diff --git a/Makefile.in b/Makefile.in
deleted file mode 100644
index d1fc1764699231231ef98afb5bf0ae733f66d14d..0000000000000000000000000000000000000000
--- a/Makefile.in
+++ /dev/null
@@ -1,763 +0,0 @@
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-
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diff --git a/src/.settings/language.settings.xml b/src/.settings/language.settings.xml
deleted file mode 100644
index 527fb011044a60d3943527299156f9d5de8be1d0..0000000000000000000000000000000000000000
--- a/src/.settings/language.settings.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<project>
- <configuration id="cdt.managedbuild.toolchain.gnu.macosx.base.481822517" name="Default">
- <extension point="org.eclipse.cdt.core.LanguageSettingsProvider">
- <provider copy-of="extension" id="org.eclipse.cdt.ui.UserLanguageSettingsProvider"/>
- <provider-reference id="org.eclipse.cdt.core.ReferencedProjectsLanguageSettingsProvider" ref="shared-provider"/>
- <provider class="org.eclipse.cdt.managedbuilder.language.settings.providers.GCCBuildCommandParser" id="org.eclipse.cdt.managedbuilder.core.GCCBuildCommandParser" keep-relative-paths="false" name="CDT GCC Build Output Parser" parameter="(g?cc)|([gc]\+\+)|(clang)" prefer-non-shared="true"/>
- <provider class="org.eclipse.cdt.managedbuilder.language.settings.providers.GCCBuiltinSpecsDetector" console="false" env-hash="-1667358530298693438" id="org.eclipse.cdt.managedbuilder.core.GCCBuiltinSpecsDetector" keep-relative-paths="false" name="CDT GCC Built-in Compiler Settings" parameter="${COMMAND} ${FLAGS} -E -P -v -dD "${INPUTS}"" prefer-non-shared="true">
- <language-scope id="org.eclipse.cdt.core.gcc"/>
- <language-scope id="org.eclipse.cdt.core.g++"/>
- </provider>
- <provider-reference id="org.eclipse.cdt.managedbuilder.core.MBSLanguageSettingsProvider" ref="shared-provider"/>
- </extension>
- </configuration>
-</project>
\ No newline at end of file
diff --git a/src/FqBaseBackend.cpp b/src/FqBaseBackend.cpp
index fd55744ca9cf9b0244491eb84cb17f61d16296c3..59013d754f882113e9d02e26f160ccd3563ccb23 100644
--- a/src/FqBaseBackend.cpp
+++ b/src/FqBaseBackend.cpp
@@ -83,14 +83,7 @@ void FqBaseBackend::openOutputFile(){
openFile4Output(o_filename,&o_f_desc);
}
-/*
-void FqBaseBackend::openUndefFile(){
- //std::cout<<qual_thres.min_correct_k_mers_in_read<<endl;
- if (qual_thres.min_correct_k_mers_in_read>=1) {
- if (undef_filename==NULL) throw std::runtime_error("No file currently associated to this backend for undefined reads.");
- openFile4Output(undef_filename,&undef_f_desc);
- }
-}*/
+
void FqBaseBackend::openFile4Output(char * filename, int * f_desc) {
mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
@@ -119,39 +112,6 @@ void FqBaseBackend::closeOutputFile() {
}
}
-/*void FqBaseBackend::closeUndefFile() {
- if (undef_f_desc!=-1) {
- if (close(undef_f_desc)==-1) err(errno,"cannot close file: %s.",undef_filename);
- undef_f_desc=-1;
- }
-}*/
-
-/*
-void FqBaseBackend::writeStrToUndefFile(char * start_in_buf, int len) {
- if (write(undef_f_desc,start_in_buf,len)==-1) err(errno,"cannot write in file: %s.",undef_filename);
-}*/
-
-/*
- * Writes a fq record to the file containing "undefined" reads.
- * Undefined reads are those who don't contain the minimum number of valid k-mer.
- * The thing is that:
- * - when called from mainBackend, the \n terminating the fastq record has not been counted yet.
- * - when called fromAuxBackend, the final \n has already been counted
- * So, values for buf_info.pchar and buf_info.cnt may or may not contain the final \n.
- * This is why I use the addCR parameter to add it or not.
