Fixed the new alignpaired end to work after ngsfilter with the 9879847

possible cases

python/obitools3/commands/alignpairedend.pyx

@@ -15,16 +15,12 @@ from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
 from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
-
+from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
 
 import sys
 import os
 
 
-REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"
-REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"
-
-
 __title__="Aligns paired-ended reads"
 
 
@@ -106,8 +102,7 @@ def alignmentIterator(entries, aligner):
         else:
             seqF = Nuc_Seq.new_from_stored(entries[i])
             seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality=seqF[REVERSE_QUALITY_COLUMN_NAME])
-            seqF.pop(REVERSE_SEQ_COLUMN_NAME)
+            seqR.index = i
-            seqF.pop(REVERSE_QUALITY_COLUMN_NAME)
         
         ali = aligner(seqF, seqR)
         
@@ -196,7 +191,7 @@ def run(config):
             reverse = entries[1]
             aligner = Kmer_similarity(forward, view2=reverse, kmer_size=config['alignpairedend']['kmersize'])
         else:
-            aligner = Kmer_similarity(entries, kmer_size=config['alignpairedend']['kmersize'])
+            aligner = Kmer_similarity(entries, column2=entries[REVERSE_SEQ_COLUMN_NAME], qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], kmer_size=config['alignpairedend']['kmersize'])
         
     ba = alignmentIterator(entries, aligner)
 

python/obitools3/dms/capi/kmer_similarity.pxd

@@ -32,6 +32,8 @@ cdef extern from "kmer_similarity.h" nogil:
                               OBIDMS_column_p column2,
                               index_t idx2,
                               index_t elt_idx2,
+                              OBIDMS_column_p qual_col1,
+                              OBIDMS_column_p qual_col2,
                               uint8_t kmer_size,
                               int32_t* kmer_pos_array,
                               int32_t* kmer_pos_array_height_p,

python/obitools3/dms/obiseq.pxd

@@ -5,6 +5,7 @@ from .view.view cimport Line
 
 cdef class Seq(dict) :
 
+    cdef int _index
     cpdef object clone(self)
     cpdef str get_str(self)
     cpdef get_symbol_at(self, int pos)
@@ -22,6 +23,7 @@ cdef class Nuc_Seq(Seq) :
     
 
 cdef class Seq_Stored(Line) :
+
     cpdef get_symbol_at(self, int pos)
     cpdef get_slice(self, slice slice_to_get)
 
@@ -31,6 +33,7 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
     cdef  Nuc_Seq _reverse_complement
     cdef  object  _quality_array
     cdef  bytes   _seq
+    
     cpdef set(self, object id, object seq, object definition=*, object quality=*, int offset=*, object tags=*)
     cpdef set_quality_int(self, list new_qual)
     cpdef set_quality_char(self, object new_qual, int offset=*)

python/obitools3/dms/obiseq.pyx

@@ -40,6 +40,7 @@ cdef class Seq(dict) :
         self.id = id
         self.seq = seq
         self.definition = definition
+        self._index = -1
         if tags is not None :
             for k in tags:
                 k_b = tobytes(k)
@@ -54,6 +55,7 @@ cdef class Seq(dict) :
     def new_from_stored(Seq_Stored seq_to_clone) :
         cdef Seq  new_seq
         new_seq = Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
+        new_seq._index = seq_to_clone._index
         return new_seq
 
     def __contains__(self, object key):
@@ -128,7 +130,16 @@ cdef class Seq(dict) :
         if new_definition is not None:
             new_definition = tobytes(new_definition)
         self[DEFINITION_COLUMN] = new_definition
-        
+
+    # sequence index (for reference in a view eventually) property getter and setter
+    @property
+    def index(self):  # @ReservedAssignment
+        return self._index
+
+    @index.setter
+    def index(self, int idx):  # @DuplicatedSignature
+        self._index = idx
+
         
 cdef class Nuc_Seq(Seq) :
 
@@ -160,6 +171,7 @@ cdef class Nuc_Seq(Seq) :
     def new_from_stored(Nuc_Seq_Stored seq_to_clone) :
         cdef Nuc_Seq new_seq
         new_seq = Nuc_Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
+        new_seq._index = seq_to_clone.index
         return new_seq
 
