From 7e557a77124e54011b43a30834c93c3814ff53f6 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Mon, 31 May 2021 15:30:08 +0200
Subject: [PATCH] did some cleaning: removed all read processing taht didn't
treat PE as single
---
src/CountMinSketch.hpp | 70 +++-------
src/Filter.hpp | 12 +-
src/FqAuxBackend.cpp | 1 -
src/ROCKparams.h | 15 ---
src/read_utils.cpp | 14 +-
src/read_utils.h | 4 +-
src/rock.cpp | 3 -
src/rock_commons.h | 6 +-
src/unit_test_cms.cpp | 245 +----------------------------------
src/unit_test_read_utils.cpp | 28 +---
10 files changed, 44 insertions(+), 354 deletions(-)
diff --git a/src/CountMinSketch.hpp b/src/CountMinSketch.hpp
index 55c2058..a8f0702 100644
--- a/src/CountMinSketch.hpp
+++ b/src/CountMinSketch.hpp
@@ -41,9 +41,6 @@ typedef struct {
int kappa;
int kappa_prime;
int max_filter_size; // max amount of RAM wanted for the CMS.
- int filter_PE_separately; // indicates whether PE reads must be treated as single by the cms. Indeed it may appear that 1 end contains useful k-mer but that other end contains k-mer such that "global" median is below threshold.
- // In this case, read is rejected by the CMS (default behavior). We want to do an experimentation to see if keeping such reads wold lead to better results in assembling.
- // Values can be 0 (process PE as single),1 (process PE separately with strict implementation for kappa_prime) or 2 (process PE separately with lenient implementation for kappa prime).
float wanted_max_collision_proba;
} CMSparams;
@@ -73,7 +70,6 @@ private:
int lambda;
int kappa;
int kappa_prime;
- int filter_PE_separately;
T ** cms_lambda_array;
T mask;
@@ -84,11 +80,11 @@ private:
}
- inline int isRCovBelowThres(const T_read_numericValues& read_val, const int& threshold);
+ inline int isRCovBelowThres(const readNumericValues& read_val, const int& threshold);
inline int isRCovBelowThresPartial(const readNumericValues& read_val, const int& threshold, const int& start=0,const int& stop=0);
- void init(int glambda,int gkappa,int gkappa_prime,int filter_PE_separately=0);
+ void init(int glambda,int gkappa,int gkappa_prime);
// for unit tests.
friend void test_CMS(int lambda,int kappa,int kappa_prime);
@@ -96,12 +92,12 @@ private:
public:
- CountMinSketch(int glambda,int gkappa,int gkappa_prime,int filter_PE_separately=0) {
- init(glambda,gkappa,gkappa_prime,filter_PE_separately);
+ CountMinSketch(int glambda,int gkappa,int gkappa_prime) {
+ init(glambda,gkappa,gkappa_prime);
}
CountMinSketch(CMSparams parms) {
- init(parms.lambda,parms.kappa,parms.kappa_prime,parms.filter_PE_separately);
+ init(parms.lambda,parms.kappa,parms.kappa_prime);
}
~CountMinSketch() {
@@ -134,15 +130,12 @@ public:
// keep that just for unit testing purpose
T getEstimatedNbOcc(const unsigned long& val);
- int addRead(const T_read_numericValues& read_val);
+ int addRead(const readNumericValues& read_val);
- int isBeneathMinKappa(const T_read_numericValues&read_val);
+ int isBeneathMinKappa(const readNumericValues&read_val);
unsigned long getNbDistinctKMers();
- int arePEFilteredAsSingle() {
- return !filter_PE_separately;
- }
};
@@ -151,24 +144,20 @@ public:
/*
* Determines whether median of k-mer coverage is below threshold or not.
*/
-//#include <stdio.h>
// this is a few seconds faster
-template<typename T> inline int CountMinSketch<T>::isRCovBelowThres(const T_read_numericValues& read_val, const int& threshold) {
+template<typename T> inline int CountMinSketch<T>::isRCovBelowThres(const readNumericValues& read_val, const int& threshold) {
int PE1_below_thres;
- int PE2_below_thres=0;
int a1=0,a2=0;
- int b1,b2=0;
+ int b1;
int j;
unsigned int h;
T min;
- int num=read_val.single_or_PE_val.size();
-
- read_val.idx_start_PE2?b1=read_val.idx_start_PE2:b1=num;
- read_val.idx_start_PE2?b2=num-b1:b2;
+ int num=read_val.size();
+ b1=num;
// this proves faster than using iterators on these data (short)
- long const * p_start=(long const * )&(read_val.single_or_PE_val[0]); // TODO: when we'll use C++11: use the data() method of the vector class to access the underlying C array.
