diff --git a/src/.settings/language.settings.xml b/src/.settings/language.settings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..527fb011044a60d3943527299156f9d5de8be1d0
--- /dev/null
+++ b/src/.settings/language.settings.xml
@@ -0,0 +1,15 @@
+<?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/ReadProcessor.cpp b/src/ReadProcessor.cpp
index 27030213a7bd5fe4ca2db89827e8b22880665bae..dde661758b9606f3f50919c0342cb5279cc885af 100644
--- a/src/ReadProcessor.cpp
+++ b/src/ReadProcessor.cpp
@@ -25,7 +25,7 @@
#include "ReadProcessor.h"
#include <iostream>
-//! Tried to inline this bur slightly slower. Stays here.
+//! Tried to inline this but slightly slower. Stays here.
unsigned long ReadProcessor::nucleoToNumberWrap(char s) {
(s=='N')?n=k:n;
n--;
@@ -36,7 +36,7 @@ void ReadProcessor::kMerAndRevToNumber(char * k_m,KmRevNumbers& numbers) {
unsigned long c,crev;
if (numbers.first) { // first k_mer conversion
int i;
- int j=k;
+ int j=k;
for (i=0;i<k;i++) {
c=nucleoToNumberWrap(k_m[i]); // do not catch exception for the moment. If nucleoToNumber throws -1 and there is no catch clause for it, the terminate() function will be called automatically. Anyway, there's not munch we can do if it returns -1.
numbers.nbr=numbers.nbr<<2;
@@ -45,7 +45,7 @@ void ReadProcessor::kMerAndRevToNumber(char * k_m,KmRevNumbers& numbers) {
numbers.nbr_rev=numbers.nbr_rev|crev;
j--;
}
- numbers.first=0;
+ numbers.first=0;
} else {
c=nucleoToNumberWrap(k_m[k-1]);
numbers.nbr=numbers.nbr<<2;
@@ -62,6 +62,7 @@ void ReadProcessor::kMerAndRevToNumber(char * k_m,KmRevNumbers& numbers) {
void ReadProcessor::getKMerNumbers(char * dnaStr,int l,std::vector<unsigned long>& my_vect) { // See simple_test.cpp and results. benchmark showed that std::vector is very slightly faster than C array and doesn't require more memory in our case. So, I am using it since it makes code simpler.
int i;
KmRevNumbers numbers;
+ initNumbers(numbers);
char * p_char=dnaStr;
int nb_k_m=l-k+1;
for (i=0; i<nb_k_m;i++) {
diff --git a/src/ReadProcessor.h b/src/ReadProcessor.h
index 62f688179fb833171cd1c1080fee81381000bede..8caa552c8da2795bf4f864211d853010ffa36c4d 100644
--- a/src/ReadProcessor.h
+++ b/src/ReadProcessor.h
@@ -35,12 +35,8 @@
#include <iostream>
using namespace std;
-//! Gather here the numbers corresponding to a kmer and it's reverse complement once they were hashed.
-typedef struct {
- unsigned long nbr;
- unsigned long nbr_rev;
- unsigned int first; //! set this to 1 before processing the 1rst kmer of the read.
-} KmRevNumbers;
+
+
class ReadProcessor {
@@ -51,6 +47,7 @@ class ReadProcessor {
std::map<char, char> nucleo_rev_cpl;
unsigned long mask_kMer;
+
void init_nucleo_rev_cpl() {
nucleo_rev_cpl['A']='T';
nucleo_rev_cpl['T']='A';
@@ -114,11 +111,24 @@ public:
init_mask(k);
}
+ //! Gather here the numbers corresponding to a kmer and it's reverse complement once they were hashed.
+ typedef struct {
+ unsigned long nbr;
+ unsigned long nbr_rev;
+ unsigned int first; //! set this to 1 before processing the 1rst kmer of the read.
