From 15d383fa8b56202d9e7a08e8138981fbac3e59cf Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 27 Jul 2017 19:24:41 +0200
Subject: [PATCH] Added possibility to specify the offset for encoding and
 decoding sequence quality character strings

---
 .../dms/column/typed_column/qual.pxd          | 18 +++++-----
 .../dms/column/typed_column/qual.pyx          | 34 +++++++++++--------
 src/obidmscolumn_qual.c                       | 22 +++++++-----
 src/obidmscolumn_qual.h                       | 18 +++++++---
 src/obiview.c                                 | 32 ++++++++---------
 src/obiview.h                                 | 32 ++++++++++++-----
 6 files changed, 95 insertions(+), 61 deletions(-)

diff --git a/python/obitools3/dms/column/typed_column/qual.pxd b/python/obitools3/dms/column/typed_column/qual.pxd
index f9cbba4..1381517 100644
--- a/python/obitools3/dms/column/typed_column/qual.pxd
+++ b/python/obitools3/dms/column/typed_column/qual.pxd
@@ -3,24 +3,24 @@
 
 from ...capi.obitypes cimport index_t
 
-from ..column cimport Column, \
-                      Column_multi_elts
+from ..column_idx cimport Column_idx, \
+                          Column_multi_elts_idx
 
 
-cdef class Column_qual(Column) :
+cdef class Column_qual(Column_idx) :
 
     cpdef object get_line(self, index_t line_nb)
-    cpdef object get_str_line(self, index_t line_nb)
+    cpdef object get_str_line(self, index_t line_nb, int offset=*)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef set_str_line(self, index_t line_nb, object value)
+    cpdef set_str_line(self, index_t line_nb, object value, int offset=*)
 
 
-cdef class Column_multi_elts_qual(Column_multi_elts) :
+cdef class Column_multi_elts_qual(Column_multi_elts_idx) :
 
     cpdef object get_item(self, index_t line_nb, object elt_id)
-    cpdef object get_str_item(self, index_t line_nb, object elt_id)
+    cpdef object get_str_item(self, index_t line_nb, object elt_id, int offset=*)
     cpdef object get_line(self, index_t line_nb)
-    cpdef object get_str_line(self, index_t line_nb)
+    cpdef object get_str_line(self, index_t line_nb, int offset=*)
     cpdef set_item(self, index_t line_nb, object elt_id, object value)
-    cpdef set_str_item(self, index_t line_nb, object elt_id, object value)
+    cpdef set_str_item(self, index_t line_nb, object elt_id, object value, int offset=*)
     
\ No newline at end of file
diff --git a/python/obitools3/dms/column/typed_column/qual.pyx b/python/obitools3/dms/column/typed_column/qual.pyx
index 070127c..3ff8ad3 100644
--- a/python/obitools3/dms/column/typed_column/qual.pyx
+++ b/python/obitools3/dms/column/typed_column/qual.pyx
@@ -6,6 +6,8 @@ from ..column cimport register_column_class
 
 from ...view.view cimport View
 
+from ..column cimport Column
+
 from obitools3.utils cimport tobytes, bytes2str, \
                              obi_errno_to_exception
 
@@ -28,7 +30,9 @@ from libc.stdint cimport uint8_t
 from libc.stdlib cimport malloc
 
 
-cdef class Column_qual(Column):
+# TODO detect type of value and call set_item_str if str or bytes
+
+cdef class Column_qual(Column_idx):
 
     @staticmethod
     def new(View    view,
@@ -59,12 +63,12 @@ cdef class Column_qual(Column):
         return result
 
     
-    cpdef object get_str_line(self, index_t line_nb):
+    cpdef object get_str_line(self, index_t line_nb, int offset=-1):
         global obi_errno
         cdef   char*  value
         cdef   object result
         cdef   int    i
-        value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
+        value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, offset)
         obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
         if value == OBIQual_char_NA :
             result = None
@@ -91,19 +95,19 @@ cdef class Column_qual(Column):
             free(value_b)
  
  
-    cpdef set_str_line(self, index_t line_nb, object value):
+    cpdef set_str_line(self, index_t line_nb, object value, int offset=-1):
         global obi_errno
         cdef   bytes value_b        
         if value is None :
-            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA) < 0:
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA, offset) < 0:
                 obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
         else :
             value_b = tobytes(value)
-            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b, offset) < 0:
                 obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
 