+ long const * p_start=(long const * )&(read_val[0]); // TODO: when we'll use C++11: use the data() method of the vector class to access the underlying C array.
int nb=0;
while(nb<b1 && 2*a1<=b1) {
j=lambda;
@@ -181,25 +170,6 @@ template<typename T> inline int CountMinSketch<T>::isRCovBelowThres(const T_read
nb++;
}
PE1_below_thres=2*a1>b1;
- if (b2) {
- nb=b1;
- while(nb<num && 2*a2<=b2) {
- j=lambda;
- min=mask;
- while (--j>=0 && min>threshold) {
- h=hash64to32(*(p_start+nb),j);
- min=cms_lambda_array[j] [h];
- }
- (min<threshold)? a2+=1:a2;
- nb++;
- }
- PE2_below_thres=2*a2>b2;
- if (threshold==kappa) return (PE1_below_thres || PE2_below_thres);
- else {
- if (filter_PE_separately==1) return(PE1_below_thres && PE2_below_thres);
- return(PE1_below_thres || PE2_below_thres);
- }
- }
return PE1_below_thres;
}
@@ -257,11 +227,10 @@ template<typename T> inline int CountMinSketch<T>::isRCovBelowThres(const T_read
-template<typename T> void CountMinSketch<T>::init(int glambda,int gkappa,int gkappa_prime,int gfilter_PE_separately) {
+template<typename T> void CountMinSketch<T>::init(int glambda,int gkappa,int gkappa_prime) {
lambda=glambda;
kappa=gkappa;
kappa_prime=gkappa_prime;
- filter_PE_separately=gfilter_PE_separately;
int j;
mask=get_mask<T>::value;
cms_lambda_array= (T**) malloc(lambda*sizeof(T*));
@@ -283,28 +252,23 @@ template<typename T> T CountMinSketch<T>::getEstimatedNbOcc(const unsigned long&
return min;
}
-template<typename T> int CountMinSketch<T>::addRead(const T_read_numericValues& read_val) {
+template<typename T> int CountMinSketch<T>::addRead(const readNumericValues& read_val) {
int keep_r=isRCovBelowThres(read_val,kappa);
if (keep_r) {
readNumericValues::const_iterator it;
// according to the intel profiler, we spend a lot of time in this loop. Try to use something slightly faster.
- long const * p=(long const *) &read_val.single_or_PE_val[0];
+ long const * p=(long const *) &read_val[0];
int cnt;
- int stop=read_val.single_or_PE_val.size();
+ int stop=read_val.size();
for (cnt=0;cnt<stop;cnt++) {
this->addKMer(*p);
p=p+1;
}
-/*
- for (it=read_val.single_or_PE_val.begin();it!=read_val.single_or_PE_val.end();it++) {
- this->addKMer(*it);
- }
-*/
}
return keep_r;
}
-template<typename T> int CountMinSketch<T>::isBeneathMinKappa(const T_read_numericValues& read_val) {
+template<typename T> int CountMinSketch<T>::isBeneathMinKappa(const readNumericValues& read_val) {
int res=isRCovBelowThres(read_val,kappa_prime);
return res;
}
diff --git a/src/Filter.hpp b/src/Filter.hpp
index 45e3de8..8537fa2 100644
--- a/src/Filter.hpp
+++ b/src/Filter.hpp
@@ -85,7 +85,7 @@ template <typename T> void Filter::underlyingfillCMS(FqBaseBackend* map_id_backe
i_dim::iterator it_offs;
k_dim::iterator it_struct;
ReadProcessor read_p(k);
- T_read_numericValues nbrKmerDecompo;
+ readNumericValues nbrKmerDecompo;
// 1rst step, open files before fetching reads in them
int i;
@@ -103,14 +103,14 @@ template <typename T> void Filter::underlyingfillCMS(FqBaseBackend* map_id_backe
init_DnaSeqStr(&a_seqs[1]);
getDNASeqstr(map_id_backend,*it_struct,j,a_seqs,qual_thres.nucl_score_threshold);
// decompose dna string into k-mers and turn k_mers into numbers.
- decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,cms->arePEFilteredAsSingle(),a_seqs);
+ decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,a_seqs);
// insert k-mers into CMS if overall read satisfies kappa condition.
ret=cms->addRead(nbrKmerDecompo);
if (!ret) {
// read is rejected, update rpos structure accordingly.
it_struct->fileid=0;
}
- nbrKmerDecompo.single_or_PE_val.clear();
+ nbrKmerDecompo.clear();
}
}
}
@@ -126,7 +126,7 @@ template <typename T> void Filter::underlyinglowFilterCMS(FqBaseBackend* map_id_
k_dim::iterator it_struct;
int ret;
ReadProcessor read_p(k);
- T_read_numericValues nbrKmerDecompo;
+ readNumericValues nbrKmerDecompo;
// 1rst step, open files before fetching reads in them
int i;
@@ -145,10 +145,10 @@ template <typename T> void Filter::underlyinglowFilterCMS(FqBaseBackend* map_id_
init_DnaSeqStr(&a_seqs[1]);
getDNASeqstr(map_id_backend,*it_struct,j,a_seqs);
// decompose dna string into k-mers and turn k_mers into numbers.
- decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,cms->arePEFilteredAsSingle(),a_seqs);
+ decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,a_seqs);
ret=cms->isBeneathMinKappa(nbrKmerDecompo);
if (ret) it_struct->fileid=0;
- nbrKmerDecompo.single_or_PE_val.clear();
+ nbrKmerDecompo.clear();
}
}
}
diff --git a/src/FqAuxBackend.cpp b/src/FqAuxBackend.cpp
index 2f6d1a6..311e5e3 100644
--- a/src/FqAuxBackend.cpp
+++ b/src/FqAuxBackend.cpp
@@ -23,7 +23,6 @@
#include "FqConstants.h"
#include <stdio.h>
-//#include <stdlib.h>
#include <fcntl.h>
#include <unistd.h>
#include <errno.h>
diff --git a/src/ROCKparams.h b/src/ROCKparams.h
index 2ff7bb4..bea282b 100755
--- a/src/ROCKparams.h
+++ b/src/ROCKparams.h
@@ -76,11 +76,9 @@ class ROCKparams{
vector<PE_files> v_PE_files;
int f_id;
unsigned long cms_size;
- //unsigned long total_machine_RAM;
float expected_collision_proba;
- //void computeLambda();
void processMainArgs(int optind, 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);
@@ -107,7 +105,6 @@ class ROCKparams{
public:
FasqQualThreshold getQualThreshold();
- //int getfilterPEMode();
ROCKparams() {
f_id=0; // to generate id of input/output fastq files. +1=total number of files.
@@ -117,7 +114,6 @@ public:
parms.kappa=70;
parms.kappa_prime=0;
parms.lambda=0;
- parms.filter_PE_separately=0;
parms.wanted_max_collision_proba=k_max_collision_proba;
qual_thres.min_correct_k_mers_in_read=1;
qual_thres.nucl_score_threshold=k_phred_32;
@@ -125,14 +121,11 @@ public:
verbose_mode=0;
cms_size=0;
expected_collision_proba=0.0; //! collision probability that is computed at the beginning of ROCK from the expected number of distinct k-mers provided by the user.
- //min_correct_k_mers_in_read=0;
- //total_machine_RAM=getNodePhysMemory();
parms.max_filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory
if (parms.max_filter_size==0) throw EXIT_FAILURE;
}
-
void initFromMainOptsArgs(int argc,char ** argv);
@@ -162,16 +155,8 @@ public:
return k;
}
- // cms_size is computed when ROCK starts.