     # is_revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence)

python/obitools3/libalign/_solexapairend.pyx

@@ -13,7 +13,7 @@ from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
 
 from obitools3.dms.view.view cimport View
 from obitools3.dms.column.column cimport Column
-
+from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
 
 from math import log10
 
@@ -182,7 +182,7 @@ def buildConsensus(ali, seq, ref_tags=None):
         col_p = column.pointer()
         # doesn't work because uint8_t* are forced into bytes by cython (nothing read/kept beyond 0 values)
         #obi_set_qual_int_with_elt_idx_and_col_p_in_view(view_p, col_p, seq.index, 0, ali.consensus_qual, ali.consensus_len)
-        seq.set(ref_tags.id+b"_CONS", ali.consensus_seq, quality=ali.consensus_qual, tags=ref_tags)
+        seq.set(ref_tags.id+b"_CONS", ali.consensus_seq, quality=ali.consensus_qual)
         seq[b'ali_length'] = ali.consensus_len
         seq[b'score_norm']=float(ali.score)/ali.consensus_len
         seq[b'shift']=ali.shift
@@ -208,7 +208,7 @@ def buildConsensus(ali, seq, ref_tags=None):
             quality[i] = min(42, round(-10*log10(p)))
             i+=1
         
-        seq.set(ali[0].wrapped.id+b"_CONS", sseq, quality=quality, tags=ali[0].wrapped)
+        seq.set(ali[0].wrapped.id+b"_CONS", sseq, quality=quality)
         
         if hasattr(ali, "counter"):
             seq[b'alignement_id']=ali.counter
@@ -224,12 +224,18 @@ def buildConsensus(ali, seq, ref_tags=None):
         seq[b'ali_length']=len(seq)-ic.seqASingle-ic.seqBSingle
         if seq[b'ali_length']>0:
             seq[b'score_norm']=float(ali.score)/seq[b'ali_length']
+        
+        ref_tags = ali[0].wrapped
 
     if hasattr(ali, "direction"):
         seq[b'ali_direction']=ali.direction
     seq[b'score']=ali.score
     seq[b'mode']=b'alignment'
-    
+
+    for tag in ref_tags:
+        if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME:
+            seq[tag] = ref_tags[tag]
+
     return seq
 
 
@@ -241,10 +247,13 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
     s = forward.seq + reverse.seq     
     quality = forward.quality
     quality.extend(reverse.quality)
-    seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality, tags=forward)
+    seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
     seq[b"score"]=ali.score
     seq[b"ali_direction"]=ali.direction
     seq[b"mode"]=b"joined"
     seq[b"pairedend_limit"]=len(forward)    
+    for tag in forward:
+        if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME:
+            seq[tag] = forward[tag]
     return seq
 

python/obitools3/libalign/shifted_ali.pxd

@@ -24,7 +24,9 @@ cdef class Kmer_similarity:
     cdef int32_t         shift_count_array_height_a[1]
     cdef Obiview_p       view1_p
     cdef OBIDMS_column_p column1_p
+    cdef OBIDMS_column_p qual_col1_p
     cdef Obiview_p       view2_p
     cdef OBIDMS_column_p column2_p
+    cdef OBIDMS_column_p qual_col2_p
     cdef bint            build_consensus
     cpdef free(self)

python/obitools3/libalign/shifted_ali.pyx

@@ -1,8 +1,7 @@
 #cython: language_level=3
 
-from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, QUALITY_COLUMN
 
-from obitools3.dms.obiseq cimport Nuc_Seq_Stored
 from obitools3.dms.capi.kmer_similarity cimport kmer_similarity, Obi_ali_p, obi_free_shifted_ali
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column
@@ -52,13 +51,14 @@ cdef class Ali_shifted:
     def direction(self):
         return self.pointer().direction
 
-    cpdef free(self):
+    cpdef free(self):  # TODO allocated memory could be kept
         obi_free_shifted_ali(self.pointer())
 
