diff --git a/Makefile.am b/Makefile.am
index 1bfdcf48680594bc8757ad43f3144bbdca65cd65..94c45230274fe7315e516349e7d59f6f4ea884fd 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1 +1 @@
-SUBDIRS=src
+SUBDIRS=src test
diff --git a/configure.ac b/configure.ac
index f810bdd7b22c2081017c2bb3038b5702f6fd656e..03c172a77162abdeaf4105685a08f6fff52b7f31 100644
--- a/configure.ac
+++ b/configure.ac
@@ -13,6 +13,6 @@ AC_PROG_RANLIB
# AC_CHECK_PROG(POD2MAN, pod2man, pod2man, :)
-AC_CONFIG_FILES(Makefile src/Makefile)
+AC_CONFIG_FILES(Makefile src/Makefile test/Makefile)
AC_OUTPUT
diff --git a/src/CountMinSketch.hpp b/src/CountMinSketch.hpp
index 53991c0f846fe9094264b1f2e3eeb019c80c8aab..d4d448a12b88c8fd8714d5e2a37f1e3f17a2262d 100644
--- a/src/CountMinSketch.hpp
+++ b/src/CountMinSketch.hpp
@@ -72,6 +72,7 @@ typedef struct {
int lambda;
int kappa;
int kappa_prime;
+ int filter_size; // max amount of RAM wanted for the CMS.
} CMSparams;
template <typename T>
diff --git a/src/Filter.hpp b/src/Filter.hpp
index dd0620be5066f685c5c07c76895a86822f2c6026..6676fc974d0c4f74a2a0e7a534d5f41e9113643b 100644
--- a/src/Filter.hpp
+++ b/src/Filter.hpp
@@ -57,8 +57,8 @@ template <typename T> void Filter::underlyingfillCMS(FqBaseBackend* map_id_backe
}
for (rit=io_sr->rbegin(); rit!=io_sr->rend(); ++rit) { //process map in reverse order (by decreasing scores).
- cout << "score="<<rit->first<<endl;
- unsigned long score=rit->first;
+ //cout << "score="<<rit->first<<endl;
+ // unsigned long score=rit->first;
for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
unsigned long j=it_offs->first;
for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
diff --git a/src/FqBaseBackend.cpp b/src/FqBaseBackend.cpp
index 83e69c83ac3c5b3d652b5196c287738088b454e7..74c8a6ae552f9b305c9673bb16a8af5f828eec34 100644
--- a/src/FqBaseBackend.cpp
+++ b/src/FqBaseBackend.cpp
@@ -140,8 +140,6 @@ int FqBaseBackend::getRead(const unsigned long& offset, char * fq_record) {
#endif
int res=lseek(i_f_desc,offset,SEEK_SET);
if (res==-1) {
- // err(errno,"fseek problem when trying to retrieve dna string.");
- // add exception for debug
#ifdef DEBUG
cout<<"Couldn't get read at offset: "<<offset<<endl;
#endif
diff --git a/src/Makefile.am b/src/Makefile.am
index 27bad12c8640c2cbcac18a677dcbb894fbf12eca..f21fe59daa1b0f0088d2abafe8f0b9b7fb13da2b 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -3,7 +3,7 @@ LINTDEFS = $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS)
AM_CPPFLAGS = -DDATADIR=\"$(pkgdatadir)\"
bin_PROGRAMS=rock
-noinst_PROGRAMS = unit_test_fqreader perf_test_fqreader unit_test_read_utils unit_test_cms unit_test_fqwriter
+noinst_PROGRAMS = unit_test_fqreader unit_test_read_utils unit_test_cms unit_test_fqwriter
## noinst_PROGRAMS =
noinst_LIBRARIES = librock.a
@@ -15,9 +15,6 @@ rock_LDADD = librock.a
unit_test_fqreader_SOURCES=unit_test_fqreader.cpp
unit_test_fqreader_LDADD=librock.a
-perf_test_fqreader_SOURCES=perf_test_fqreader.cpp