- /*void setFilterSize(unsigned long fsize) {
- cms_size=fsize;
- }*/
unsigned long getFilterSize() const {
- /*unsigned long cms_size_in_GB=cms_size/1024;
- cms_size_in_GB/=1024;
- cms_size_in_GB/=1024;
- return cms_size_in_GB;*/
return cms_size;
}
diff --git a/src/read_utils.cpp b/src/read_utils.cpp
index 6fcf98c..d223fca 100644
--- a/src/read_utils.cpp
+++ b/src/read_utils.cpp
@@ -149,21 +149,19 @@ void getDNASeqstr(FqBaseBackend* fq_files_be [],
}
-void decomposeReadInKMerNums(ReadProcessor& read_p, T_read_numericValues& nbrKmerDecompo,int k,const int& filter_PE_as_single,DnaSeqStr a_seqs[2]) {
- int nb_expected_k_mers_PE1;
- int nb_expected_k_mers_PE2=0;
- nbrKmerDecompo.idx_start_PE2=0;
+void decomposeReadInKMerNums(ReadProcessor& read_p, readNumericValues& nbrKmerDecompo,int k,DnaSeqStr a_seqs[2]) {
+ int nb_expected_k_mers,nb_expected_k_mers_PE1,nb_expected_k_mers_PE2=0;
nb_expected_k_mers_PE1=a_seqs[0].length+1-k;
if (a_seqs[1].length) nb_expected_k_mers_PE2=a_seqs[1].length+1-k;
- nbrKmerDecompo.single_or_PE_val.reserve(nb_expected_k_mers_PE1+nb_expected_k_mers_PE2);
+ nb_expected_k_mers=nb_expected_k_mers_PE1+nb_expected_k_mers_PE2;
+ nbrKmerDecompo.reserve(nb_expected_k_mers);
char * start_dna_str=a_seqs[0].fq_record_buf+a_seqs[0].start_idx;
- read_p.getKMerNumbers(start_dna_str,a_seqs[0].length,nbrKmerDecompo.single_or_PE_val);
+ read_p.getKMerNumbers(start_dna_str,a_seqs[0].length,nbrKmerDecompo);
if (a_seqs[1].length) { // case of PE reads
- if (!filter_PE_as_single) nbrKmerDecompo.idx_start_PE2=nbrKmerDecompo.single_or_PE_val.size();
start_dna_str=a_seqs[1].fq_record_buf+a_seqs[1].start_idx;
- read_p.getKMerNumbers(start_dna_str,a_seqs[1].length,nbrKmerDecompo.single_or_PE_val);
+ read_p.getKMerNumbers(start_dna_str,a_seqs[1].length,nbrKmerDecompo);
}
}
diff --git a/src/read_utils.h b/src/read_utils.h
index 48c12c0..5bb504c 100644
--- a/src/read_utils.h
+++ b/src/read_utils.h
@@ -36,8 +36,6 @@ void getDNASeqstr(FqBaseBackend* [],
void init_DnaSeqStr(DnaSeqStr * dna_seq);
-void decomposeReadInKMerNums(ReadProcessor& read_p, T_read_numericValues& nbrKmerDecompo,int k,const int &,DnaSeqStr a_seqs[2]);
-// void decomposeReadInKMerNums(ReadProcessor& read_p, T_read_numericValues& nbrKmerDecompo,int k,int DnaSeqStr a_seqs[2] );
-
+void decomposeReadInKMerNums(ReadProcessor& read_p, readNumericValues& nbrKmerDecompo,int k,DnaSeqStr a_seqs[2]);
#endif /* READ_UTILS_H_ */
diff --git a/src/rock.cpp b/src/rock.cpp
index 6fce394..55673a7 100755
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -74,7 +74,6 @@ void printCMSparams(const CMSparams& p) {
cout<<"kappa="<<p.kappa<<endl;
cout<<"kappa_prime="<<p.kappa_prime<<endl;
cout<<"filter_size="<<p.max_filter_size<<endl;
- cout<<"filter_PE_separately="<<p.filter_PE_separately<<endl;
}
const void printVerboseInfo(const ROCKparams& Rparms,const Filter& filter,const T_read_counters& rc,\
@@ -142,9 +141,7 @@ int main(int argc,char * argv[]) {
main_parms.initFromMainOptsArgs(argc,argv);
int f_id=main_parms.get_f_id();
CMSparams parms=main_parms.getCMSparams();
- //printCMSparams(parms);
FasqQualThreshold qual_thres=main_parms.getQualThresholds();
- //printFastqQualThreshold(qual_thres);
std::vector<IO_fq_files> single_files=main_parms.get_single_files();
vector<PE_files> v_PE_files=main_parms.get_PE_files();
diff --git a/src/rock_commons.h b/src/rock_commons.h
index 78e5ae1..a6fc52d 100644
--- a/src/rock_commons.h
+++ b/src/rock_commons.h
@@ -72,11 +72,9 @@ typedef struct {
typedef std::vector<unsigned long> readNumericValues;
-typedef struct {
+/*typedef struct {
readNumericValues single_or_PE_val;
- int idx_start_PE2; // In he case where PE reads are not treated as single;
- // indicate at which index the single_or_PE_val array starts containing values for PE2 k-mers.
