diff --git a/NEWS b/NEWS
index e16d2968ce40675b15c8da496e49618c5d017852..a1d3c41ec3febef608ed8eb128f07f1ecbad8314 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,6 @@
+New in version 1.2
+ * -v option for verbose mode.
+
New in version 1.1
* input file names can be provided as arguments in command-line. -i option is no more mandatory.
* output filenames are generated by ROCK if -o option is not used. -o option is no more mandatory.
diff --git a/configure b/configure
index 332dd0853a93b3a30e168d2ae76dcbc704209343..38895ab85417a30bf7d581ccf233d82a7b819e94 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for rock 1.1.
+# Generated by GNU Autoconf 2.69 for rock 1.2.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -576,8 +576,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='rock'
PACKAGE_TARNAME='rock'
-PACKAGE_VERSION='1.1'
-PACKAGE_STRING='rock 1.1'
+PACKAGE_VERSION='1.2'
+PACKAGE_STRING='rock 1.2'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -1226,7 +1226,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures rock 1.1 to adapt to many kinds of systems.
+\`configure' configures rock 1.2 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1297,7 +1297,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of rock 1.1:";;
+ short | recursive ) echo "Configuration of rock 1.2:";;
esac
cat <<\_ACEOF
@@ -1383,7 +1383,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-rock configure 1.1
+rock configure 1.2
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1438,7 +1438,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by rock $as_me 1.1, which was
+It was created by rock $as_me 1.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2217,7 +2217,7 @@ fi
# Define the identity of the package.
PACKAGE='rock'
- VERSION='1.1'
+ VERSION='1.2'
cat >>confdefs.h <<_ACEOF
@@ -3726,7 +3726,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by rock $as_me 1.1, which was
+This file was extended by rock $as_me 1.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -3783,7 +3783,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-rock config.status 1.1
+rock config.status 1.2
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index be1a23ea68322b8596d7f185fc2d79de070c4da6..2235b95494d21ba35729a1699deb188c72666cd3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,7 +1,7 @@
dnl Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT(rock, 1.1)
+AC_INIT(rock, 1.2)
AC_CANONICAL_SYSTEM
diff --git a/doc/rock.pod b/doc/rock.pod
index 89cd73a54141a295bb0cf6b463958c61705d5d52..54f67120a9a73fc1f086af5de43dd935d0e7b916 100644
--- a/doc/rock.pod
+++ b/doc/rock.pod
@@ -65,6 +65,10 @@ Default is to use the minumum between
1) all the machine's memory minus a constant for storing imput fastq files indexes.
2) a default value of 4.
+=item -v
+
+verbose mode. At the end of execution displays a recap ofall ROCK parameters (name of input files, values of, kappa and happa_prime) plus, CMS size in Bytes, plus if -n was provided, the expected probability of collision.
+
=item -h
Usage display.
diff --git a/src/Filter.hpp b/src/Filter.hpp
index a0acab56fd18c9aaa79bb11191f9ac71d0e4f9df..5ecea7614bb3ae5f45fb3c32e4f5c17a2fdd6208 100644
--- a/src/Filter.hpp
+++ b/src/Filter.hpp
@@ -25,6 +25,12 @@ class Filter {
ByteCountMinSketch * pByteCMS;
ShortCountMinSketch * pShortCMS;
+#// long CMS_size_in_Bytes;
+ long nb_bytes_before_fill_CMS,nb_bytes_after_fill_CMS;
+
+ void getRSS(int before_fill=0);
+
+
template <typename T> void underlyingfillCMS(FqBaseBackend* map_id_backend[],int nb_be, int k, srp* io_sr, CountMinSketch<T>* cms);
template <typename T> void underlyinglowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k,srp* io_sr, CountMinSketch<T>* pcms);
@@ -33,13 +39,18 @@ public:
Filter(const CMSparams& parms) {
pByteCMS=NULL;
pShortCMS=NULL;
+ getRSS();
if (parms.kappa<ubytemask) pByteCMS=new ByteCountMinSketch(parms);
- else pShortCMS=new ShortCountMinSketch(parms);
+ else pShortCMS=new ShortCountMinSketch(parms);
+ //CMS_size_in_Bytes=0;
+
+ nb_bytes_after_fill_CMS=0;
}
void fillCMS(FqBaseBackend* map_id_backend[],int nb_be,int k,srp* io_sr);
void lowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k, srp* io_sr);
unsigned long getApproxNbDistinctKMers();
+ unsigned long getSize();
};
template <typename T> void Filter::underlyingfillCMS(FqBaseBackend* map_id_backend[],int nb_be, int k, srp* io_sr, CountMinSketch<T>* cms) {
@@ -127,6 +138,7 @@ template <typename T> void Filter::underlyinglowFilterCMS(FqBaseBackend* map_id_
void Filter::fillCMS(FqBaseBackend* map_id_backend[],int nb_be,int k,srp* io_sr) {
if (pByteCMS!=NULL) underlyingfillCMS<unsigned char>(map_id_backend,nb_be, k, io_sr,pByteCMS);
else underlyingfillCMS<unsigned short>(map_id_backend,nb_be, k, io_sr,pShortCMS);
+ getRSS(1);
}
void Filter::lowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k, srp* io_sr) {
@@ -139,4 +151,18 @@ unsigned long Filter::getApproxNbDistinctKMers() {
else return pShortCMS->getNbDistinctKMers();
}
+void Filter::getRSS(int before_fill) {
+ struct rusage usage;
+ int res2=getrusage(RUSAGE_SELF,&usage);
+ if (res2==-1) err(errno,"cannot get resource usage.");
+ if (before_fill==0) nb_bytes_before_fill_CMS=usage.ru_maxrss;
+ else nb_bytes_after_fill_CMS=usage.ru_maxrss;
+}
+
+unsigned long Filter::getSize() {
+ unsigned long cms_size=nb_bytes_after_fill_CMS-nb_bytes_before_fill_CMS;
+ // cms_size/=8; ru_maxrss seems to be already in Bytes.