- */
-/*
-void FqBaseBackend::writeToUndefFile(const T_buf_info& buf_info,const int& addCR) {
- int l=strlen(cur_fq_record);
- if (l==0) {
- writeStrToUndefFile(buf_info.p_start_cur_rec,buf_info.pchar-buf_info.p_start_cur_rec+addCR);
- } else {
- memcpy(cur_fq_record+l,buf_info.p_start_cur_rec,buf_info.cnt+addCR);
- l+=buf_info.cnt;
- cur_fq_record[l+addCR]='\0';
- writeStrToUndefFile(cur_fq_record,strlen(cur_fq_record)); // Try that, if there is performance problem due to resolving inheritance, will find a different way
- }
-}*/
diff --git a/src/FqMainBackend.cpp b/src/FqMainBackend.cpp
index bb37e787a25ef842a92038791da334508815024e..a259053d242b70435a27d96694ec8a555a51826d 100644
--- a/src/FqMainBackend.cpp
+++ b/src/FqMainBackend.cpp
@@ -137,8 +137,8 @@ void FqMainBackend::onEndFastqRecord(T_fq_rec_info& rec_info,const T_buf_info& b
void FqMainBackend::processBuf(T_buf_info& buf_info,unsigned char f_id,unsigned long cur_offset) {
static T_fq_rec_info fq_rec_info;
- static int num_l_in_rec; /* counter to know on which line inside the fastq record we are */
- static int qual_score=0;
+ static int num_l_in_rec=5; /* counter to know on which line inside the fastq record we are */
+ //static int qual_score=0;
static int n;
int start_rec_in_buf=0;
@@ -146,7 +146,7 @@ void FqMainBackend::processBuf(T_buf_info& buf_info,unsigned char f_id,unsigned
while (buf_info.cnt<=buf_info.real_bufsize-1) {
switch (*buf_info.pchar){
case k_read_id_start:
- if (qual_score) goto inc_score;
+ if (num_l_in_rec==4) goto inc_score;
else {
buf_info.p_start_cur_rec=buf_info.pchar;
fq_rec_info.rstart_offset=cur_offset-buf_info.real_bufsize+buf_info.cnt;
@@ -155,31 +155,23 @@ void FqMainBackend::processBuf(T_buf_info& buf_info,unsigned char f_id,unsigned
num_l_in_rec=1;
fq_rec_info.nb_nucleotides_in_read=0;
fq_rec_info.nb_nucleotides_in_read_PE2=0;
+ fq_rec_info.nb_k_mers_in_error=0;
+ fq_rec_info.nb_k_mers_in_error_in_PE2=0;
+ fq_rec_info.st=0;
+ fq_rec_info.idx_nucl_in_read=0;
+ n=0; // counter for k-mers in error
}
break;
- case k_read_qual_start:
- if (qual_score) goto inc_score; // In this case we are already processing the read score. The + char is simply phred score 43-33=10 if phred33.
- qual_score=1;
- fq_rec_info.nb_k_mers_in_error=0;
- fq_rec_info.nb_k_mers_in_error_in_PE2=0;
- fq_rec_info.st=0;
- fq_rec_info.idx_nucl_in_read=0;
- n=0; // counter for k-mers in error
- break;
case '\n':
//debug_processBuf(on_line_end,buf_info,fq_rec_info.rstart_offset);
- (qual_score==1)?qual_score++:qual_score;
num_l_in_rec+=1;
- if (num_l_in_rec==5) {
- qual_score=0;/* end of fastq record */
- onEndFastqRecord(fq_rec_info,buf_info);
- }
+ if (num_l_in_rec==5) onEndFastqRecord(fq_rec_info,buf_info);
break;
default:
//debug_processBuf(on_store_read_id,buf_info,fq_rec_info.rstart_offset);
(num_l_in_rec==2)?fq_rec_info.nb_nucleotides_in_read++:fq_rec_info.nb_nucleotides_in_read;
inc_score:
- { if (qual_score==2) onIncScore(fq_rec_info,buf_info,n);
+ { if (num_l_in_rec==4) onIncScore(fq_rec_info,buf_info,n);
}
break;
}
diff --git a/src/Makefile.in b/src/Makefile.in
deleted file mode 100644
index a112f5c9051215ae924245e59465707aaa2d90ae..0000000000000000000000000000000000000000
--- a/src/Makefile.in
+++ /dev/null
@@ -1,737 +0,0 @@
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-