-}T_read_numericValues;
+}T_read_numericValues;*/
typedef struct {
unsigned int nb_input_reads;
diff --git a/src/unit_test_cms.cpp b/src/unit_test_cms.cpp
index 6060174..21bee4a 100644
--- a/src/unit_test_cms.cpp
+++ b/src/unit_test_cms.cpp
@@ -47,10 +47,8 @@ void test_getBestLambdaForN() {
assert(best==1);
nb_k_mer=10000000000;
best=Rparms.getBestLambdaForN(nb_k_mer,5,UINT_MAX,0.1);
- //cout<<best<<endl;
assert(best==1);
best=Rparms.getBestLambdaForN(nb_k_mer,1,UINT_MAX,0.05);
- //cout<<best<<endl;
assert(best==8);
nb_k_mer=50000000000;
@@ -137,19 +135,16 @@ void test_CMS(int lambda,int kappa,int kappa_prime) {
}
// Now, check that our k-mer is present in the CMS.
int min=cms.getEstimatedNbOcc(num);
- //std::cout<<"min="<<min<<endl;
assert((min==num) || (min==num-get_mask<unsigned char>::value-1)); // addKmer doesn't check kappa.
unsigned long nb_distinct_k_mers=cms.getNbDistinctKMers();
- //cout<<nb_distinct_k_mers<<endl;
assert(nb_distinct_k_mers==1);
// mimic a read (as given by part 2 output).
- T_read_numericValues read_values;
+ readNumericValues read_values;
for (i=1;i<=400;i++) {
- read_values.single_or_PE_val.push_back(i*1000-1);
+ read_values.push_back(i*1000-1);
}
- read_values.idx_start_PE2=0;
ret=cms.addRead(read_values); // read should be accepted since none of the values that it contains is equal to those I inserted previously.
assert(ret!=rej_expected);
@@ -157,13 +152,12 @@ void test_CMS(int lambda,int kappa,int kappa_prime) {
assert(nb_distinct_k_mers==401);
// mimic a vector that contains a lot of k_mers already present in the CMS and check that it is rejected.
- T_read_numericValues read_values2;
- read_values2.idx_start_PE2=0;
+ readNumericValues read_values2;
for (i=1;i<=199;i++) {
- read_values2.single_or_PE_val.push_back(i*1000-1);
+ read_values2.push_back(i*1000-1);
}
for (i=200;i<=400;i++) {
- read_values2.single_or_PE_val.push_back(num);
+ read_values2.push_back(num);
}
ret=cms.addRead(read_values2);
assert(ret==rej_expected);
@@ -178,231 +172,7 @@ void test_CMS(int lambda,int kappa,int kappa_prime) {
-void testCMS_with_PE_NotasSingle(int lambda,int kappa,int kappa_prime) {
- // int filter_PE_as_single=0;
- int filter_PE_separately=1;
- CountMinSketch<unsigned char>* cms=new CountMinSketch<unsigned char>(lambda,kappa,kappa_prime,filter_PE_separately);
- int i;
- cout<<"size of the CMS component: "<<sizeof(cms)<<endl;
- int num=200;
- //int rej_expected=0;
- int ret;
- for (i=0;i<kappa;i++) {
- cms->addKMer(num);
- }
- int min=cms->getEstimatedNbOcc(num);
- assert(min==kappa);
- // mimic a PE read (as given by part 2 output).
- T_read_numericValues read_values;
-
- // mimic a PE read in which PE1 contains k-mer that appear rarely in the CMS and PE2 contains k_mers that already appear kappa times in the CMS.
- for (i=1;i<=200;i++) {
- read_values.single_or_PE_val.push_back(i*1000-1);
- }
- read_values.idx_start_PE2=200;
- for (i=1;i<=239;i++) {
- read_values.single_or_PE_val.push_back(num);
- }
- read_values.single_or_PE_val.push_back(50);
- read_values.single_or_PE_val.push_back(55);
- ret=cms->addRead(read_values); // read should be accepted since PE1 is nor over covered.
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values); // read should not be considered under covered since only PE1 is under covered.
- assert(ret==0);
-
- // Now, change PE1 a little and insert it kappa times in the CMS
- for (int j=1;j<=kappa;j++) {
- read_values.single_or_PE_val[2]=j;
- ret=cms->addRead(read_values);
- if (j<=kappa-1) assert(ret>0); // read should be accepted as long as we haven't inserted PE1 kappa times.
- else assert(ret==0); //otherwise it is rejected.