+ return cms_size;
+}
+
#endif
diff --git a/src/Makefile.am b/src/Makefile.am
index d83e7beef20b4d53967e70d775d2be0beb8cb95d..8176ea400dbac74fb73c19791aef892be93c1516 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -29,5 +29,5 @@ unit_test_main_utils_LDADD=librock.a
librock_a_SOURCES = $(SRC)
-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
+SRC = fqreader.cpp FqBaseBackend.cpp FqAuxBackend.cpp FqMainBackend.cpp read_utils.cpp ReadProcessor.cpp fqwriter.cpp main_utils.cpp ROCKparams.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 ROCKparams.h
diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..947c64c1caa1794bd88d97426931a28d230b5ac0
--- /dev/null
+++ b/src/ROCKparams.cpp
@@ -0,0 +1,224 @@
+/*
+ * ROCKparams.cpp
+ *
+ * Created on: Jul 25, 2016
+ * Author: vlegrand
+ */
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <vector>
+#include <cmath>
+#include "ROCKparams.h"
+using namespace std;
+
+
+void ROCKparams::computeLambda() {
+ unsigned long tmp=parms.filter_size;
+ tmp*=1073741824; // this is in fact 1024*1024*1024.
+ parms.lambda=tmp/INT_MAX;
+ if (parms.kappa>get_mask<unsigned char>::value) parms.lambda=parms.lambda/sizeof(unsigned short);
+}
+
+
+void ROCKparams::processMainArgs(int optind, const int argc, char ** argv,std::vector<string>& v_input_lines) {
+ if (optind==argc) return; // no arguments
+ while (optind<argc) { // otherwise, only arguments expected are names of files to filter.
+ string iline=argv[optind];
+ v_input_lines.push_back(iline);
+ optind++;
+ }
+ }
+
+
+void ROCKparams::optArgConsistency(const string& input_file,const string& output_file,
+ const int& g,CMSparams& parms,const int& nb_k_mers,
+ const std::vector<string>& v_input_lines) {
+ if (input_file.empty() && v_input_lines.empty()) {
+ std::cout<<"You must provide filename via -i or arguments to indicate ROCK what to filter." <<std::endl;
+ usage(EXIT_FAILURE);
+ }
+ if (!input_file.empty() && !v_input_lines.empty()) {
+ std::cout<<"files to filter are provided via the -i option or as arguments. It cannot be both." <<std::endl;
+ usage(EXIT_FAILURE);
+ }
+ 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 number of k-mers=> 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 if (g!=0) {
+ parms.filter_size=g;
+ computeLambda();
+ }
+ 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);
+ }
+
+ if (parms.lambda==0) {
+ // This happens when the user doesn't specify lambda nor g nor nb_k_mers.
+ computeLambda();
+ parms.lambda=min(parms.lambda,proposedLambda);
+ if (parms.lambda==0) {
+ cout<<"Not enough RAM on the machine. TotalRAM -1GB must be bigger than INT_MAX to allow at least 1 array in the CMS."<<endl;
+ exit(EXIT_FAILURE);
+ }
+ }
+#ifdef DEBUG
+ cout<<"parms.lambda="<<parms.lambda<<" INT_MAX="<<INT_MAX<<endl;
+#endif
+ unsigned long cms_size=INT_MAX;
+ cms_size*=parms.lambda;
+ //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);
+ }
+}
+
+
+/*
+ * Loads the content of a text file (containing input fastq file names to be filtered or names of files that ROCK must generate).