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-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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-.PRECIOUS: Makefile
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/src/unit_test_fqreader.cpp b/src/unit_test_fqreader.cpp
index bb727735c1ad197f6e59e1ae63557415a225218c..b5eb927d67da46feb759cbb4858d09f2c69c14bc 100644
--- a/src/unit_test_fqreader.cpp
+++ b/src/unit_test_fqreader.cpp
@@ -647,14 +647,11 @@ AAAAAEEAEEEEEEEEE6EE/EEEEEEEEAEEAEEEEEEEEEEEEEEAEEEA/A/EEEAEEEEEE/EE</EAEEEEEE/E
FqBaseBackend::setQualThreshold(qual_thres);
FqMainBackend::setTreatPEMode(0);
FqMainBackend be(&sr);
- //be.setUndefFile((char *) "../test/data/unit/test_processBuf.undef.fq");
buf_info.buf=buf;
buf_info.pchar=buf;
buf_info.cnt=0;
buf_info.real_bufsize=strlen(buf);
- //be.openUndefFile();
be.processBuf(buf_info,f_id1,348);
- //be.closeUndefFile();
// check that read is rejected
for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
@@ -664,18 +661,65 @@ AAAAAEEAEEEEEEEEE6EE/EEEEEEEEAEEAEEEEEEEEEEEEEEAEEEA/A/EEEAEEEEEE/EE</EAEEEEEE/E
}
}
assert(cnt_read==0);
- /*std::ifstream t("../test/data/unit/test_processBuf.undef.fq");
- std::string rej_str;
-
- t.seekg(0, std::ios::end);
- rej_str.reserve(t.tellg());
- t.seekg(0, std::ios::beg);
-
- rej_str.assign((std::istreambuf_iterator<char>(t)),
- std::istreambuf_iterator<char>());
- assert(strcmp(rej_str.c_str(),buf)==0);
+}
+
+void test_processBufSinglePlusCharBug() {
+ srp::reverse_iterator rit;
+ i_dim::iterator it_offs;
+ k_dim::iterator it_struct;
+ std::string bufstr="@SRR001666.4 071112_SLXA-EAS1_s_7:5:1:792:346/2\n\
+AAAGTTAACGAACGCGCGAAAGGTCTGGAAGGTATC\n\
++\n\
+IIIIIIII@+IIIIIIIIB@7IIF=III+CIID0I+\n\
+@NB501291:419:HWLVNBGXK:1:11101:20148:1052 2:N:0:ATCTCAGG+NGGAGAGA\n\
+GATTTTAAANNNNNNNNNAAATNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNAANTTAANGNAANCTGATTACCATGNTAGNNCATATTAGTTNGANCGCCGCGTTNTTCNANACATANNGTAATCNNANTNACTAAGTATTCNTNCGGTA\n\
++\n\
+AAAA/EEEE#########EEEE###############E##############EE#EEEE#E#EE#/EEEEEEEAEEE#EEE##<AAEEEEEEE#AE#6EE/EEE<E#EEE#E#EEEA/##/EEEE<##<#/#/<AE/AA/EE/#A#/AAA/\n\
+@NB501291:419:HWLVNBGXK:1:11101:11957:1078 2:N:0:ATCTCAGG+CGGAGAGA\n\
+ATTATATGATGCAGTAAAAGCCATTGGTGAAGAGCTATGCCCACAATTAGGTATTACTATTCCGGTGGGTAAGGACTCAATGTCCATGAAAACGCGTTGGCAAGATGATCAAGGGAAAACGAAAGAAGTTATTTCACCGCTCTCTTTAGTT\n\
++\n\
+AAAAAEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEE<EEEAEEEEA<EAEEEEEEEAAAAE<EEEE/EEEEAAEEEEEEE<EEEEAAEEE<AE<EE<EEEEAEE/EE/EEEE<EE/EE/E/EEEEEAE<E</<<<AE<AAAEEE/AE\n";
+ char * buf=(char *) bufstr.c_str();
+ srp sr;
+ T_buf_info buf_info;
+ FasqQualThreshold qual_thres;
+ qual_thres.min_correct_k_mers_in_read=1;
+ qual_thres.nucl_score_threshold=k_phred_32;
+ qual_thres.k=25;
+ FqBaseBackend::setQualThreshold(qual_thres);
+ FqMainBackend::setTreatPEMode(0);
+ FqMainBackend be(&sr);
+ buf_info.buf=buf;
+ buf_info.pchar=buf;
+ buf_info.cnt=0;
+ buf_info.real_bufsize=strlen(buf);
+ unsigned char f_id1=1;
+ be.processBuf(buf_info,f_id1,855);
+ int cnt_read=0;
+ for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
+ int score=rit->first;
+ for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
+ unsigned int q=it_offs->first;
+ assert(q==0);
+ for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
+ cnt_read++;
+ if (cnt_read==1) {
+ assert(score==9); // real score is 5016+151*k_phred_32 but it is normalized by taking the quotient of a division by 1000.