- }
-
- ret=cms->isBeneathMinKappa(read_values); // read should not be considered under covered since PE1 was inserted kappa times.
- assert(ret==0);
-
- // mimic a PE read (as given by part 2 output).
- T_read_numericValues read_values2;
-
- // mimic a PE read that will be inserted in the CMS kappa_prime+1 times to check low filter.
- for (i=1;i<=150;i++) {
- read_values2.single_or_PE_val.push_back(i*1500-1);
- }
- read_values2.idx_start_PE2=150;
- for (i=1;i<=151;i++) {
- read_values2.single_or_PE_val.push_back(i*1600-1);
- }
- for (i=0;i<kappa_prime+1;i++) {
- ret=cms->addRead(read_values2);
- assert(ret>0);
- }
-
- ret=cms->isBeneathMinKappa(read_values2);
- assert(ret==0);
- //mimic a read for which PE1 is under kappa_prime and PE2 too. Such a read is expected to be removed by low filter
- T_read_numericValues read_values3;
-
- for (i=1;i<=200;i++) {
- read_values3.single_or_PE_val.push_back(i);
- }
- read_values3.idx_start_PE2=201;
- for (i=1;i<=205;i++) {
- read_values3.single_or_PE_val.push_back(i);
- }
- ret=cms->addRead(read_values3);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values3);
- assert(ret>0);
-
- //mimic a read for which PE1 is over kappa_prime but not PE2
- T_read_numericValues read_values4;
- for (i=201;i<=399;i++) {
- read_values4.single_or_PE_val.push_back(200);
- }
- read_values4.idx_start_PE2=199;
- for (i=201;i<=399;i++) {
- read_values4.single_or_PE_val.push_back(i);
- }
- ret=cms->addRead(read_values4);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values4);
- assert(ret==0);
-
- //mimic a read for which PE2 is over kappa_prime but not PE1
- T_read_numericValues read_values5;
- for (i=201;i<=399;i++) {
- read_values5.single_or_PE_val.push_back(i);
- }
- read_values5.idx_start_PE2=199;
- for (i=201;i<=399;i++) {
- read_values5.single_or_PE_val.push_back(200);
- }
- ret=cms->addRead(read_values5);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values5);
- assert(ret==0);
-
- delete cms;
-}
-
-/* Test new implementation of PE as single.
- * In this implementation, we process PE separately and we keep a PE if med(cov(PE1)) or med((covPE2)) < C and
- * med(cov(PE1)) or med(cov(PE2)<c .*/
-void testCMS_with_PE_NotasSingle2(int lambda,int kappa,int kappa_prime) {
- int filter_PE_separately=2;
- CountMinSketch<unsigned char>* cms=new CountMinSketch<unsigned char>(lambda,kappa,kappa_prime,filter_PE_separately);
- int i;
- cout<<"size of the CMS component: "<<sizeof(cms)<<endl;
- int num=200;
- //int rej_expected=0;
- int ret;
- for (i=0;i<kappa;i++) {
- cms->addKMer(num);
- }
- int min=cms->getEstimatedNbOcc(num);
- assert(min==kappa);
- // mimic a PE read (as given by part 2 output).
- T_read_numericValues read_values;
-
- // mimic a PE read in which PE1 contains k-mer that appear rarely in the CMS and PE2 contains k_mers that already appear kappa times in the CMS.
- for (i=1;i<=200;i++) {
- read_values.single_or_PE_val.push_back(i*1000-1);
- }
- read_values.idx_start_PE2=200;
- for (i=1;i<=239;i++) {
- read_values.single_or_PE_val.push_back(num);
- }
- read_values.single_or_PE_val.push_back(50);
- read_values.single_or_PE_val.push_back(55);
- ret=cms->addRead(read_values); // read should be accepted since PE1 is nor over covered.
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values); // read should be considered under covered since PE1 is under covered.
- assert(ret>0);
-
- // Now, change PE1 a little and insert it kappa times in the CMS
- for (int j=1;j<=kappa;j++) {
- read_values.single_or_PE_val[2]=j;
- ret=cms->addRead(read_values);
- if (j<=kappa-1) assert(ret>0); // read should be accepted as long as we haven't inserted PE1 kappa times.
- else assert(ret==0); //otherwise it is rejected.
- }
-
- ret=cms->isBeneathMinKappa(read_values); // read should not be considered under covered since PE1 was inserted kappa times.
- assert(ret==0);
-
- // mimic a PE read (as given by part 2 output).