+ */
+int ROCKparams::loadFileArgs(const std::string& afile,std::vector<string>& v_lines) {
+ ifstream infiles_names(afile.c_str());
+ if (!infiles_names) cout<<"couldn't open file: "<<afile<<endl;
+ while (infiles_names) {
+ string iline;
+ if (!getline(infiles_names,iline)) break;
+ v_lines.push_back(iline);
+ }
+ if (!infiles_names.eof())
+ {
+ std::cout<<"error while reading input or output file"<<std::endl;
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
+}
+
+/*
+ * 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 ROCKparams::loadInOutFileArgs(const std::string& input_file,const std::string& output_file,std::vector<string>& v_input_lines,std::vector<string>& v_output_lines) {
+ int reti=EXIT_SUCCESS;
+ int reto=EXIT_SUCCESS;
+ reti=loadFileArgs(input_file,v_input_lines);
+ if (!output_file.empty()) {
+ reto=loadFileArgs(output_file,v_output_lines);
+ }
+ if (reti==EXIT_SUCCESS && reto==EXIT_SUCCESS) return EXIT_SUCCESS;
+ else return EXIT_FAILURE;
+}
+
+void ROCKparams::removePathfromFName(string& FName) {
+ std::size_t i_found2 =FName.find_last_of(path_sep); // remove path from filename.
+ if (i_found2!=std::string::npos) {
+ FName=FName.substr(i_found2+1);
+ }
+}
+
+void ROCKparams::changeExtension(string& FName) { // changes .fq into .rock.fq or adds .rock.fq
+ std::size_t o_found = FName.find_last_of(k_ext);
+ if (o_found!=std::string::npos) FName.replace(o_found,1,".rock.");
+ else FName.append(".rock.fq");
+}
+
+void ROCKparams::genOutFilenames(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines) {
+ std::vector<string>::const_iterator it_in;
+ string o_line;
+ for (it_in=v_input_lines.begin();it_in!=v_input_lines.end();++it_in) {
+ std::size_t i_found = (*it_in).find_first_of(k_sep_pair_end);
+ if (i_found!=std::string::npos) {// PE files are separared by a ','
+ string i_name_PE1=(*it_in).substr(0,i_found);
+ removePathfromFName(i_name_PE1);
+ string i_name_PE2=(*it_in).substr(i_found+1);
+ removePathfromFName(i_name_PE2);
+ changeExtension(i_name_PE1);
+ changeExtension(i_name_PE2);
+ o_line=i_name_PE1;
+ o_line+=k_sep_pair_end;
+ o_line.append(i_name_PE2);
+
+ } else {
+ o_line=*it_in;
+ removePathfromFName(o_line);
+ changeExtension(o_line);
+ }
+ v_output_lines.push_back(o_line);
+ }
+}
+
+int ROCKparams::processInOutFileArgs(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines,std::vector<IO_fq_files>& single_files,vector<PE_files>& v_PE_files,int& f_id) {
+ if (v_output_lines.empty()) {
+ // in that case, generate output filenames from input filenames
+ genOutFilenames(v_input_lines,v_output_lines);
+ }
+ if (v_input_lines.size()!=v_output_lines.size()) {
+ cout<< "Inconsistency between input and output files lists!"<<endl;
+ return EXIT_FAILURE;
+ } else {
+ std::vector<string>::const_iterator it_in;
+ std::vector<string>::const_iterator it_out;
+ it_in=v_input_lines.begin();
+ it_out=v_output_lines.begin();
+ while (it_in!=v_input_lines.end()) {
+ std::size_t i_found = (*it_in).find_first_of(k_sep_pair_end);
+ if (i_found!=std::string::npos) {
+ // this is PE
+ f_id+=2;
+ string i_name_PE1=(*it_in).substr(0,i_found);
+ string i_name_PE2=(*it_in).substr(i_found+1);
+ std::size_t o_found = (*it_out).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=(*it_out).substr(0,o_found);
+ checkDirExists(o_name_PE1);
+ string o_name_PE2=(*it_out).substr(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=*it_in;
+ checkDirExists(*it_out);
+ p.out_fq_file=*it_out;
+ single_files.push_back(p);
+ }
+ ++it_in;
+ ++it_out;
+ }
+ 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;
+}
diff --git a/src/ROCKparams.h b/src/ROCKparams.h
new file mode 100644
index 0000000000000000000000000000000000000000..5448008ea62115fbeddaae8b691afb16d7db8516
--- /dev/null
+++ b/src/ROCKparams.h
@@ -0,0 +1,192 @@
+/*
+ * ROCKparams.h
+ *
+ * Created on: Jul 25, 2016
+ * Author: vlegrand
+ */
+
+#ifndef ROCKPARAMS_H_
+#define ROCKPARAMS_H_
+
+
+#include <cstdlib>
+#include <string>
+#include <vector>
+#include <getopt.h>
+#include "CountMinSketch.hpp"
+#include "main_utils.h"
+
+#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.