-perf_test_fqreader_LDADD=librock.a
-
unit_test_read_utils_SOURCES=unit_test_read_utils.cpp
unit_test_read_utils_LDADD=librock.a
@@ -29,5 +26,5 @@ unit_test_fqwriter_LDADD=librock.a
librock_a_SOURCES = $(SRC)
-SRC = fqreader.cpp FqBaseBackend.cpp FqAuxBackend.cpp FqMainBackend.cpp read_utils.cpp ReadProcessor.cpp fqwriter.cpp
-HDR = srp.h fqreader.h FqConstants.h FqBaseBackend.h FqAuxBackend.h FqMainBackend.h ReadProcessor.h rock_commons.h read_utils.h CountMinSketch.hpp Filter.hpp fqwriter.h
+SRC = fqreader.cpp FqBaseBackend.cpp FqAuxBackend.cpp FqMainBackend.cpp read_utils.cpp ReadProcessor.cpp fqwriter.cpp main_utils.cpp
+HDR = srp.h fqreader.h FqConstants.h FqBaseBackend.h FqAuxBackend.h FqMainBackend.h ReadProcessor.h rock_commons.h read_utils.h CountMinSketch.hpp Filter.hpp fqwriter.h main_utils.h
diff --git a/src/main_utils.cpp b/src/main_utils.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..83386c689e6c4402c5db1dffdaaae9534b183544
--- /dev/null
+++ b/src/main_utils.cpp
@@ -0,0 +1,153 @@
+/*
+ * main_utils.cpp
+ *
+ * Created on: May 9, 2016
+ * Author: vlegrand
+ */
+
+#include <sys/types.h>
+#include <sys/sysctl.h>
+#include <sys/stat.h>
+#include <string.h>
+#include <iostream>
+#include <fstream>
+#include <cmath>
+#include "main_utils.h"
+
+using namespace std;
+
+/*
+ * Use this function to get the amount of RAM on the machine (used or not).
+ * Aim is to make sure that ROCK can run on the current machine with the requirements that the user gave.
+ */
+unsigned long getNodePhysMemory() {
+#ifdef __linux__
+ return sysconf(_SC_PHYS_PAGES)*sysconf(_SC_PAGESIZE)/1024/1024/1024;
+#elif __APPLE__
+ int64_t mem;
+ size_t len = sizeof(mem);
+ int ret=sysctlbyname("hw.memsize", (void*) &mem, &len, NULL,0); // total RAM is given in bytes; so convert it to MB.*/
+ if (ret==-1) {
+ cout<<"Couldn't determine how much RAM is usable on your system."<<errno<<endl;
+ return errno;
+ }
+ return mem/1024/1024/1024;
+#else
+ cout<<"ROCK has not been tested on this operating system, please contact author."<<endl;
+ return unknown_os;
+#endif
+}
+
+
+/*
+ * Given a filename (including full path), determine if parent directory exists.
+ * If is doesn't, display error message and exit.
+ */
+void checkDirExists(const string o_file) {
+ std::size_t o_found = o_file.find_last_of("/");
+ if (o_found!=string::npos) {
+ string parent_dir=o_file.substr(0,o_found);
+ cout<<parent_dir<<endl;
+ struct stat info;
+ if (stat(parent_dir.c_str(),&info)!=0) {
+ cout<<"parent directory for output files: "<<parent_dir<<" doesn't exist."<<endl;
+ exit(EXIT_FAILURE);
+ }
+ }
+}
+
+
+/*
+ * Reads the names of input and output fastq files that ROCK must process from text files whose names are passed as
+ * argument of the -i/-o options. Fills the appropriate structures.
+ * orresponding output files are supposed to be in the same order as input files. No checking here. It is ut to the user to give something correct in input.