- T_read_numericValues read_values2;
-
- // mimic a PE read that will be inserted in the CMS kappa_prime+1 times to check low filter.
- for (i=1;i<=150;i++) {
- read_values2.single_or_PE_val.push_back(i*1500-1);
- }
- read_values2.idx_start_PE2=150;
- for (i=1;i<=151;i++) {
- read_values2.single_or_PE_val.push_back(i*1600-1);
- }
- for (i=0;i<kappa_prime+1;i++) {
- ret=cms->addRead(read_values2);
- assert(ret>0);
- }
-
- ret=cms->isBeneathMinKappa(read_values2);
- assert(ret==0);
-
- //mimic a read for which PE1 is under kappa_prime and PE2 too. Such a read is expected to be removed by low filter
- T_read_numericValues read_values3;
-
- for (i=1;i<=200;i++) {
- read_values3.single_or_PE_val.push_back(i);
- }
- read_values3.idx_start_PE2=201;
- for (i=1;i<=205;i++) {
- read_values3.single_or_PE_val.push_back(i);
- }
- ret=cms->addRead(read_values3);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values3);
- assert(ret>0);
-
- //mimic a read for which PE1 is over kappa_prime but not PE2
- T_read_numericValues read_values4;
- for (i=201;i<=399;i++) {
- read_values4.single_or_PE_val.push_back(200);
- }
- read_values4.idx_start_PE2=199;
- for (i=201;i<=399;i++) {
- read_values4.single_or_PE_val.push_back(i);
- }
- ret=cms->addRead(read_values4);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values4);
- assert(ret>0);
-
- //mimic a read for which PE2 is over kappa_prime but not PE1
- T_read_numericValues read_values5;
- for (i=201;i<=399;i++) {
- read_values5.single_or_PE_val.push_back(i);
- }
- read_values5.idx_start_PE2=199;
- for (i=201;i<=399;i++) {
- read_values5.single_or_PE_val.push_back(200);
- }
- ret=cms->addRead(read_values5);
- assert(ret>0);
-
- ret=cms->isBeneathMinKappa(read_values5);
- assert(ret>0);
-
- delete cms;
-}
/*
* TODO: move this somewhere else.
@@ -470,11 +240,6 @@ int main(int argc, char **argv) {
test_ROCKparams();
cout<<"testing CMS with lambda="<<lambda<<endl;
test_CMS(lambda,kappa,kappa_prime); // Finally using C arrays (maps implied storing hash keys : 4 Bytes per k_mer overhead) but each array is of size INT_MAX...
- //cout<<"testing CMS with PE not as single strict kappa prime implementation"<<endl;
- // VL comment these tests since AC says That the best option is to treat PE as single.
- /*testCMS_with_PE_NotasSingle(lambda,kappa,kappa_prime);
- cout<<"testing CMS with PE not as single lenient kappa prime implementation"<<endl;
- testCMS_with_PE_NotasSingle2(lambda,kappa,kappa_prime);*/
cout<<"done"<<endl;
// profiling_CMS_fill();
diff --git a/src/unit_test_read_utils.cpp b/src/unit_test_read_utils.cpp
index 648af9a..5b22586 100644
--- a/src/unit_test_read_utils.cpp
+++ b/src/unit_test_read_utils.cpp
@@ -202,7 +202,7 @@ void test_getReadPEWithNQST() {
void test_decomposeReadInkMerNums() {
int k=5;
ReadProcessor read_p(k);
- T_read_numericValues nbrKmerDecompo;
+ readNumericValues nbrKmerDecompo;
DnaSeqStr a_seqs[2];
init_DnaSeqStr(&a_seqs[0]);
@@ -212,26 +212,19 @@ void test_decomposeReadInkMerNums() {
strcpy(seq1->fq_record_buf,"@fake_stuff\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+\n....@\n");
seq1->start_idx=12;
seq1->length=75;
- decomposeReadInKMerNums(read_p,nbrKmerDecompo,k,1,a_seqs);
- assert(nbrKmerDecompo.single_or_PE_val.size()==71);
- assert(nbrKmerDecompo.idx_start_PE2==0);
+ decomposeReadInKMerNums(read_p,nbrKmerDecompo,k,a_seqs);
+ assert(nbrKmerDecompo.size()==71);
readNumericValues::iterator it;
- for (it=nbrKmerDecompo.single_or_PE_val.begin();it!=nbrKmerDecompo.single_or_PE_val.end();it++) {
+ for (it=nbrKmerDecompo.begin();it!=nbrKmerDecompo.end();it++) {
assert(*it==1023);
}
DnaSeqStr * seq2=&a_seqs[1];
strcpy(seq2->fq_record_buf,"@another_fake_stuff\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\n+\n....@\n");
seq2->start_idx=20;
seq2->length=80;
- nbrKmerDecompo.single_or_PE_val.clear();
- decomposeReadInKMerNums(read_p,nbrKmerDecompo,k,1,a_seqs);
- assert(nbrKmerDecompo.single_or_PE_val.size()==147);
- assert(nbrKmerDecompo.idx_start_PE2==0);
-
- T_read_numericValues nbrKmerDecompo2;
- decomposeReadInKMerNums(read_p,nbrKmerDecompo2,k,0,a_seqs);
- assert(nbrKmerDecompo2.single_or_PE_val.size()==147);
- assert(nbrKmerDecompo2.idx_start_PE2==71);
+ nbrKmerDecompo.clear();
+ decomposeReadInKMerNums(read_p,nbrKmerDecompo,k,a_seqs);
+ assert(nbrKmerDecompo.size()==147);
}
@@ -312,8 +305,6 @@ void testDNAToNumberMoreComplex() { // TODO in main, check that k<=32.