+ //assert(it_struct->read_a1==429);
+ }
+ else if (cnt_read==2) {
+ assert(score==8); // real score is 3076 + 151*k_phred_32
+ //assert(it_struct->read_a1==120);
+ }
+ else if (cnt_read==3) {
+ assert(score==2); // real score is 1256 + 36*k_phred_32 (we don't do the substraction to gain calculation time).
+ //assert(it_struct->read_a1==0);
+ }
+ }
+ }
+ }
+ assert(cnt_read==3);
- assert(remove((char *) "../test/data/unit/test_processBuf.undef.fq")==0);*/
}
void test_processBufPE() {
@@ -707,10 +751,8 @@ AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEE
FqMainBackend::setTreatPEMode(0);
FqMainBackend be(&sr);
- //be.setUndefFile((char *) "../test/data/unit/test_processBuf_PE1.undef.fq");
FqAuxBackend be2;
- //be2.setUndefFile((char *) "../test/data/unit/test_processBuf_PE2.undef.fq");
buf_info.buf=buf_PE1;
@@ -726,11 +768,7 @@ AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEE
be.setAuxProcessor(&be2);
- //be.openUndefFile();
- //be2.openUndefFile();
be.processBuf(buf_info,f_id1,348);
- //be.closeUndefFile();
- //be2.closeUndefFile();
// check that read is selected
for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
@@ -741,16 +779,6 @@ AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEE
}
}
assert(cnt_read==1);
-
- /*struct stat fileStat;
- stat("../test/data/unit/test_processBuf_PE1.undef.fq", &fileStat);
- assert(fileStat.st_size==0);
-
- stat("../test/data/unit/test_processBuf_PE2.undef.fq", &fileStat);
- assert(fileStat.st_size==0);
-
- assert(remove((char *) "../test/data/unit/test_processBuf_PE1.undef.fq")==0);
- assert(remove((char *) "../test/data/unit/test_processBuf_PE2.undef.fq")==0);*/
}
@@ -782,7 +810,6 @@ void Aux_MimicBigPEFilesWithMQOptions(const FasqQualThreshold& qual_thres,const
int cnt_read=0;
for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
- //unsigned long score=rit->first;
for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
cnt_read++;
@@ -790,15 +817,6 @@ void Aux_MimicBigPEFilesWithMQOptions(const FasqQualThreshold& qual_thres,const
}
}
assert(cnt_read==nb_expected_reads);
- /*if (nb_expected_reads==6) {
- assert(compareFilesLileByLine(fq_1_test_undef,fq_1_expected_undef_100)==0);
- assert(compareFilesLileByLine(fq_2_test_undef,fq_2_expected_undef_100)==0);
- } else {
- assert(compareFilesLileByLine(fq_1_test_undef,fq_1_expected_undef_180)==0);
- assert(compareFilesLileByLine(fq_2_test_undef,fq_2_expected_undef_180)==0);
- }
- assert(remove((char *) "../test/data/unit/09-4607_S43_R1.undef.fastq")==0);
- assert(remove((char *) "../test/data/unit/09-4607_S43_R2.undef.fastq")==0);*/
}
@@ -826,6 +844,8 @@ void test_MimicBigPEFilesWithMQOptions() {
}
int main(int argc, char **argv) {
+ cout<<"test for the case where there are + characters in read score and or read id"<<endl;
+ test_processBufSinglePlusCharBug();
cout<<"test for single file"<<endl;
test_processSingleFile();
cout<<"test for PE files"<<endl;
diff --git a/test/Makefile.in b/test/Makefile.in
deleted file mode 100644
index 2c01e42a55b7f525f8f4b99d382fd4f4f7f0b8be..0000000000000000000000000000000000000000
--- a/test/Makefile.in
+++ /dev/null
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