Merge branch 'feature-a/3250-shift-kmer-ascii-value-for-ambiguous-and-unknown' into 'dev'

Feature a/3250 shift kmer ascii value for ambiguous and unknown

Closes #3250

See merge request !220

algo/core/kmeraffect.cpp

@@ -66,6 +66,12 @@ string toString(const affect_t &a) {
 }
 
 string toStringValues(const affect_t &a){
+  if(a == AFFECT_UNKNOWN.affect){
+    return AFFECT_UNKNOWN_TO_STRING;
+  }
+  if(a == AFFECT_AMBIGUOUS.affect){
+    return AFFECT_AMBIGUOUS_TO_STRING;
+  }
   return string(1,affect_char(a));
 }
 
@@ -149,7 +155,7 @@ int KmerAffect::getStrand() const{
 }
 
 string KmerAffect::getLabel() const {
-  return string(1, affect_char(affect));
+ return ::toStringValues(affect);
 }
 
 unsigned char KmerAffect::getLength() const {

algo/core/kmeraffect.h

@@ -170,11 +170,16 @@ bool operator!=(const KmerAffect &a1, const KmerAffect &a2);
 ostream &operator<<(ostream &os, const KmerAffect &kmer);
 
 #define AFFECT_NOT_UNKNOWN_SYMBOL "*"
-#define AFFECT_AMBIGUOUS_SYMBOL "?"
-#define AFFECT_UNKNOWN_SYMBOL "_"
+#define AFFECT_AMBIGUOUS_SYMBOL "\0"
+#define AFFECT_UNKNOWN_SYMBOL "\1"
 #define AFFECT_AMBIGUOUS_CHAR (AFFECT_AMBIGUOUS_SYMBOL[0])
 #define AFFECT_UNKNOWN_CHAR (AFFECT_UNKNOWN_SYMBOL[0])
 
+/* Define how an ambiguous kmeraffect looks like in a string */
+#define AFFECT_AMBIGUOUS_TO_STRING "?"
+
+/* Define how an unknown kmeraffect looks like in a string */
+#define AFFECT_UNKNOWN_TO_STRING "_"
 
 /**
  * Constant defining any not-unknown affectation

algo/tests/unit-tests/testAutomaton.cpp

@@ -114,7 +114,7 @@ void testGetMultiResults(){
   /* Check if there is at least one Kmer unknown when no matching K-mer */
   unsigned int i = 0;
   for(auto const& x : results){
-    if(x.first.toStringValues() == AFFECT_UNKNOWN_SYMBOL){
+    if(x.first.toStringValues() == AFFECT_UNKNOWN_TO_STRING){
       break;
     }
     ++i;

algo/tests/unit-tests/testKmerAffect.cpp

@@ -57,8 +57,8 @@ void testAffect() {
   TAP_TEST_EQUAL(toString(Vminus), "-V", TEST_AFFECT_TO_STRING, toString(Vminus));
   TAP_TEST_EQUAL(toString(Vplus), "+V", TEST_AFFECT_TO_STRING, toString(Vplus));
   TAP_TEST_EQUAL(toString(Jplus), "+J", TEST_AFFECT_TO_STRING, toString(Jplus));
-  TAP_TEST_EQUAL(toString(AFFECT_UNKNOWN.affect), " " AFFECT_UNKNOWN_SYMBOL, TEST_AFFECT_TO_STRING, "");
-  TAP_TEST_EQUAL(toString(AFFECT_AMBIGUOUS.affect), " " AFFECT_AMBIGUOUS_SYMBOL, TEST_AFFECT_TO_STRING, "");
+  TAP_TEST_EQUAL(toString(AFFECT_UNKNOWN.affect), " " AFFECT_UNKNOWN_TO_STRING, TEST_AFFECT_TO_STRING, "");
+  TAP_TEST_EQUAL(toString(AFFECT_AMBIGUOUS.affect), " " AFFECT_AMBIGUOUS_TO_STRING, TEST_AFFECT_TO_STRING, "");
 
   ostringstream oss;
   oss << Vminus;
@@ -104,13 +104,13 @@ void testKmerAffectClass() {
   TAP_TEST(unknown == AFFECT_UNKNOWN, TEST_KMERAFFECT_CONSTRUCTOR, "");
   TAP_TEST(unknown.isUnknown(), TEST_KMERAFFECT_UNKNOWN, "");
   TAP_TEST_EQUAL(unknown.getStrand(), 0, TEST_KMERAFFECT_STRAND, "");
-  TAP_TEST_EQUAL(unknown.getLabel(), AFFECT_UNKNOWN_SYMBOL, TEST_KMERAFFECT_LABEL, "");
+  TAP_TEST_EQUAL(unknown.getLabel(), AFFECT_UNKNOWN_TO_STRING, TEST_KMERAFFECT_LABEL, "");
   unknown += KAVm;
   TAP_TEST(unknown.affect == KAVm, TEST_KMERAFFECT_ADD, "");
   unknown += KAJp;
   TAP_TEST(unknown == AFFECT_AMBIGUOUS, TEST_KMERAFFECT_ADD, "");
   TAP_TEST(unknown.isAmbiguous(), TEST_KMERAFFECT_AMBIGUOUS, "");
-  TAP_TEST_EQUAL(unknown.getLabel(), AFFECT_AMBIGUOUS_SYMBOL, TEST_KMERAFFECT_LABEL, "");
+  TAP_TEST_EQUAL(unknown.getLabel(), AFFECT_AMBIGUOUS_TO_STRING, TEST_KMERAFFECT_LABEL, "");
   TAP_TEST_EQUAL(unknown.getStrand(), 0, TEST_KMERAFFECT_STRAND, "");
   TAP_TEST_EQUAL(unknown.getLength(), 4, TEST_KMERAFFECT_AMBIGUOUS, "");