int nb_expected_k_mers=strlen(dnaStr)+1;
nb_expected_k_mers-=k;
nbrKmerDecompo.reserve(nb_expected_k_mers);
- // unsigned long expected=read_p.kMerToNumber((char *) "GCTACCATAACACCAACTGTTTTCACCATA",NULL);
- // unsigned long expected_rev=read_p.kMerToNumber((char *) "TATGGTGAAAACAGTTGGTGTTATGGTAGC",NULL);
read_p.getKMerNumbers((char *) dnaStr,strlen(dnaStr),nbrKmerDecompo);
assert(nbrKmerDecompo.size()==nb_expected_k_mers); // for each k_mer, we also expect to have a number for its reverse complement.
@@ -356,7 +347,6 @@ void testDNAToNumberMoreComplex() { // TODO in main, check that k<=32.
}
}
-// NTTTTNGGTGCTACCATAACACCAACTGTTTTCACCATAATTTTAANATCAAGCATTAGAGACGCTTCTCTAATGTATTGCAAATCTAGTTCTACCATTTGATGAAAATCTAATTCATTTCTTCCACTAACCTGCCATAATCCAGTACAACCTGGTATAACGGTCAAACGCTTTTTATCATAGGAACTGTATTCTCCTACCTCACGTGGCAAAGGAGGTCTTGGACCAACAATTGCCATGTCTCCTTTAACCACATTCCAAAGCTGTGGTA
/*
* Tests the handling of N nucleotides.
@@ -405,7 +395,6 @@ void test_getReadWithNQST() {
assert(my_struct1.read_a1==639);
assert(my_struct2.read_a1==1228);
srp io_sr;
- //unsigned int j=0;
DnaSeqStr a_seqs;
char dna_read[MAX_READ_LENGTH];
@@ -424,8 +413,6 @@ void test_getReadWithNQST() {
tmp+=a_seqs.start_idx;
memcpy(dna_read,tmp,a_seqs.length);
dna_read[a_seqs.length]='\0';
- /*std::cout<<"modified dna read:"<<endl;
- std::cout<<dna_read<<endl;*/
assert(strcmp(dna_read,"NNNNNAGGTGCTACCATAACACCAACTGTTTTCACNATAATTTTAAAATCAAGCATTAGAGACGCNTCTCTAATGTATTGCAAATCTAGTTCTACCATTTGATGAAAATCTAATTNATTTCTTCCACTANCCTGCCATAATCCAGTACAACCTGGTATAACGGNCAANCGCTTTTTATCATAGGANCTGTATTCTCCTACCTCACGTGGCAAAGGAGGNCTTGGACCAACAATTGCCATGTCTCCTTTAACCACATTCCAAAGCTGNNNNN")==0);
init_DnaSeqStr(&a_seqs);
@@ -434,7 +421,6 @@ void test_getReadWithNQST() {
tmp=(char *) a_seqs.fq_record_buf;
tmp+=a_seqs.start_idx;
memcpy(dna_read,tmp,a_seqs.length);
- // std::cout<<dna_read<<endl;
assert(strcmp(dna_read,"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN")==0);
// now test the same thing with PE reads
--
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