+ } KmRevNumbers;
+
+ void initNumbers(KmRevNumbers& numbers) {
+ numbers.first=1;
+ numbers.nbr=0;
+ numbers.nbr_rev=0;
+ }
+
// Do not inline this; it is slightly slower.
// These functions are no more used. Now using the same loop to convert hash kmer and reverse complement.
/*unsigned long kMerToNumberReverse(char * k_m,unsigned long * p_prev);
unsigned long kMerToNumber(char * k_m,unsigned long * p_prev);*/
-
+ //! The 2 previous methods are now replacs by the one below.
void kMerAndRevToNumber(char * k_m,KmRevNumbers& numbers);
unsigned long nucleoToNumberWrap(char s);
diff --git a/src/unit_test_cms b/src/unit_test_cms
new file mode 100755
index 0000000000000000000000000000000000000000..27b3a8364dac9209abcb6410d8a5fb313c7b7b36
Binary files /dev/null and b/src/unit_test_cms differ
diff --git a/src/unit_test_fqreader b/src/unit_test_fqreader
new file mode 100755
index 0000000000000000000000000000000000000000..056c2b1304d00ab6a76e4bcae8e3a99ed54f62eb
Binary files /dev/null and b/src/unit_test_fqreader differ
diff --git a/src/unit_test_fqwriter b/src/unit_test_fqwriter
new file mode 100755
index 0000000000000000000000000000000000000000..c13adacc2b01f4236a8ba2c702d175fc36616b55
Binary files /dev/null and b/src/unit_test_fqwriter differ
diff --git a/src/unit_test_math_utils b/src/unit_test_math_utils
new file mode 100755
index 0000000000000000000000000000000000000000..2b841e519706a85f8914034929fbccc3909d2173
Binary files /dev/null and b/src/unit_test_math_utils differ
diff --git a/src/unit_test_read_utils b/src/unit_test_read_utils
new file mode 100755
index 0000000000000000000000000000000000000000..fcb34f67c20c3b60f24feb096ea77ae0940c29db
Binary files /dev/null and b/src/unit_test_read_utils differ
diff --git a/src/unit_test_read_utils.cpp b/src/unit_test_read_utils.cpp
index 3e6439964b89c3e060874bbe4e5639f8ade0f8e5..44560b997ed5b4905bf5c3bb64927f946d2a90e1 100644
--- a/src/unit_test_read_utils.cpp
+++ b/src/unit_test_read_utils.cpp
@@ -226,7 +226,18 @@ void test_decomposeReadInkMerNums() {
decomposeReadInKMerNums(read_p,nbrKmerDecompo,k,a_seqs);
assert(nbrKmerDecompo.size()==147);
}
-
+/*
+void initNumbers(KmRevNumbers& numbers) {
+ numbers.first=1;
+ numbers.nbr=0;
+ numbers.nbr_rev=0;
+}*/
+
+void savNumbers(ReadProcessor::KmRevNumbers& numbers,ReadProcessor::KmRevNumbers& numbers_sav) {
+ numbers_sav.first=numbers.first;
+ numbers_sav.nbr=numbers.nbr;
+ numbers_sav.nbr_rev=numbers.nbr_rev;
+}
/*
* Test the basic methods of the ReadProcessor object.
@@ -244,32 +255,42 @@ void testDNAToNumberSimple() {
assert(read_p.nucleoToNumber('N')==0);
// unsigned long * p_prev=NULL;
- KmRevNumbers numbers;
+ ReadProcessor::KmRevNumbers numbers;
+ read_p.initNumbers(numbers);
read_p.set_k(4);
read_p.kMerAndRevToNumber((char *) "AAAA",numbers);
assert(numbers.nbr==0); // TODO : this method should be private in ReadProcessor. Design a friend class to test them or declare this testing function friend in ReadProcessor.