+
+#define proposedLambda 4
+
+using namespace std;
+
+
+class ROCKparams{
+ CMSparams parms;
+ int g; // max RAM to use for the CMS if specified by the user.
+ int nb_k_mers; // expected number of k-mers in input data if specified by the user.
+ int k; // size of the k-mers
+ int verbose_mode;
+ std::string input_file,output_file;
+
+ std::vector<IO_fq_files> single_files;
+ vector<PE_files> v_PE_files;
+ int f_id;
+ unsigned long cms_size;
+ float expected_collision_proba;
+
+
+ void computeLambda();
+ void processMainArgs(int optind, const int argc, char ** argv,std::vector<string>& v_input_lines);
+ int loadInOutFileArgs(const std::string& input_file,const std::string& output_file,std::vector<string>& v_input_lines,std::vector<string>& v_output_lines);
+ int loadFileArgs(const std::string& afile,std::vector<string>& v_lines);
+ void removePathfromFName(string& FName);
+ void changeExtension(string& FName);
+ void genOutFilenames(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines);
+ int processInOutFileArgs(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines,std::vector<IO_fq_files>& single_files,vector<PE_files>& v_PE_files,int& f_id);
+
+ /*
+ * 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,
+ const std::vector<string>& v_input_lines);
+
+ friend void test_processIOFileArgs();
+
+public:
+
+ ROCKparams() {
+ f_id=0; // to generate id of input/output fastq files. +1=total number of files.
+ g=0;
+ k=30;
+ nb_k_mers=0;
+ parms.kappa=50;
+ parms.kappa_prime=0;
+ parms.lambda=0;
+ verbose_mode=0;
+ cms_size=0;
+ expected_collision_proba=0.0;
+ parms.filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory
+ if (parms.filter_size==0) throw EXIT_FAILURE;
+ }
+
+
+
+ void initFromMainOptsArgs(int argc,char * argv[]) {
+ int i;
+ std::vector<string> v_input_lines;
+ std::vector<string> v_output_lines;
+
+ while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:v")) != -1) {
+ switch(i) {
+ case 'i':
+ input_file=optarg;break;
+ case 'c':
+ parms.kappa_prime=atoi(optarg);break;
+ case 'h':
+ usage(EXIT_SUCCESS); break;
+ case 'o':
+ output_file=optarg; break;
+ case 'C':
+ 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':
+ 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);
+ 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':
+ nb_k_mers=atoi(optarg);break; // number of distinct k-mers
+ case 'g':
+ // cout<<optarg<<endl;
+ g=atoi(optarg);
+ break;
+ case 'v':
+ verbose_mode=1;
+ break;
+ default:
+ usage(EXIT_FAILURE); break; }
+ }
+ processMainArgs(optind, argc, argv,v_input_lines);
+ optArgConsistency(input_file,output_file,g,parms,nb_k_mers,v_input_lines);
+ if (nb_k_mers) {
+ expected_collision_proba=getCollisionProba(nb_k_mers,parms.lambda);
+ }
+ if (v_input_lines.empty() && (loadInOutFileArgs(input_file,output_file,v_input_lines,v_output_lines)==EXIT_FAILURE)) throw EXIT_FAILURE;
+ if (processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id)!=EXIT_SUCCESS) throw EXIT_FAILURE;
+ }
+
+ CMSparams getCMSparams() {
+ return parms;
+ }
+
+ int get_f_id() {
+ return f_id;
+ }
+
+ std::vector<IO_fq_files> get_single_files() {
+ return single_files;
+ }
+
+ vector<PE_files> get_PE_files() {
+ return v_PE_files;
+ }
+
+ int get_k() {
+ return k;
+ }
+
+ void printVerboseInfo() {
+ std::vector<IO_fq_files>::iterator it_s;
+ vector<PE_files>::iterator it_pe;
+ cout<<"Input files: "<<endl;
+ cout<<"single:"<<endl;
+ for (it_s=single_files.begin();it_s!=single_files.end();it_s++) {
+ cout<<" "<<it_s->in_fq_file<<endl;
+ }
+ cout<<"pair-end:"<<endl;
+ for (it_pe=v_PE_files.begin();it_pe!=v_PE_files.end();it_pe++) {
+ cout<<" "<<it_pe->PE1.in_fq_file<<" "<<it_pe->PE2.in_fq_file<<endl;
+ }
+ cout<<endl;
+ cout<<"k="<<k<<endl;
+ cout<<"kappa="<<parms.kappa<<endl;
+ cout<<"kappa prime="<<parms.kappa_prime;
+ cout<<endl;
+ cout<<"CMS size="<<cms_size<<" Bytes for "<<parms.lambda<<" arrays."<<endl;
+ cout<<endl;
+ if (nb_k_mers!=0) cout<<"expected probability of collision was: "<<expected_collision_proba<<endl;
+ }
+
+ void setFilterSize(unsigned long fsize) {
+ cms_size=fsize;
+ }
+
+ int is_verbose() {
+ return verbose_mode;
+ }
+
+};
+
+
+#endif /* ROCKPARAMS_H_ */
diff --git a/src/main_utils.cpp b/src/main_utils.cpp
index 6b6a02a46069a2a61f58f42a548781d0795dfd97..dc1ba44e4f854658141f2ed8bf5dd009590cfdb7 100644
--- a/src/main_utils.cpp
+++ b/src/main_utils.cpp
@@ -62,139 +62,6 @@ void checkDirExists(const string o_file) {
}
-void removePathfromFName(string& FName) {
- std::size_t i_found2 =FName.find_last_of(path_sep); // remove path from filename.
