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angsd.cpp
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angsd.cpp
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/*
copyright (gpl) 19 sep 2012.
Thorfinn Sand Korneliussen [email protected]
Anders albrechtsen [email protected]
use wiki for updated list of bugfixes and documentation
http://www.popgen.dk/angsd
*/
#include "version.h"
#include <cassert>
#include <iostream>//for printing time
#include <cstring> //for cstring functions
#include <cstdlib> //for exit()
#include <cstdio> //for fprintf
#include <signal.h>//for catching ctrl+c, allow threads to finish
#include <htslib/hts.h>
#include "cigstat.h"
#include "shared.h"
#include "multiReader.h"
extern std::vector <char *> dumpedFiles;
int SIG_COND =1;//if we catch signal then quit program nicely
int VERBOSE =1;
extern pthread_mutex_t mUpPile_mutex;//mutex for not deleting mUppile data untill end of data
void printTime(FILE *fp){
time_t rawtime;
struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
fprintf (fp, "\t-> %s", asctime (timeinfo) );
}
//this function is called from within the bamreader
void callBack_bambi(fcb *fff){
if(fff==NULL){
// fprintf(stderr,"SEnding NULL this is a killswitch");
selector(NULL);//<-send NULL which acts as a killswitch
}else{
funkyPars *fp = funkyPars_init();
fp->for_callback=fff;
fp->refId = fp->for_callback->refId;
selector(fp);
}
}
int really_kill =3;
void handler(int s) {
if(VERBOSE)
fprintf(stderr,"\n\t-> Caught SIGNAL: Will try to exit nicely (no more threads are created.\n\t\t\t We will wait for the current threads to finish)\n");
if(--really_kill!=3)
fprintf(stderr,"\n\t-> If you really want angsd to exit uncleanly ctrl+c: %d more times\n",really_kill+1);
fflush(stderr);
if(!really_kill)
exit(0);
VERBOSE=0;
SIG_COND=0;
pthread_mutex_unlock(&mUpPile_mutex);
}
//we are threading so we want make a nice signal handler for ctrl+c
void catchkill(){
struct sigaction sa;
sigemptyset (&sa.sa_mask);
sa.sa_flags = 0;
sa.sa_handler = handler;
sigaction(SIGPIPE, &sa, 0);
sigaction(SIGINT, &sa, 0);
}
//print nice info
void printProgInfo(FILE *fp){
fprintf(fp,"\n\t-> angsd version: %s (htslib: %s) build(%s %s)\n",ANGSD_VERSION,hts_version(),__DATE__,__TIME__);
fprintf(fp,"\t-> Please use the website \"http://www.popgen.dk/angsd\" as reference\n");
fprintf(fp,"\t-> Use -nThreads or -P for number of threads allocated to the program\n");
fprintf(fp,"Overview of methods:\n");
fprintf(fp,"\t-GL\t\tEstimate genotype likelihoods\n");
fprintf(fp,"\t-doCounts\tCalculate various counts statistics\n");
fprintf(fp,"\t-doAsso\t\tPerform association study\n");
fprintf(fp,"\t-doMaf\t\tEstimate allele frequencies\n");
fprintf(fp,"\t-doError\tEstimate the type specific error rates\n");
fprintf(fp,"\t-doAncError\tEstimate the errorrate based on perfect fastas\n");
fprintf(fp,"\t-HWE_pval\tEst inbreedning per site or use as filter\n");
fprintf(fp,"\t-doGeno\t\tCall genotypes\n");
fprintf(fp,"\t-doFasta\tGenerate a fasta for a BAM file\n");
fprintf(fp,"\t-doAbbababa\tPerform an ABBA-BABA test\n");
fprintf(fp,"\t-sites\t\tAnalyse specific sites (can force major/minor)\n");
fprintf(fp,"\t-doSaf\t\tEstimate the SFS and/or neutrality tests genotype calling\n");
fprintf(fp,"\t-doHetPlas\tEstimate hetplasmy by calculating a pooled haploid frequency\n");
fprintf(fp,"\n\tBelow are options that can be usefull\n");
fprintf(fp,"\t-bam\t\tOptions relating to bam reading\n\t-doMajorMinor\tInfer the major/minor using different approaches\n");
fprintf(fp,"\t-ref/-anc\tRead reference or ancestral genome\n");
fprintf(fp,"\t-doSNPstat\tCalculate various SNPstat\n");
fprintf(fp,"\t-cigstat\tPrintout CIGAR stat across readlength\n");
fprintf(fp,"\tmany others\n\n");
fprintf(fp,"Output files:\n\t In general the specific analysis outputs specific files, but we support basic bcf output\n");
fprintf(fp,"\t-doBcf\t\tWrapper around -dopost -domajorminor -dofreq -gl -dovcf docounts\n");
fprintf(fp,"For information of specific options type: \n\t./angsd METHODNAME eg \n\t\t./angsd -GL\n\t\t./angsd -doMaf\n\t\t./angsd -doAsso etc\n");
fprintf(fp,"\t\t./angsd sites for information about indexing -sites files\n");
fprintf(fp,"Examples:\n\tEstimate MAF for bam files in 'list'\n\t\t\'./angsd -bam list -GL 2 -doMaf 2 -out RES -doMajorMinor 1\'\n");
}
void parseArgStruct(argStruct *arguments){
//validate that there are no duplicate parameters