 
 cdef class Kmer_similarity:
-    def __init__(self, View_NUC_SEQS view1, Column column1=None, View_NUC_SEQS view2=None, Column column2=None, uint8_t kmer_size=3, build_consensus=True) :
+    def __init__(self, View_NUC_SEQS view1, Column column1=None, Column qual_column1=None, View_NUC_SEQS view2=None, Column column2=None, Column qual_column2=None, uint8_t kmer_size=3, build_consensus=True) :
         cdef Column default_seq_col
+        cdef Column default_qual_col
         if kmer_size < 1 or kmer_size > 3:
             raise Exception("Kmer size to compute kmer similarity must be >=1 or <=4")
         self.kmer_pos_array_p = NULL
@@ -89,13 +89,28 @@ cdef class Kmer_similarity:
                 raise Exception("Kmer similarity with no sequence column given must be given a NUC_SEQS view")
             default_seq_col = view2[NUC_SEQUENCE_COLUMN]
             self.column2_p = default_seq_col.pointer()
+        if qual_column1 is not None:
+            self.qual_col1_p = qual_column1.pointer()
+        else:
+            if type(view1) != View_NUC_SEQS:
+                raise Exception("Kmer similarity with no quality column given must be given a NUC_SEQS view")
+            default_qual_col = view1[QUALITY_COLUMN]
+            self.qual_col1_p = default_qual_col.pointer()
+        if qual_column2 is not None:
+            self.qual_col2_p = qual_column2.pointer()
+        else:
+            if type(view2) != View_NUC_SEQS:
+                raise Exception("Kmer similarity with no quality column given must be given a NUC_SEQS view")
+            default_qual_col = view2[QUALITY_COLUMN]
+            self.qual_col2_p = default_qual_col.pointer()
+
     
-    
+    def __call__(self, object seq1, object seq2):
-    def __call__(self, Nuc_Seq_Stored seq1, Nuc_Seq_Stored seq2):
         cdef Obi_ali_p ali_p
         cdef Ali_shifted ali
         ali_p = kmer_similarity(self.view1_p, self.column1_p, seq1.index, 0, \
                                self.view2_p, self.column2_p, seq2.index, 0, \
+                               self.qual_col1_p, self.qual_col2_p, \
                                self.kmer_size, \
                                self.kmer_pos_array_p, self.kmer_pos_array_height_a, \
                                self.shift_array_p, self.shift_array_height_a, \

src/kmer_similarity.c

@@ -64,19 +64,18 @@ void obi_free_shifted_ali(Obi_ali_p ali)
 
 
 Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1, index_t elt_idx1,
-							Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
+						  Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
-							uint8_t kmer_size,
+						  OBIDMS_column_p qual_col1, OBIDMS_column_p qual_col2,
-							int32_t* kmer_pos_array, int32_t* kmer_pos_array_height_p,
+						  uint8_t kmer_size,
-							int32_t* shift_array, int32_t* shift_array_height_p,
+						  int32_t* kmer_pos_array, int32_t* kmer_pos_array_height_p,
-							int32_t* shift_count_array, int32_t* shift_count_array_length_p,
+						  int32_t* shift_array, int32_t* shift_array_height_p,
-							bool build_consensus)
+						  int32_t* shift_count_array, int32_t* shift_count_array_length_p,
+						  bool build_consensus)
 {
 	Obi_ali_p       ali = NULL;
 	int 			i, j;
 	bool 			switched_seqs;
 	bool			left_ali;
-	OBIDMS_column_p qual_col1;
-	OBIDMS_column_p qual_col2;
 	double 			score = 0.0;
 	Obi_blob_p      blob1 = NULL;
 	Obi_blob_p   	blob2 = NULL;
@@ -106,6 +105,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	int32_t         overlap_len;
 	int32_t         consensus_len;
 	int32_t  		cons_shift;
+	int32_t  		copy_start;
+	int32_t  		copy_len;
 	uint8_t   		kmer;
 	byte_t          nuc;
 	uint8_t         encoding;
@@ -116,6 +117,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	int32_t         shift_array_height       = *shift_array_height_p;
 	int32_t         shift_count_array_length = *shift_count_array_length_p;
 	bool			free_blob1 = false;
+	bool			keep_seq1_start;
+	bool			keep_seq2_start;
+	bool			keep_seq1_end;
+	bool			keep_seq2_end;
 
 	// Check kmer size
 	if ((kmer_size < 1) || (kmer_size > 4))
@@ -143,7 +148,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	switched_seqs = false;
 	len1 = blob1->length_decoded_value;
 	len2 = blob2->length_decoded_value;
-	if (len2 > len1)
+	if (len2 < len1)
 	{
 		switched_seqs = true;
 		temp_len = len1;
@@ -334,7 +339,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	// Find the most represented shift
 	best_shift_idx = 0;
 	max_common_kmers = 0;
-	empty_part = (shift_count_array_length-1)/2 - len1;
+	//empty_part = (shift_count_array_length-1)/2 - len1; //TODO wrong in some cases (len1 shorter than overlap or something like that)
+	empty_part = 0;
 	for (i=empty_part; i < (shift_count_array_length - empty_part); i++)  // skipping empty parts of the array
 	{
 		if (shift_count_array[i] > max_common_kmers)
@@ -345,10 +351,44 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	}
 	best_shift = best_shift_idx - len1;
 