+ */
+int processInOutFileArgs(const std::string& input_file,const std::string output_file,std::vector<IO_fq_files>& single_files,vector<PE_files>& v_PE_files,int& f_id) {
+ ifstream infiles_names(input_file.c_str());
+ if (!infiles_names) cout<<"couldn't open file: "<<input_file<<endl;
+ ifstream ofiles_names(output_file.c_str());
+ if (!ofiles_names) cout<<"couldn't open file: "<<output_file<<endl;
+ /*cout<<"processing in/out files: "<<input_file<<" "<<output_file<<endl;
+ cout<<f_id<<endl;*/
+ while (infiles_names && ofiles_names && f_id<=k_max_input_files) {
+ // cout<<"entering while loop"<<endl;
+ string iline;
+ string oline;
+ if (!getline(infiles_names,iline)) break;
+ if (!getline(ofiles_names,oline)) break;
+ /*cout<< iline<<endl;
+ cout<<oline<<endl;*/
+ std::size_t i_found = iline.find_first_of(k_sep_pair_end);
+ if (i_found!=std::string::npos) {
+ // this is PE
+ f_id+=2;
+ string i_name_PE1=iline.substr(0,i_found);
+ string i_name_PE2=iline.substr(i_found+1);
+ std::size_t o_found = oline.find_first_of(k_sep_pair_end);
+ if (o_found==std::string::npos) {
+ cout<< "Inconsistency between input and output files lists!"<<endl;
+ return EXIT_FAILURE;
+ }
+ string o_name_PE1=oline.substr(0,o_found);
+ checkDirExists(o_name_PE1);
+ string o_name_PE2=oline.substr(0,o_found+1);
+ //cout<<o_name_PE2<<endl;
+ checkDirExists(o_name_PE2);
+ PE_files pe;
+ pe.PE1.in_fq_file=i_name_PE1;
+ pe.PE1.out_fq_file=o_name_PE1;
+ pe.PE2.in_fq_file=i_name_PE2;
+ pe.PE2.out_fq_file=o_name_PE2;
+ v_PE_files.push_back(pe);
+
+ } else {
+ // this is single.
+ f_id+=1;
+ IO_fq_files p;
+ p.in_fq_file=iline;
+ checkDirExists(oline);
+ p.out_fq_file=oline;
+ single_files.push_back(p);
+ }
+ }
+ if (!infiles_names.eof())
+ {
+ std::cout<<"error while reading input or output file"<<std::endl;
+ return EXIT_FAILURE;
+ }
+ /*if (!ofiles_names.eof())
+ {
+ std::cout<<"error while reading input or output file"<<std::endl;
+ return EXIT_FAILURE;
+ }*/
+
+ if (f_id>k_max_input_files) {
+ cout<<"ROCK cannot handle more than "<<k_max_input_files<<" input files."<<endl;
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
+}
+
+
+/*
+ * Minimize lambda for a given number of k-mers.
+ * We want p<=0.01,
+ * so choose smallest lambda so that [1-(1-1/m)exp n] exp lambda<=0.01
+ */
+int getBestLambdaForN(const unsigned long& nb_k_mers,const int& lambda_max) {
+ int lambda=2;
+ int min_lambda=lambda;
+ float tmp=1/INT_MAX;
+ tmp=1-tmp;
+ tmp=pow(tmp,nb_k_mers);
+ tmp=1-tmp;
+ while (lambda<=lambda_max) {
+ min_lambda=lambda;
+ float p=pow(tmp,lambda);
+ if (p<=0.01) break;
+ lambda+=1;
+ }
+ return min_lambda;
+}
+
+
diff --git a/src/main_utils.h b/src/main_utils.h
new file mode 100644
index 0000000000000000000000000000000000000000..80cd267c29f1a5960dd32b27faa1d80f92d99ffe
--- /dev/null
+++ b/src/main_utils.h
@@ -0,0 +1,22 @@
+/*
+ * main_utils.h
+ *
+ * Created on: May 9, 2016
+ * Author: vlegrand
+ */
+
+#ifndef MAIN_UTILS_H_
+#define MAIN_UTILS_H_
+
+#define k_max_input_files 15
+#define k_sep_pair_end ','
+
+#include <vector>
+#include "rock_commons.h"
+
+unsigned long getNodePhysMemory();
+int processInOutFileArgs(const std::string& input_file,const std::string output_file,std::vector<IO_fq_files>& single_files,std::vector<PE_files>& v_PE_files,int& f_id);
+int getBestLambdaForN(const unsigned long& nb_k_mers,const int& lambda_max);
+
+
+#endif /* MAIN_UTILS_H_ */
diff --git a/src/rock.cpp b/src/rock.cpp
index 938f6ee64c3823d3b5b4f51861e9c9250bca9aa9..fbe8f1f2d2018b5e9d239f4e0f1af8fca3d7b38d 100644
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -7,14 +7,15 @@
Description : see : https://projets.pasteur.fr/projects/homogeneisation-couverture-pre-assemblage/wiki
============================================================================
*/
-
+#include <sys/sysctl.h>
#include <cstdlib>
#include <string.h>
#include <getopt.h>
#include <iostream>
-#include <fstream>
+//#include <fstream>
#include <map>
#include <vector>
+#include <unistd.h>
#include "CountMinSketch.hpp"
#include "rock_commons.h"
@@ -22,13 +23,17 @@
#include "FqMainBackend.h"
#include "fqreader.h"
-// #include "ReadProcessor.h"
-// #include "read_utils.h"
#include "fqwriter.h"
#include "Filter.hpp"
+#include "main_utils.h"
+
+
-#define k_max_input_files 15
-#define k_sep_pair_end ','
+#define unknown_os 1
+#define defaultGRPMAXSize 1 //(in gigabytes) Default maximum size of srp structure but of course this size depends of the number of reads we are processing.