- if (i_found2!=std::string::npos) {
- FName=FName.substr(i_found2+1);
- }
-}
-
-void changeExtension(string& FName) { // changes .fq into .rock.fq or adds .rock.fq
- std::size_t o_found = FName.find_last_of(k_ext);
- if (o_found!=std::string::npos) FName.replace(o_found,1,".rock.");
- else FName.append(".rock.fq");
-}
-
-void genOutFilenames(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines) {
- std::vector<string>::const_iterator it_in;
- string o_line;
- for (it_in=v_input_lines.begin();it_in!=v_input_lines.end();++it_in) {
- std::size_t i_found = (*it_in).find_first_of(k_sep_pair_end);
- if (i_found!=std::string::npos) {// PE files are separared by a ','
- string i_name_PE1=(*it_in).substr(0,i_found);
- removePathfromFName(i_name_PE1);
- string i_name_PE2=(*it_in).substr(i_found+1);
- removePathfromFName(i_name_PE2);
- changeExtension(i_name_PE1);
- changeExtension(i_name_PE2);
- o_line=i_name_PE1;
- o_line+=k_sep_pair_end;
- o_line.append(i_name_PE2);
-
- } else {
- o_line=*it_in;
- removePathfromFName(o_line);
- changeExtension(o_line);
- }
- v_output_lines.push_back(o_line);
- }
-}
-
-
-int processInOutFileArgs(const std::vector<string>& v_input_lines,std::vector<string>& v_output_lines,std::vector<IO_fq_files>& single_files,vector<PE_files>& v_PE_files,int& f_id) {
- if (v_output_lines.empty()) {
- // in that case, generate output filenames from input filenames
- genOutFilenames(v_input_lines,v_output_lines);
- }
- if (v_input_lines.size()!=v_output_lines.size()) {
- cout<< "Inconsistency between input and output files lists!"<<endl;
- return EXIT_FAILURE;
- } else {
- std::vector<string>::const_iterator it_in;
- std::vector<string>::const_iterator it_out;
- it_in=v_input_lines.begin();
- it_out=v_output_lines.begin();
- while (it_in!=v_input_lines.end()) {
- std::size_t i_found = (*it_in).find_first_of(k_sep_pair_end);
- if (i_found!=std::string::npos) {
- // this is PE
- f_id+=2;
- string i_name_PE1=(*it_in).substr(0,i_found);
- string i_name_PE2=(*it_in).substr(i_found+1);
- std::size_t o_found = (*it_out).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=(*it_out).substr(0,o_found);
- checkDirExists(o_name_PE1);
- string o_name_PE2=(*it_out).substr(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=*it_in;
- checkDirExists(*it_out);
- p.out_fq_file=*it_out;
- single_files.push_back(p);
- }
- ++it_in;
- ++it_out;
- }
- 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;
-}
-
-
-/*
- * Loads the content of a text file (containing input fastq file names to be filtered or names of files that ROCK must generate).
- */
-int loadFileArgs(const std::string& afile,std::vector<string>& v_lines) {
- ifstream infiles_names(afile.c_str());
- if (!infiles_names) cout<<"couldn't open file: "<<afile<<endl;
- while (infiles_names) {
- string iline;
- if (!getline(infiles_names,iline)) break;
- v_lines.push_back(iline);
- }
- if (!infiles_names.eof())
- {
- std::cout<<"error while reading input or output file"<<std::endl;
- return EXIT_FAILURE;
- }
- return EXIT_SUCCESS;
-}
-
-/*
- * 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 loadInOutFileArgs(const std::string& input_file,const std::string& output_file,std::vector<string>& v_input_lines,std::vector<string>& v_output_lines) {
- int reti=EXIT_SUCCESS;
- int reto=EXIT_SUCCESS;
- reti=loadFileArgs(input_file,v_input_lines);
- if (!output_file.empty()) {
- reto=loadFileArgs(output_file,v_output_lines);
- }
- if (reti==EXIT_SUCCESS && reto==EXIT_SUCCESS) return EXIT_SUCCESS;
- else return EXIT_FAILURE;
-}
-
-
/*
* Minimize lambda for a given number of k-mers.