+	keep_seq1_start = false;
+	keep_seq1_end = false;
+	keep_seq2_start = false;
+	keep_seq2_end = false;
+
+	// The 873863 cases of hell
 	if (best_shift > 0)
-	    overlap_len = len2 - best_shift;
+	{
-	else
+		overlap_len = len2 - best_shift;
+		if (len1 <= overlap_len)
+		{
+			overlap_len = len1;
+			if (! switched_seqs)
+				keep_seq2_end = true;
+			else
+				keep_seq2_start = true;
+		}
+		else if (switched_seqs)
+		{
+			keep_seq2_start = true;
+			keep_seq1_end = true;
+		}
+	}
+	else if (best_shift < 0)
+	{
 	    overlap_len = len1 + best_shift;
+	    if (!switched_seqs)
+	    {
+	    	keep_seq1_start = true;
+	    	keep_seq2_end = true;
+	    }
+	}
+	else
+	{
+		overlap_len = len1;
+		if ((!switched_seqs) && (len2 > len1))
+			keep_seq2_end = true;
+	}
 
 	score = max_common_kmers + kmer_size - 1;
 
@@ -369,7 +409,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	ali->shift = abs_shift;
 	ali->consensus_seq = NULL;
 	ali->consensus_qual = NULL;
-	if (((best_shift < 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
+	if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
 	{
 		left_ali = true;
 		strcpy(ali->direction, "left");
@@ -383,33 +423,17 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	// Build the consensus sequence if asked
 	if (build_consensus)
 	{
-		// Get the quality columns
-		qual_col1 = obi_view_get_column(view1, QUALITY_COLUMN);
-		if (qual_col1 == NULL)
-		{
-			obi_set_errno(OBI_ALIGN_ERROR);
-			obidebug(1, "\nError when computing the kmer similarity between two sequences: can't open quality column to build the consensus sequence");
-			return NULL;
-		}
-		qual_col2 = obi_view_get_column(view2, QUALITY_COLUMN);
-		if (qual_col2 == NULL)
-		{
-			obi_set_errno(OBI_ALIGN_ERROR);
-			obidebug(1, "\nError when computing the kmer similarity between two sequences: can't open quality column to build the consensus sequence");
-			return NULL;
-		}
-
 		// Get the quality arrays
 		qual1 = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view1, qual_col1, idx1, 0, &qual1_len);
 		if (qual1 == NULL)
 		{
-			obidebug(1, "\nError getting the blob of the 1st sequence when computing the kmer similarity between two sequences");
+			obidebug(1, "\nError getting the quality of the 1st sequence when computing the kmer similarity between two sequences");
 			return NULL;
 		}
 		qual2 = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view2, qual_col2, idx2, 0, &qual2_len);
 		if (qual2 == NULL)
 		{
-			obidebug(1, "\nError getting the blob of the 1st sequence when computing the kmer similarity between two sequences");
+			obidebug(1, "\nError getting the quality of the 2nd sequence when computing the kmer similarity between two sequences");
 			return NULL;
 		}
 
@@ -417,10 +441,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 		if (seq1 == NULL)
 			seq1 = obi_blob_to_seq(blob1);
 
-		if (left_ali)
+		if (! switched_seqs)
-		    consensus_len = len1 + len2 - overlap_len;
+		    consensus_len = len2 - best_shift;
 		else
-		    consensus_len = overlap_len;
+		    consensus_len = len1 + best_shift;
 
 		// Allocate memory for consensus sequence
 		consensus_seq = (char*) malloc(consensus_len + 1 * sizeof(char)); // TODO keep malloced too maybe
@@ -447,30 +471,27 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 		// Compute consensus-relative shift for each sequence
 		if (best_shift > 0)
 		{
-			shift1 = best_shift;
+			shift1 = 0;
-			shift2 = 0;
+			shift2 = best_shift;
 		}
 		else
 		{
-			shift1 = 0;
+			shift1 = -(best_shift);
-			shift2 = -(best_shift);
+			shift2 = 0;
 		}
 