for(int i=0;i<arguments->argc;i++){
if(strcasecmp("-realSFS",arguments->argv[i])==0){
fprintf(stderr,"-realSFS is now called -doSaf\n");
exit(0);
}
if(strcasecmp("-minLRT",arguments->argv[i])==0){
fprintf(stderr,"-minLRT is now called -SNP_pval\n");
exit(0);
}
if(strcasecmp("-doSNP",arguments->argv[i])==0){
fprintf(stderr,"-doSNP is now called -SNP_pval\n");
exit(0);
}
if(strcasecmp("-soap",arguments->argv[i])==0){
fprintf(stderr,"-doHWE is deprecated, convert soap file to bam\n");
exit(0);
}
if(strcasecmp("-tglf",arguments->argv[i])==0){
fprintf(stderr,"-tglf is deprecated, merge files and use -glf\n");
exit(0);
}
if(strcasecmp("-sim1",arguments->argv[i])==0){
fprintf(stderr,"-sim1 is deprecated, use -glf filename and -isSim 1\n");
exit(0);
}
}
for(int i=0;i<arguments->argc-1;i++)
if(arguments->argv[i][0]=='-') {
for(int ii=i+1;ii<arguments->argc;ii++){
if(arguments->argv[ii][0]=='-'){
if(0==strcasecmp(arguments->argv[i],arguments->argv[ii])){
fprintf(stderr,"\t-> Duplicate parameter: %s supplied, will exit\n",arguments->argv[i]);
exit(0);
}
}
}
}
for(int i=1;i<arguments->argc;i++){
if(arguments->usedArgs[i]==0){
fprintf(stderr,"%d argument \t%s is unknown will exit\n",i,arguments->argv[i]);
fflush(stderr);
exit(0);
}
}
if(arguments->hd==NULL){
fprintf(stderr,"\t-> Error: You must supply a -fai file such that we know the sizes of the genomes (version .4486)\n");
exit(0);
}
}
int main(int argc, char** argv){
fprintf(stderr,"\t-> angsd version: %s (htslib: %s) build(%s %s)\n",ANGSD_VERSION,hts_version(),__DATE__,__TIME__);
//no arguments supplied -> print info
if(argc==1||(argc==2&&(strcasecmp(argv[1],"--version")==0||strcasecmp(argv[1],"--help")==0))){//if haven't been supplied with arguments, load default,print, and exit
printProgInfo(stderr);
return 0;
}
if(!strcasecmp("sites",argv[1])){
//from prep_sites.* used for indexing -sites files
int main_sites(int argc,char **argv);
main_sites(--argc,++argv);
return 0;
}
//print time
clock_t t=clock();
time_t t2=time(NULL);
//intialize our signal handler for ctrl+c
catchkill();
argStruct *args=NULL;
if(argc==2){
fprintf(stderr,"\t-> Analysis helpbox/synopsis information:\n");
multiReader mr(argc,argv);
args = mr.getargs();
init(args);//program dies here after printing info, if a match is found
fprintf(stderr,"\nUnknown argument supplied: \'%s\'\n\n",argv[1]);
printProgInfo(stderr);
exit(0);//important otherwise the abc classes will try to clean up, which doesnt make sense in this context
// return 0;
}
multiReader *mr= new multiReader(argc,argv);
args = mr->getargs();
init(args);
parseArgStruct(args);
//Below is main loop which will run until nomore data
assert(args->hd);
assert(args->revMap);
extern int cigstat;
if(cigstat)
cigstat_init(args->outfiles);
int lastRefId=-1;
while(SIG_COND) {
funkyPars *tmp = mr->fetch(); //YES MISTER FETCH
if(tmp==NULL)
break;
if(lastRefId==-1||lastRefId!=tmp->refId){
lastRefId=tmp->refId;
void changeChr(int refId);//<-ugly is located in shared.cpp, to force a change of chr, when notusing bamfiles
changeChr(lastRefId);
}
selector(tmp);
}
//now we have no more data lets wait and cleanup
fprintf(stderr,"\t-> Done reading data waiting for calculations to finish\n");
destroy_shared();
//printout the filenames generated
fprintf(stderr,"\t-> Output filenames:\n");
for(int i=0;i<(int)dumpedFiles.size();i++){
fprintf(stderr,"\t\t->\"%s\"\n",dumpedFiles[i]);
fprintf(args->argumentFile,"\t\t->\"%s\"\n",dumpedFiles[i]);
free(dumpedFiles[i]);
}
// fprintf(stderr,"\n");
fprintf(args->argumentFile,"\n");
// fprintf(stderr,"\t");
printTime(stderr);
//print out nice messages
extern size_t total_number_of_sites_unfiltred,total_number_of_sites_filtered;
fprintf(stderr,"\t-> Arguments and parameters for all analysis are located in .arg file\n");
fprintf(stderr,"\t-> Total number of sites analyzed: %lu\n\t-> Number of sites retained after filtering: %lu \n",total_number_of_sites_unfiltred,total_number_of_sites_filtered);
fprintf(stderr, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(stderr, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
fprintf(args->argumentFile, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(args->argumentFile, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
//make better below
extern int *bamSortedIds;
delete [] bamSortedIds;
delete mr;
//check
extern htsFormat *dingding2;
free(dingding2);
return 0;
}