* We want p<=0.01,
@@ -235,3 +102,17 @@ float getCollisionProba(const unsigned long& nb_k_mers,const int& lambda) {
//return p;
}
+void usage(int status) {
+ cout<<"usage: rock [options] [args]"<<endl<<endl;
+ cout<<" -i <file> .... file name containing the list of the FASTQ files to process."<<endl;
+ cout<<" -o <file> .... file name containing the list of the output FASTQ file names."<<endl;
+ cout<<" -h .... Print this message and exit."<<endl;
+ cout<<" -k <int> .... k-mer size. (default 30)."<<endl;
+ cout<<" -c <int> .... lower coverage threshold (default: 0)."<<endl;
+ cout<<" -C <int> .... upper coverage threshold (default: 50; max: 65535)."<<endl;
+ cout<<" -l <int> .... size of the count min sketch (default: at most 4, depending on the available RAM)"<<endl;
+ cout<<" -n <int> .... (expected) number of distinct k-mers within the processed reads."<<endl;
+ cout<<" -g <int> .... maximum RAM to use (in Gb) for the CMS."<<endl;
+ cout<<" -v .... verbose"<<endl;
+ exit(status); }
+
diff --git a/src/main_utils.h b/src/main_utils.h
index 7f3a8c296f318bea70a124a56bd6dfc67204c41b..ed50a9cea471b62d7e0f7cc1303248a54778bc8a 100644
--- a/src/main_utils.h
+++ b/src/main_utils.h
@@ -13,14 +13,17 @@
#define k_ext '.'
#define path_sep '/'
+#include <string>
#include <vector>
#include "rock_commons.h"
unsigned long getNodePhysMemory();
-int loadInOutFileArgs(const std::string& input_file,const std::string& output_file,std::vector<std::string>& v_input_lines,std::vector<std::string>& v_output_lines);
-int processInOutFileArgs(const std::vector<std::string>& v_input_lines,std::vector<std::string>& v_output_lines,std::vector<IO_fq_files>& single_files,std::vector<PE_files>& v_PE_files,int& f_id);
+void checkDirExists(const std::string o_file);
+/*int loadInOutFileArgs(const std::string& input_file,const std::string& output_file,std::vector<std::string>& v_input_lines,std::vector<std::string>& v_output_lines);
+int processInOutFileArgs(const std::vector<std::string>& v_input_lines,std::vector<std::string>& v_output_lines,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,int lambda_max);
float getCollisionProba(const unsigned long& nb_k_mers,const int& lambda);
+void usage(int status);
#endif /* MAIN_UTILS_H_ */
diff --git a/src/rock.cpp b/src/rock.cpp
index 33fc9a23d81c296a13bd0e9a23d2ef878111c516..b53e64cf3ad3c610cdefdd6223e73e01b9e49fc8 100644
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -9,8 +9,9 @@
*/
#include <sys/sysctl.h>
#include <cstdlib>
+#include "err.h"
#include <string.h>
-#include <getopt.h>
+
#include <iostream>
#include <map>
#include <vector>
@@ -26,15 +27,9 @@
#include "fqwriter.h"
#include "Filter.hpp"
#include "main_utils.h"
+#include "ROCKparams.h"
-
-#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.
-#define proposedLambda 4
-
using namespace std;
@@ -53,115 +48,6 @@ void printRUsage() {
-static void usage(int status) {
- cout<<"usage: rock [options] [args]"<<endl<<endl;
- cout<<" -i <file> .... file name containing the list of the FASTQ files to process."<<endl;
- cout<<" -o <file> .... file name containing the list of the output FASTQ file names."<<endl;
- cout<<" -h .... Print this message and exit."<<endl;
- cout<<" -k <int> .... k-mer size. (default 30)."<<endl;
- cout<<" -c <int> .... lower coverage threshold (default: 0)."<<endl;
- cout<<" -C <int> .... upper coverage threshold (default: 50; max: 65535)."<<endl;
- cout<<" -l <int> .... size of the count min sketch (default: at most 4, depending on the available RAM)"<<endl;
- cout<<" -n <int> .... (expected) number of distinct k-mers within the processed reads."<<endl;
- cout<<" -g <int> .... maximum RAM to use (in Gb) for the CMS."<<endl;
- exit(status); }
-
-
-void computeLambda(CMSparams& parms) {
- /*cout<<ULONG_MAX<<endl;
- cout<<UINT_MAX<<endl;
- cout<<INT_MAX<<endl;*/
- unsigned long tmp=parms.filter_size;
- tmp*=1073741824; // this is in fact 1024*1024*1024.