+ // 1 GB is enough to store approx 82 millions of reads (must take into account memory needed for stl containers).
+ // This constant is used only if you use rock's default behavior (use 90% of the machine's RAM).
+ // If you specify a lambda, it is possible to use more memory for storing more reads and less memory for the CMS.
using namespace std;
@@ -48,91 +53,76 @@ void printRUsage() {
-
-
-static void usage(int status) { //TODO write me.
- /* FILE *f = stdout;
- (void)fprintf(f, "usage: %s [options] <dbase:name> <dbase:name> <dbase:name>...\n\n", prog);
- (void)fprintf(f, "options:\n");
- (void)fprintf(f, " -a ... Search query by accession number.\n");
- (void)fprintf(f, " -c ... Check query.\n");
- (void)fprintf(f, " -h ... Prints this message and exit.\n");
- (void)fprintf(f, " -i ... Search query by entry name.\n");
- (void)fprintf(f, " -l ... List available databases.\n");
- (void)fprintf(f, " -o <file> ... Place output into <file>.\n");
- (void)fprintf(f, " -f <file1> <file2> <file3>... Read input from <file1> <file2> <file3>.\n");*/
+static void usage(int status) {
+ cout<<"usage: rock [options]"<<endl<<endl;
+ cout<<" -i <input_filename.txt> .... In input_filename.txt put the names of the fastq files to filter."<<endl;
+ cout<<" -o <output_filename.txt> .... In output_filename.txt put the names of the filtered fastq files."<<endl;
+ cout<<" -h .... Print this message and exit."<<endl;
+ cout<<" -k <k_mer_size> .... Specify k-mer size. Default is 30."<<endl;
+ cout<<" -c <kappa_prime> .... Specify lower threshold for coverage. Defaut is 0 (None)."<<endl;
+ cout<<" -C <kappa> .... Specify upper threshold for coverage. Default is 50. Max is 65535."<<endl;
+ cout<<" -l <lambda> .... Indicate number of arrays wanted in the CMS. Default is biggest l so that l<B/(b*MAX_INT) where b is 1 or 2 depending on kappa and B is the RAM quantity on the machine."<<endl;
+ cout<<" -n <nb_distinct_k_mer> .... Indicate the number of distinct k-mer. Useful to compute lambda if not specified with -l."<<endl;
+ cout<<" -g <size in GB> .... Wanted size for the CMS."<<endl;
exit(status); }
-
-
-
-
-
-
-
/*
- * Reads the names of input and output fastq files that ROCK must process from text files whose names are passed as
- * argument of the -i/-o options. Fills the appropriate structures.
- * orresponding output files are supposed to be in the same order as input files. No checking here. It is ut to the user to give something correct in input.