assert(numbers.nbr_rev==255);
read_p.set_k(5);
+ read_p.initNumbers(numbers);
read_p.kMerAndRevToNumber((char *) "AANAA",numbers);
assert(numbers.nbr==0);
assert(numbers.nbr_rev==975);
read_p.set_k(14);
+ read_p.initNumbers(numbers);
read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGG",numbers);
assert(numbers.nbr==219386);
assert(numbers.nbr_rev==84779983);
+ ReadProcessor::KmRevNumbers numbers_orig,numbers_w;
+ savNumbers(numbers,numbers_orig);
+ savNumbers(numbers_orig,numbers_w);
read_p.set_k(15);
- read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGA",numbers);
- assert(numbers.nbr==877544);
- read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGN",numbers);
- assert(numbers.nbr==877544);
- read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGC",numbers);
- assert(numbers.nbr==877545);
- read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGG",numbers);
- assert(numbers.nbr==877546);
- read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGT",numbers);
- assert(numbers.nbr==877547);
+ read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGA",numbers_w);
+ assert(numbers_w.nbr==877544);
+ savNumbers(numbers_orig,numbers_w);
+ read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGN",numbers_w);
+ assert(numbers_w.nbr==877544);
+ savNumbers(numbers_orig,numbers_w);
+ read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGC",numbers_w);
+ assert(numbers_w.nbr==877545);
+ savNumbers(numbers_orig,numbers_w);
+ read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGG",numbers_w);
+ assert(numbers_w.nbr==877546);
+ savNumbers(numbers_orig,numbers_w);
+ read_p.kMerAndRevToNumber((char *) "AANAATCCGATTGGT",numbers_w);
+ assert(numbers_w.nbr==877547);
read_p.set_k(1);
assert(read_p.nucleoToNumberReverse('A',1)==3);
@@ -285,30 +306,31 @@ void testDNAToNumberSimple() {
assert(read_p.nucleoToNumberReverse('T',20)==0);
assert(read_p.nucleoToNumberReverse('N',20)==0);
- numbers.nbr=84779983;
+ numbers.nbr_rev=84779983;
read_p.set_k(14);
read_p.kMerAndRevToNumber((char *)"ANAATCCGATTGGA",numbers);
assert(numbers.nbr_rev==222521587);
- numbers.nbr=84779983;
+ numbers.nbr_rev=84779983;
read_p.kMerAndRevToNumber((char *)"ANAATCCGATTGGN",numbers);
assert(numbers.nbr_rev==21194995);
- numbers.nbr=84779983;
+ numbers.nbr_rev=84779983;
read_p.kMerAndRevToNumber((char *)"ANAATCCGATTGGT",numbers);
assert(numbers.nbr_rev==21194995);
- numbers.nbr=84779983;
+ numbers.nbr_rev=84779983;
read_p.kMerAndRevToNumber((char *)"ANAATCCGATTGGC",numbers);
assert(numbers.nbr_rev==155412723);
- numbers.nbr=84779983;
+ numbers.nbr_rev=84779983;
read_p.kMerAndRevToNumber((char *)"ANAATCCGATTGGG",numbers);
assert(numbers.nbr_rev==88303859);
}
+
+
/*
* Test the ReadProcessor method that will be called by the main program : the one who takes as input a dna string and returns
* a serie of numbers all corresponding to its k-mer composition + reverse complement.
*/
-
void testDNAToNumberMoreComplex() { // TODO in main, check that k<=32.
// from a dna string a found in fq files, return its k-mer decomposition; k-mers are numbers.
char dnaStr[]="TTTTTAGGTGCTACCATAACACCAACTGTTTTCACCATAATTTTAAAATCAAGCATTAGAGACGCTTCTCTAATGTATTGCAAATCTAGTTCTACCATTTGATGAAAATCTAATTCATTTCTTCCACTAACCTGCCATAATCCAGTACAACCTGGTATAACGGTCAAACGCTTTTTATCATAGGAACTGTATTCTCCTACCTCACGTGGCAAAGGAGGTCTTGGACCAACAATTGCCATGTCTCCTTTAACCACATTCCAAAGCTGTGGTA";
@@ -325,35 +347,44 @@ void testDNAToNumberMoreComplex() { // TODO in main, check that k<=32.