- parms.lambda=tmp/INT_MAX;
- //cout<<"parms.lambda="<<parms.lambda<<endl;
- if (parms.kappa>get_mask<unsigned char>::value) parms.lambda=parms.lambda/sizeof(unsigned short);
-}
-
-
-/*
- * 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,
- const std::vector<string>& v_input_lines) {
- if (input_file.empty() && v_input_lines.empty()) {
- std::cout<<"You must provide filename via -i or arguments to indicate ROCK what to filter." <<std::endl;
- usage(EXIT_FAILURE);
- }
- if (!input_file.empty() && !v_input_lines.empty()) {
- std::cout<<"files to filter are provided via the -i option or as arguments. It cannot be both." <<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 number of k-mers=> 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 if (g!=0) {
- parms.filter_size=g;
- computeLambda(parms);
- }
- 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);
- }
-
- if (parms.lambda==0) {
- // This happens when the user doesn't specify lambda nor g nor nb_k_mers.
- computeLambda(parms);
- parms.lambda=min(parms.lambda,proposedLambda);
- if (parms.lambda==0) {
- cout<<"Not enough RAM on the machine. TotalRAM -1GB must be bigger than INT_MAX to allow at least 1 array in the CMS."<<endl;
- exit(EXIT_FAILURE);
- }
- }
-#ifdef DEBUG
- cout<<"parms.lambda="<<parms.lambda<<" INT_MAX="<<INT_MAX<<endl;
-#endif
- unsigned long cms_size=INT_MAX;
- cms_size*=parms.lambda;
- //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);
- }
-
-}
-
-void processArgs(int optind, const int argc, char ** argv,std::vector<string>& v_input_lines) {
- if (optind==argc) return; // no arguments
- while (optind<argc) { // otherwise, only arguments expected are names of files to filter.
- string iline=argv[optind];
- v_input_lines.push_back(iline);
- optind++;
- }
-}
-
-
-
int main(int argc,char * argv[]) {
#ifdef BENCHMARK
@@ -169,74 +55,12 @@ int main(int argc,char * argv[]) {
printRUsage();
#endif
srp sr;
- int i,g;
- std::string input_file,output_file;
- std::vector<string> v_input_lines;
- 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;
- int f_id=0;
- // cout<<getNodePhysMemory()<<endl;
- // cout<<getNodePhysMemory()/100.0*90<<endl;
- parms.filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory
- if (parms.filter_size==0) return EXIT_FAILURE;
- while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:")) != -1) {
- /*cout<<i<<endl;
- cout<<optind<<endl;*/
- switch(i) {
- case 'i':
- input_file=optarg;break;
- case 'c':
- parms.kappa_prime=atoi(optarg);break;
- case 'h':
- usage(EXIT_SUCCESS); break;
- case 'o':
- output_file=optarg; break;
- case 'C':
- 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':
- 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);
- 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':
- 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; }
- }
- /*cout<<optind<<endl;
- cout<<*argv<<endl;*/
- processArgs(optind, argc, argv,v_input_lines);
- optArgConsistency(input_file,output_file,g,parms,nb_k_mers,v_input_lines);
- std::vector<string> v_output_lines;
- if (v_input_lines.empty() && (loadInOutFileArgs(input_file,output_file,v_input_lines,v_output_lines)==EXIT_FAILURE)) return EXIT_FAILURE;
- std::vector<IO_fq_files> single_files;
- vector<PE_files> v_PE_files;
- if (processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id)!=EXIT_SUCCESS) return EXIT_FAILURE;
- //cout<<"f_id="<<f_id<<endl;
+ ROCKparams main_parms;
+ main_parms.initFromMainOptsArgs(argc,argv);
+ int f_id=main_parms.get_f_id();
+ CMSparams parms=main_parms.getCMSparams();
+ std::vector<IO_fq_files> single_files=main_parms.get_single_files();
+ vector<PE_files> v_PE_files=main_parms.get_PE_files();
FqBaseBackend * map_id_backend[k_max_input_files];
Filter the_filter(parms);
@@ -252,6 +76,9 @@ int main(int argc,char * argv[]) {
printRUsage();
cout<<"Now going to fill CMS"<<endl;
#endif
+
+ int k=main_parms.get_k();
+
the_filter.fillCMS(map_id_backend,f_id,k, &sr);
#ifdef BENCHMARK
@@ -268,6 +95,7 @@ int main(int argc,char * argv[]) {
cout<<"Now going to remove read with cov<kappa_prime"<<endl;
#endif
+ main_parms.setFilterSize(the_filter.getSize());
// Now, remove reads that are beneath kappa_prime
if (parms.kappa_prime) the_filter.lowFilterCMS(map_id_backend,f_id,k,&sr);
@@ -283,6 +111,7 @@ int main(int argc,char * argv[]) {