-		// If left alignment, copy first part of first sequence
+		// Copy first part of first or second sequence depending on cases
-		if (left_ali)
+		if (keep_seq1_start)
 		{
-			if (switched_seqs)
+			strncpy(consensus_seq, seq1, abs_shift);
-			{
+			memcpy(consensus_qual, qual1, abs_shift*sizeof(uint8_t));
-				strncpy(consensus_seq, seq2, abs_shift);
+			cons_shift = abs_shift;
-				memcpy(consensus_qual, qual2, abs_shift*sizeof(uint8_t));
+		}
-				cons_shift = abs_shift;
+		else if (keep_seq2_start)
-			}
+		{
-			else
+			strncpy(consensus_seq, seq2, abs_shift);
-			{
+			memcpy(consensus_qual, qual2, abs_shift*sizeof(uint8_t));
-				strncpy(consensus_seq, seq1, abs_shift);
+			cons_shift = abs_shift;
-				memcpy(consensus_qual, qual1, abs_shift*sizeof(uint8_t));
-				cons_shift = abs_shift;
-			}
 		}
 		else
 			cons_shift = 0;
@@ -485,19 +506,26 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
  			consensus_qual[pos+cons_shift] = round((qual1[pos+shift1] + qual2[pos+shift2])/2);    // TODO maybe use the (p1*(1-p2/3)) formula (but parenthesis bug???)
 		}
 
-		// If left alignment, copy last part of first sequence
+		// Copy last part of first or second sequence depending on cases
-		if (left_ali)
+		if (keep_seq1_end)
 		{
-			if (switched_seqs)
+			strncpy(consensus_seq+cons_shift+overlap_len, seq1+overlap_len, len1 - overlap_len);
+			memcpy(consensus_qual+cons_shift+overlap_len, qual1+overlap_len, (len1 - overlap_len)*sizeof(uint8_t));
+		}
+		if (keep_seq2_end)
+		{
+			if (best_shift <= 0)
 			{
-				strncpy(consensus_seq+cons_shift+overlap_len, seq1+overlap_len, len1-overlap_len);
+				copy_start = overlap_len;
-				memcpy(consensus_qual+cons_shift+overlap_len, qual1+overlap_len, (len1-overlap_len)*sizeof(uint8_t));
+				copy_len = len2 - overlap_len;
 			}
-			else
+			if (best_shift > 0)
 			{
-				strncpy(consensus_seq+cons_shift+overlap_len, seq2+overlap_len, len2-overlap_len);
+				copy_start = overlap_len + best_shift;
-				memcpy(consensus_qual+cons_shift+overlap_len, qual2+overlap_len, (len2-overlap_len)*sizeof(uint8_t));
+				copy_len = len2 - overlap_len - best_shift;
 			}
+			strncpy(consensus_seq+cons_shift+overlap_len, seq2+copy_start, copy_len);
+			memcpy(consensus_qual+cons_shift+overlap_len, qual2+copy_start, copy_len*sizeof(uint8_t));
 		}
 
 		consensus_seq[consensus_len] = '\0';

src/kmer_similarity.h

@@ -33,9 +33,9 @@ typedef struct Obi_ali {
 	 	 	 	 	 	 	 	 */
 	int      overlap_length;	/**< Length of the overlap between the aligned sequences.
 	 	 	 	 	 	 	 	 */
-	char*    consensus_seq; 	/**< Consensus sequence built with the computed overlap.
+	char*    consensus_seq; 	/**< Consensus sequence built as to reconstruct a pairedend read.
 	 	 	 	 	 	 	 	 */
-	uint8_t* consensus_qual;	/**< Consensus quality built with the computed overlap.
+	uint8_t* consensus_qual;	/**< Consensus quality built as to reconstruct a pairedend read.
 	 	 	 	        	 	 */
 	int		 shift;   		    /**< Shift chosen to align the sequences (for shifted alignment).
 	 	 	 	 	 	 	 	 */
@@ -91,7 +91,7 @@ void obi_free_shifted_ali(Obi_ali_p ali);
  *        If needed, reallocated to a bigger size.
  * @param shift_count_array_height_p A pointer on an integer corresponding to the size (number of elements)
  *        allocated for shift_count_array. Updated by the function as needed.
- * @param build_consensus A boolean indicating whether the function should build the consensus sequence and quality. // TODO option to build consensus without quality?
+ * @param build_consensus A boolean indicating whether the function should build the consensus sequence and quality as to reconstruct a pairedend read. // TODO option to build consensus without quality?
  *
  * @returns A pointer on an Obi_ali_p structure containing the results.
  * @retval NULL if an error occurred.
@@ -107,6 +107,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1,
 						  OBIDMS_column_p column2,
 						  index_t idx2,
 						  index_t elt_idx2,
+						  OBIDMS_column_p qual_col1,
+						  OBIDMS_column_p qual_col2,
 						  uint8_t kmer_size,
 						  int32_t* kmer_pos_array,
 						  int32_t* kmer_pos_array_height_p,