- */
-int processInOutFileArgs(const std::string& input_file,const std::string output_file,std::vector<IO_fq_files>& single_files,vector<PE_files>& v_PE_files,int& f_id) {
- ifstream infiles_names(input_file.c_str());
- ifstream ofiles_names(output_file.c_str());
- while (infiles_names && ofiles_names && f_id<=k_max_input_files) {
- string iline;
- string oline;
- if (!getline(infiles_names,iline)) break;
- if (!getline(ofiles_names,oline)) break;
- std::size_t i_found = iline.find_first_of(k_sep_pair_end);
- if (i_found!=std::string::npos) {
- // this is PE
- f_id+=2;
- string i_name_PE1=iline.substr(0,i_found);
- string i_name_PE2=iline.substr(i_found+1);
- std::size_t o_found = oline.find_first_of(k_sep_pair_end);
- if (o_found==std::string::npos) {
- cout<< "Inconsistency between input and output files lists!"<<endl;
- return EXIT_FAILURE;
- }
- string o_name_PE1=oline.substr(0,o_found);
- string o_name_PE2=oline.substr(o_found+1);
- /* debug stuff, TODO comment that */
- /*cout<<"PE1="<<name_PE1<<endl;
- cout<<"PE2="<<name_PE2<<endl;*/
- /* */
- PE_files pe;
- pe.PE1.in_fq_file=i_name_PE1;
- pe.PE1.out_fq_file=o_name_PE1;
- pe.PE2.in_fq_file=i_name_PE2;
- pe.PE2.out_fq_file=o_name_PE2;
- v_PE_files.push_back(pe);
-
- } else {
- // this is single.
- f_id+=1;
- // cout<<"single="<<iline;
- IO_fq_files p;
- p.in_fq_file=iline;
- p.out_fq_file=oline;
- single_files.push_back(p);
- }
-
- }
- if (!infiles_names.eof())
- {
- std::cout<<"error while reading input file"<<std::endl;
- return EXIT_FAILURE;
- }
- if (f_id>k_max_input_files) {
- cout<<"ROCK cannot handle more than "<<k_max_input_files<<" input files."<<endl;
- return EXIT_FAILURE;
+ * Checks options and arguments consistency (ex kappa_prime not superior to kappa; output file directory exists and so on...)
+ * Also set some CMS parameters depending on value of other options.
+*/
+void optArgConsistency(const string& input_file,const string& output_file,const int& g,CMSparams& parms,const int& nb_k_mers) {
+ if (input_file.empty()) {
+ std::cout<<"input file name is mandatory" <<std::endl;
+ usage(EXIT_FAILURE);
+ }
+ if (output_file.empty()) {
+ std::cout<<"output file name is mandatory" <<std::endl;
+ usage(EXIT_FAILURE);
+ }
+ cout<<"g="<<g<<endl;
+ cout<<"lambda="<<parms.lambda<<endl;
+ if (g!=0 and parms.lambda!=0) {// user set both lambda and cms size=> inconsistency.
+ cout<<"-l and -g options are mutually exclusive."<<endl;
+ usage(EXIT_FAILURE);
+ }
+ if (nb_k_mers!=0 and parms.lambda!=0) {// user set both lambda and cms size=> inconsistency.
+ cout<<"-l and -n options are mutually exclusive."<<endl;
+ usage(EXIT_FAILURE);
+ }
+ float avail_mem=getNodePhysMemory()-defaultGRPMAXSize;
+ //cout<<avail_mem;
+ if (g>avail_mem) {
+ std::cout<<"This machine only has "<<getNodePhysMemory()<<" Gigabytes of RAM. This is not enough to run ROCK with a CMS of size: "<<g<<endl;
+ exit(EXIT_FAILURE);
+ } else {
+ parms.filter_size=g;
+ // compute lambda if not set by the user.
+ if (parms.lambda==0) {
+ parms.lambda=parms.filter_size/INT_MAX;
+ if (parms.kappa>get_mask<unsigned char>::value) parms.lambda=parms.lambda/sizeof(unsigned short);
}
- /*if (!ofiles_names.eof())
- {
- std::cout<<"error while reading output file"<<std::endl;
- return EXIT_FAILURE;
- }*/
- return EXIT_SUCCESS;
+ }
+ if (nb_k_mers) { // user indicated number of k-mers; use it to minimize parms.lambda
+ parms.lambda=getBestLambdaForN(nb_k_mers,parms.lambda);
+ }
+ if (parms.kappa_prime>=parms.kappa) {
+ cout<<"ERROR lower filter is higher than high filter!"<<endl;
+ exit(EXIT_FAILURE);
+ }
+
+ //cout<<"parms.lambda="<<parms.lambda<<" INT_MAX="<<INT_MAX<<endl;
+ unsigned long cms_size=INT_MAX;
+ cms_size*=2;
+ //cout<<"minimum cms size:"<<cms_size<<endl;
+ if (parms.kappa>get_mask<unsigned char>::value) cms_size=cms_size*sizeof(unsigned short);
+ //cout<<"cms_size in B="<<cms_size<<endl;
+ cms_size=ceil(cms_size/1024.0/1024/1024); // convert to gigabytes.