printRUsage();
cout<<"Should now free memory"<<endl;
#endif
+ int i;
for (i=1;i<=f_id;i++) {
// cout<<"deleting backend: "<<i-1<<endl;
delete map_id_backend[i-1];
@@ -297,6 +126,8 @@ int main(int argc,char * argv[]) {
cout<<"estimated probability of collision:"<<p<<endl;
cout<<"estimated number of distinct k-mers:"<<approx_nb_k_mers<<endl;
+ if (main_parms.is_verbose()) main_parms.printVerboseInfo();
+
#ifdef BENCHMARK
cout<<"finished,going to exit "<<endl;
printRUsage();
diff --git a/src/unit_test_main_utils.cpp b/src/unit_test_main_utils.cpp
index 0e9947dc24af06088496f7007cca6b4a17ce8382..5d05fa1646b6a1f2688d27bdf3917b2d6e975508 100644
--- a/src/unit_test_main_utils.cpp
+++ b/src/unit_test_main_utils.cpp
@@ -15,32 +15,34 @@ using namespace std;
#include "rock_commons.h"
#include "main_utils.h"
+#include "ROCKparams.h"
void test_processIOFileArgs() {
std::vector<IO_fq_files> single_files;
vector<PE_files> v_PE_files;
std::vector<string> v_input_lines;
std::vector<string> v_output_lines;
+ ROCKparams main_parms;
int f_id=0;
- int ret=loadInOutFileArgs("../test/data/unit/list_input1.txt","../test/data/unit/list_output1.txt",v_input_lines,v_output_lines);
+ int ret=main_parms.loadInOutFileArgs("../test/data/unit/list_input1.txt","../test/data/unit/list_output1.txt",v_input_lines,v_output_lines);
assert(ret==EXIT_SUCCESS);
- ret=processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
+ ret=main_parms.processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
assert(ret==EXIT_FAILURE);
f_id=0;
v_PE_files.clear();
single_files.clear();
v_input_lines.clear();
v_output_lines.clear();
- ret=loadInOutFileArgs("../test/data/unit/list_input2.txt","../test/data/unit/list_output2.txt",v_input_lines,v_output_lines);
- ret=processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
+ ret=main_parms.loadInOutFileArgs("../test/data/unit/list_input2.txt","../test/data/unit/list_output2.txt",v_input_lines,v_output_lines);
+ ret=main_parms.processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
assert(ret==EXIT_FAILURE);
f_id=0;
v_PE_files.clear();
single_files.clear();
v_input_lines.clear();
v_output_lines.clear();
- ret=loadInOutFileArgs("../test/data/unit/list_input3.txt","../test/data/unit/list_output3.txt",v_input_lines,v_output_lines);
- ret=processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
+ ret=main_parms.loadInOutFileArgs("../test/data/unit/list_input3.txt","../test/data/unit/list_output3.txt",v_input_lines,v_output_lines);
+ ret=main_parms.processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
assert(ret==EXIT_SUCCESS);
assert(f_id==14);
assert(single_files.size()==2);
@@ -56,8 +58,8 @@ void test_processIOFileArgs() {
v_input_lines.clear();
v_PE_files.clear();
single_files.clear();
- ret=loadInOutFileArgs("../test/data/unit/list_input3.txt","",v_input_lines,v_output_lines);
- ret=processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
+ ret=main_parms.loadInOutFileArgs("../test/data/unit/list_input3.txt","",v_input_lines,v_output_lines);
+ ret=main_parms.processInOutFileArgs(v_input_lines,v_output_lines,single_files,v_PE_files,f_id);
s=single_files[0];
assert(s.out_fq_file.compare("fifi.rock.fq")==0);
s2=v_PE_files[5];
diff --git a/test/rock_mem.sh b/test/rock_mem.sh
index 970acad63e0cd7b2ac06306d7b334e6eeff2503c..b1e4023bfea696a6c5f2f660597a46e67fe9d65f 100755
--- a/test/rock_mem.sh
+++ b/test/rock_mem.sh
@@ -66,6 +66,19 @@ rm -fr "klebsiella_100_2.rock.fq" || exit 1817
rm -fr "test_single.rock.fq"|| exit 1818
rm -fr "test_single2.rock.fq"|| exit 1819
+# test the -v option
+echo " "
+echo "##################################################################################"
+echo "testing verbose mode"
+../src/rock -C 100 -c 1 -l 2 -v ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "CMS size=" >/dev/null || exit 182
+
+../src/rock -C 100 -c 1 -v -n 1000 ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "expected probability of collision was:" >/dev/null || exit 182
+
+echo "erasing test result files"
+rm -fr "klebsiella_100_1.rock.fq" || exit 1816
+rm -fr "klebsiella_100_2.rock.fq" || exit 1817
+rm -fr "test_single.rock.fq"|| exit 1818
+rm -fr "test_single2.rock.fq"|| exit 1819
echo " "
echo "##################################################################################"