_file,data_files,n_files,over,qual);
else {
TApplication theApp("App",0,0);
maker.pe(data_files,n_files,over,qual);
theApp.Run();
}
}
if (option == OPT_SPARTITION) { // spartition
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.partition(chroms,n_chroms,true,useATcorr,useGCcorr,false,range);
}
if (option == OPT_HIS_NEW) { // his_new
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.setDataDir(dir);
maker.produceHistogramsNew(chroms,n_chroms);
}
// EXOnator options
if (option == OPT_PANEL) { // panel
EXOnator exonator(out_root_file);
exonator.makeTables();
}
if (option == OPT_FIT) { // fit
EXOnator exonator(out_root_file);
exonator.fit(group_name);
}
if (option == OPT_AGGREGATE) { // aggregate
HisMaker maker(out_root_file,bin,useGCcorr,genome);
maker.setDataDir(dir);
maker.aggregate(root_files,n_root_files,chroms,n_chroms);
}
if (option == OPT_LS) { // aggregate
IO io(out_root_file);
io.ls();
}
}
return 0;
}