+ //cout<<"cms_size in GB="<<cms_size<<endl;
+ if (cms_size>getNodePhysMemory()-defaultGRPMAXSize) {
+ cout<<"Not enough RAM on the machine to run rock with a CMS of size:"<<cms_size<<" GB."<<endl;
+ exit(EXIT_FAILURE);
+ }
+
}
@@ -143,51 +133,67 @@ int main(int argc,char * argv[]) {
printRUsage();
#endif
srp sr;
- int i;
+ int i,g;
std::string input_file,output_file;
- int kappa,kappa_prime,lambda,k,n;
- while((i = getopt(argc, argv, "i:o:l:k:c:C")) != -1) {
+ int k,nb_k_mers;
+ g=0;
+ k=30;
+ nb_k_mers=0;
+ CMSparams parms;
+ parms.kappa=50;
+ parms.kappa_prime=0;
+ parms.lambda=0;
+ parms.filter_size=getNodePhysMemory()/100*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory
+
+ if (parms.filter_size==unknown_os) return EXIT_FAILURE;
+ while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:")) != -1) {
switch(i) {
case 'i':
input_file=optarg;break;
case 'c':
- kappa_prime=atoi(optarg);break;
+ parms.kappa_prime=atoi(optarg);break;
case 'h':
usage(EXIT_SUCCESS); break;
case 'o':
output_file=optarg; break;
case 'C':
- kappa=atoi(optarg);break;
+ parms.kappa=atoi(optarg);
+ if (parms.kappa<=0 || parms.kappa>get_mask<unsigned short>::value) {
+ cout<<"Bad value for kappa. Must choose kappa so that 0<kappa<="<<get_mask<unsigned short>::value<<endl;
+ usage(EXIT_FAILURE);
+ }
+ break;
case 'l':
- lambda = atoi(optarg); break;
+ parms.lambda = atoi(optarg);
+ if (parms.lambda<=0) {
+ cout<<"Bad value for lambda. Choose a value that is >0 or let ROCK choose for you."<<endl;
+ usage(EXIT_FAILURE);
+ }
+ break;
case 'k':
- k=atoi(optarg); break;
+ k=atoi(optarg);
+ if (k<=0 || k>32) {
+ cout<<"Bad value for k. Must choose k so that 0<k<=32."<<endl;
+ usage(EXIT_FAILURE);
+ }
+ break;
case 'n':
- n=atoi(optarg);break;
+ nb_k_mers=atoi(optarg);break; // number of distinct k-mers
+ case 'g':
+ cout<<optarg<<endl;
+ g=atoi(optarg);
+ break;
default:
usage(EXIT_FAILURE); break; }
}
- /* for the moment, use default values for k, kappa_prime, lambda and kappa*/
- k=30;
- CMSparams parms;
- parms.kappa=50;
- parms.kappa_prime=20;
- parms.lambda=4;
- if (input_file.empty()) {
- std::cout<<"input file name is mandatory" <<std::endl;
- return EXIT_FAILURE;
- }
- if (output_file.empty()) {
- std::cout<<"output file name is mandatory" <<std::endl;
- return EXIT_FAILURE;
+ cout<<"g="<<g<<endl;
+ optArgConsistency(input_file,output_file,g,parms,nb_k_mers);
- }
int f_id=0;
std::vector<IO_fq_files> single_files;
vector<PE_files> v_PE_files;
if (processInOutFileArgs(input_file,output_file,single_files,v_PE_files,f_id)!=EXIT_SUCCESS) return EXIT_FAILURE;
- cout<<"f_id="<<f_id<<endl;
-
+ //cout<<"f_id="<<f_id<<endl;
FqBaseBackend * map_id_backend[k_max_input_files];
Filter the_filter(parms);
@@ -228,8 +234,6 @@ int main(int argc,char * argv[]) {
cout<<"Should now free memory"<<endl;
#endif
for (i=1;i<=f_id;i++) delete map_id_backend[i-1];
- // free(map_id_backend);
- // delete pcms;
#ifdef BENCHMARK
cout<<"finished,going to exit "<<endl;
printRUsage();