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Commit 2fee4abc authored by Veronique Legrand's avatar Veronique Legrand
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disabled the -p option. Default is now to process PE as single

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src/CountMinSketch.hpp
+ 1
− 1
View file @ 2fee4abc
......@@ -148,7 +148,7 @@ private:
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=1);
void init(int glambda,int gkappa,int gkappa_prime,int filter_PE_separately=0);
// for unit tests.
friend void test_CMS(int lambda,int kappa,int kappa_prime);
......
src/ROCKparams.cpp
+ 6
− 6
View file @ 2fee4abc
......@@ -24,10 +24,10 @@ void ROCKparams::computeLambda() {
parms.lambda=tmp/UINT_MAX;
if (parms.kappa>get_mask<unsigned char>::value) parms.lambda=parms.lambda/sizeof(unsigned short);
}
/*
int ROCKparams::getfilterPEMode() {
return parms.filter_PE_separately;
}
}*/
void ROCKparams::processMainArgs(int optind, const int argc, char ** argv,std::vector<string>& v_input_lines) {
......@@ -279,7 +279,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
//int option_index=0;
// while((i = getopt_long(argc, argv, "i:o:l:k:c:C:g:n:vq:m:",long_options,&option_index)) != -1) {
while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:vq:m:p:")) != -1) {
while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:vq:m:")) != -1) {
switch(i) {
case 0:
break;
......@@ -321,7 +321,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
case 'v':
verbose_mode=1;
break;
case 'p':
/* case 'p':
if (strlen(optarg)>1) {
cout<<"value for -p option must be 0, 1 or 2";
usage(EXIT_FAILURE);
......@@ -331,7 +331,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
cout<<"value for -p option must be 0, 1 or 2";
usage(EXIT_FAILURE);
}
break;
break;*/
case 'q':
q=atoi(optarg);
if (q<0) {
......@@ -356,7 +356,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
cout<<"Incompatible options: when PE are processed independently, minimum number of correct k-mers in each end is 1."<<endl;
usage(EXIT_FAILURE);
}*/
parms.filter_PE_separately=PE_separately;
//parms.filter_PE_separately=PE_separately;
//cout<<PE_as_single<<endl;
processMainArgs(optind, argc, argv,v_input_lines);
optArgConsistency(input_file,output_file,g,parms,nb_k_mers,v_input_lines);
......
src/ROCKparams.h
+ 2
− 2
View file @ 2fee4abc
......@@ -79,7 +79,7 @@ class ROCKparams{
public:
FasqQualThreshold getQualThreshold();
int getfilterPEMode();
//int getfilterPEMode();
ROCKparams() {
f_id=0; // to generate id of input/output fastq files. +1=total number of files.
......@@ -89,7 +89,7 @@ public:
parms.kappa=70;
parms.kappa_prime=5;
parms.lambda=0;
parms.filter_PE_separately=1;
//parms.filter_PE_separately=1;
qual_thres.min_correct_k_mers_in_read=1;
qual_thres.nucl_score_threshold=10+k_phred_32;
qual_thres.k=k;
......
src/rock.cpp
+ 1
− 1
View file @ 2fee4abc
......@@ -69,7 +69,7 @@ int main(int argc,char * argv[]) {
cout<<"processed input args; going to start reading fastq files"<<endl;
printRUsage();
#endif
processInputFiles(single_files,v_PE_files,map_id_backend,main_parms.getQualThreshold(),&sr,main_parms.getfilterPEMode());
processInputFiles(single_files,v_PE_files,map_id_backend,main_parms.getQualThreshold(),&sr,0); // Removing -p option, set default mode to 0 (PE processed as single).
#ifdef BENCHMARK
cout<<"finished loading fastq file into sr structure"<<endl;
cout<<"size of srp structure="<<sizeof(sr)<<endl;
......
test/rock.sh
+ 11
− 11
View file @ 2fee4abc
......@@ -55,19 +55,19 @@ mkdir data/fastq.filtered || exit 6
echo " "
echo "##################################################################################"
echo "doing more checks on options and error messages"
../src/rock -C 500000 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for kappa" >/dev/null || exit 7
../src/rock -C 500 -c 600 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "ERROR lower filter is higher than high filter" >/dev/null || exit 8
../src/rock -C 500 -c 400 -k 60 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for k" >/dev/null || exit 9
../src/rock -C 500 -c 400 -k 10 -l 0 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for lambda" >/dev/null || exit 10
../src/rock -C 500 -c 400 -k 10 -l 500 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Not enough RAM on the machine" >/dev/null || exit 11
../src/rock -C 500000 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for kappa" >/dev/null || exit 7
../src/rock -C 500 -c 600 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "ERROR lower filter is higher than high filter" >/dev/null || exit 8
../src/rock -C 500 -c 400 -k 60 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for k" >/dev/null || exit 9
../src/rock -C 500 -c 400 -k 10 -l 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for lambda" >/dev/null || exit 10
../src/rock -C 500 -c 400 -k 10 -l 500 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Not enough RAM on the machine" >/dev/null || exit 11
../src/rock -C 500 -c 400 -k 10 -l 12 -g 25 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "options are mutually exclusive" >/dev/null|| exit 12
../src/rock -C 500 -c 400 -k 10 -g 10000 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "This machine only has" >/dev/null || exit 13
../src/rock -C 500 -c 400 -k 10 -l 12 -n 85000000 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "options are mutually exclusive">/dev/null || exit 14
../src/rock -C 500 -c 400 -k 10 -q 3 -m 0 -p 0 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "minimum number of valid k-mer for keeping a read must be an integer">/dev/null || exit 15
../src/rock -C 500 -c 400 -k 10 -q -1 -m 2 -p 0 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "q must be">/dev/null || exit 16
../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 10 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 1,5 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 18
../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p -1 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
../src/rock -C 500 -c 400 -k 10 -q 3 -m 0 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "minimum number of valid k-mer for keeping a read must be an integer">/dev/null || exit 15
../src/rock -C 500 -c 400 -k 10 -q -1 -m 2 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "q must be">/dev/null || exit 16
#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 10 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 1,5 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 18
#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p -1 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
#../src/rock -C 500 -c 400 -k 10 -q 2 -m 2 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "Incompatible options">/dev/null || exit 161
......@@ -75,7 +75,7 @@ echo "doing more checks on options and error messages"
../src/unit_test_cms CHECK_MEM
if [ $? = 0 ] ## we have enough memory to run the tests in rock_mem.sh
then
${srcdir}/rock_mem.sh ||exit 255
${srcdir}/rock_mem.sh ||exit 255
fi
# unit tests
......
test/rock_mem.sh
+ 395
− 395
View file @ 2fee4abc
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