assert(nbrKmerDecompo.size()==nb_expected_k_mers); // for each k_mer, we also expect to have a number for its reverse complement.
int cnt_k_mer=0;
unsigned long num,num2;
+ ReadProcessor::KmRevNumbers numbers,numbers_start;
+ read_p.initNumbers(numbers);
+ read_p.initNumbers(numbers_start);
+ read_p.kMerAndRevToNumber((char *) "TTTTTAGGTGCTACCATAACACCAACTGTT",numbers);
+ // 1rst k-mer is : TTTTTAGGTGCTACCATAACACCAACTGTT.
+ // its reverse complement is : AACAGTTGGTGTTATGGTAGCACCTAAAAA
for (it=nbrKmerDecompo.begin();it!=nbrKmerDecompo.end();it++) {
cnt_k_mer++;
- // 1rst k-mer is : TTTTTAGGTGCTACCATAACACCAACTGTT.
- // its reverse complement is : AACAGTTGGTGTTATGGTAGCACCTAAAAA
if (cnt_k_mer==1) {
assert(*it==1151987406330741231);
- num=*it;
+ assert(*it==max(numbers.nbr,numbers.nbr_rev));
+ //num=*it;
}
if (cnt_k_mer==2) {
// 2nd k-mer is : TTTTAGGTGCTACCATAACACCAACTGTTT
- num2=read_p.kMerToNumber((char *) "TTTTAGGTGCTACCATAACACCAACTGTTT",NULL);
- assert(*it==num2);
- unsigned long num3=read_p.kMerToNumber((char *) "TTTTAGGTGCTACCATAACACCAACTGTTT",&num);
- assert(num3==num2);
+ read_p.kMerAndRevToNumber((char *) "TTTTAGGTGCTACCATAACACCAACTGTTT",numbers_start);
+ cout<<numbers_start.nbr<<endl;
+ cout<<numbers_start.nbr_rev<<endl;
+ cout<<*it<<endl;
+ assert(*it==numbers_start.nbr);
+ read_p.kMerAndRevToNumber((char *) "TTTTAGGTGCTACCATAACACCAACTGTTT",numbers);
+ assert(numbers.nbr==numbers_start.nbr);
}
if (cnt_k_mer==3) {
- num=read_p.kMerToNumber((char *) "TTTAGGTGCTACCATAACACCAACTGTTTT",NULL);
- unsigned long num_rev=read_p.kMerToNumber((char *) "AAAACAGTTGGTGTTATGGTAGCACCTAAA",NULL);
- assert(max(num,num_rev)==*it);
+ read_p.initNumbers(numbers);
+ read_p.kMerAndRevToNumber((char *) "TTTAGGTGCTACCATAACACCAACTGTTTT",numbers);
+ assert(max(numbers.nbr,numbers.nbr_rev)==*it);
}
if (cnt_k_mer==4) {
- num=read_p.kMerToNumber((char *) "TTAGGTGCTACCATAACACCAACTGTTTTC",NULL);
- assert(num==*it);
+ read_p.initNumbers(numbers);
+ read_p.kMerAndRevToNumber((char *) "TTAGGTGCTACCATAACACCAACTGTTTTC",numbers);
+ assert(numbers.nbr==*it);
}
// k-mer number 10 is GCTACCATAACACCAACTGTTTTCACCATA
// its reverse complement is : TATGGTGAAAACAGTTGGTGTTATGGTAGC
if (cnt_k_mer==10) {
- num=read_p.kMerToNumber((char *) "GCTACCATAACACCAACTGTTTTCACCATA",NULL);
+ //num=read_p.kMerToNumber((char *) "GCTACCATAACACCAACTGTTTTCACCATA",NULL);
assert(*it==max(704021989794238796,930978566989888201));
}
/*if (cnt_k_mer==20) {