  
-cdef class Column_multi_elts_qual(Column_multi_elts):
+cdef class Column_multi_elts_qual(Column_multi_elts_idx):
  
     cpdef object get_item(self, index_t line_nb, object elt_id):
         global obi_errno
@@ -126,15 +130,15 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
         return result
 
     
-    cpdef object get_str_item(self, index_t line_nb, object elt_id):
+    cpdef object get_str_item(self, index_t line_nb, object elt_id, int offset=-1):
         global obi_errno
         cdef   char*  value
         cdef   object result
         if type(elt_id) == int :
-            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
+            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, offset)
         else :
             elt_name = tobytes(elt_id)
-            value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
+            value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, offset)
         obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
         if value == OBIQual_char_NA :
             result = None
@@ -176,7 +180,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
         return result
 
 
-    cpdef object get_str_line(self, index_t line_nb) :
+    cpdef object get_str_line(self, index_t line_nb, int offset=-1) :
         global obi_errno
         cdef   char*           value
         cdef   object          value_in_result
@@ -192,7 +196,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
         column_p = self.pointer()
         elements_names = self.elements_names
         for i in range(self.nb_elements_per_line) :
-            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
+            value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, offset)
             obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
             if value != OBIQual_char_NA :
                 value_in_result = bytes2str(value)
@@ -232,7 +236,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
             free(value_b)
     
 
-    cpdef set_str_item(self, index_t line_nb, object elt_id, object value):
+    cpdef set_str_item(self, index_t line_nb, object elt_id, object value, int offset=-1):
         global obi_errno
         cdef   bytes value_b
         cdef   bytes elt_name
@@ -243,11 +247,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
             value_b = tobytes(value)
    
         if type(elt_id) == int :
-            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0 :
+            if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b, offset) < 0 :
                 obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
         else :
             elt_name = tobytes(elt_id)
-            if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
+            if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b, offset) < 0:
                 obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
 
 
diff --git a/src/obidmscolumn_qual.c b/src/obidmscolumn_qual.c
index 7faf04e..1197d7c 100644
--- a/src/obidmscolumn_qual.c
+++ b/src/obidmscolumn_qual.c
@@ -26,13 +26,16 @@
  *
  **********************************************************************/
 
-int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
+int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value, int offset)
 {
 	uint8_t* int_value;
 	int      int_value_length;
 	int 	 i;
 	int		 ret_value;
 
+	if (offset == -1)
+		offset = QUALITY_ASCII_BASE;
+
 	// Check NA value
 	if (value == OBIQual_char_NA)
 	{
@@ -45,7 +48,7 @@ int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t lin
 
 		// Convert in uint8_t array to index in that format
 		for (i=0; i<int_value_length; i++)
-			int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
+			int_value[i] = ((uint8_t)(value[i])) - offset;
 		ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
 		free(int_value);
 	}
@@ -101,13 +104,16 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
 }
 
 
-char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int offset)
 {
 	char* 		   value;
 	const uint8_t* int_value;
 	int			   int_value_length;
 	int			   i;
 
+	if (offset == -1)
+		offset = QUALITY_ASCII_BASE;
+
 	int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length);
 
 	// Check NA
@@ -118,7 +124,7 @@ char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t l
 
 	// Encode int quality to char quality
 	for (i=0; i<int_value_length; i++)
-		value[i] = (char)(int_value[i] + QUALITY_ASCII_BASE);
+		value[i] = (char)(int_value[i] + offset);
 
 	value[i] = '\0';
 
@@ -143,13 +149,13 @@ const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, i
 }
 
 
-int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
+int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value, int offset)
 {
 	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
 
-	return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value);
+	return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value, offset);
 }
 
 
@@ -163,13 +169,13 @@ int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t lin
 }
 
 
-char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int offset)
 {
 	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return OBIQual_char_NA;
 
-	return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx, offset);
 }
 
 
diff --git a/src/obidmscolumn_qual.h b/src/obidmscolumn_qual.h
index 90178de..91e5dfc 100644
--- a/src/obidmscolumn_qual.h
+++ b/src/obidmscolumn_qual.h
@@ -22,7 +22,7 @@
 #include "obitypes.h"
 
 
-#define QUALITY_ASCII_BASE (33)   		/**< The ASCII base of sequence quality.
+#define QUALITY_ASCII_BASE (33)   		/**< The default ASCII base of sequence quality.
 										 *   Used to convert sequence qualities from characters to integers
 										 *   and the other way around.
                                 	 	 */
@@ -40,6 +40,8 @@
  * @param line_nb The number of the line where the value should be set.
  * @param element_idx The index of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around. If -1, the default base is used.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -48,7 +50,7 @@
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
+int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value, int offset);
 
 
 /**
@@ -84,6 +86,8 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
  * @param column A pointer as returned by obi_create_column().
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_idx The index of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around. If -1, the default base is used.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -91,7 +95,7 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int offset);
 
 
 /**
@@ -126,6 +130,8 @@ const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, i
  * @param line_nb The number of the line where the value should be set.
  * @param element_name The name of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around. If -1, the default base is used.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -134,7 +140,7 @@ const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, i
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
+int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value, int offset);
 
 
 /**
@@ -170,6 +176,8 @@ int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t lin
  * @param column A pointer as returned by obi_create_column() or obi_clone_column().
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_name The name of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around. If -1, the default base is used.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -177,7 +185,7 @@ int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t lin
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int offset);
 
 
 /**
diff --git a/src/obiview.c b/src/obiview.c
index 53907c5..8e76047 100644
--- a/src/obiview.c
+++ b/src/obiview.c
@@ -2942,11 +2942,11 @@ obiint_t obi_get_int_with_elt_name_and_col_name_in_view(Obiview_p view, const ch
 
 /*********** FOR QUAL COLUMNS ***********/
 
-int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
+int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value, int offset)
 {
 	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
 		return -1;
-	return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value);
+	return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value, offset);
 }
 
 
@@ -2958,11 +2958,11 @@ int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colum
 }
 
 
-char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, int offset)
 {
 	if (prepare_to_get_value_from_column(view, &line_nb) < 0)
 		return OBIQual_char_NA;
-	return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx, offset);
 }
 
 
@@ -2974,12 +2974,12 @@ const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, O
 }
 
 
-int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
+int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value, int offset)
 {
 	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return -1;
-	return obi_set_qual_char_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx, value);
+	return obi_set_qual_char_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx, value, offset);
 }
 
 
@@ -2992,12 +2992,12 @@ int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_colu
 }
 
 
-char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
+char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, int offset)
 {
 	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
 	if (element_idx == OBIIdx_NA)
 		return OBIQual_char_NA;
-	return obi_get_qual_char_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx);
+	return obi_get_qual_char_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx, offset);
 }
 
 
@@ -3010,43 +3010,43 @@ const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
 }
 
 
-int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value)
+int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value, int offset)
 {
 	OBIDMS_column_p column_p;
 	column_p = obi_view_get_column(view, column_name);
 	if (column_p == NULL)
 		return -1;
-	return obi_set_qual_char_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name, value);
+	return obi_set_qual_char_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name, value, offset);
 }
 
 
-int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value)
+int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value, int offset)
 {
 	OBIDMS_column_p column_p;
 	column_p = obi_view_get_column(view, column_name);
 	if (column_p == NULL)
 		return -1;
-	return obi_set_qual_char_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx, value);
+	return obi_set_qual_char_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx, value, offset);
 }
 
 
-char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx)
+char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, int offset)
 {
 	OBIDMS_column_p column_p;
 	column_p = obi_view_get_column(view, column_name);
 	if (column_p == NULL)
 		return OBIQual_char_NA;
-	return obi_get_qual_char_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx);
+	return obi_get_qual_char_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx, offset);
 }
 
 
-char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name)
+char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, int offset)
 {
 	OBIDMS_column_p column_p;
 	column_p = obi_view_get_column(view, column_name);
 	if (column_p == NULL)
 		return OBIQual_char_NA;
-	return obi_get_qual_char_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name);
+	return obi_get_qual_char_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name, offset);
 }
 
 
diff --git a/src/obiview.h b/src/obiview.h
index 60b26c9..c9b43b3 100644
--- a/src/obiview.h
+++ b/src/obiview.h
@@ -1276,6 +1276,8 @@ obiint_t obi_get_int_with_elt_name_and_col_name_in_view(Obiview_p view, const ch
  * @param line_nb The number of the line where the value should be set.
  * @param element_idx The index of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -1284,7 +1286,7 @@ obiint_t obi_get_int_with_elt_name_and_col_name_in_view(Obiview_p view, const ch
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const char* value);
+int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const char* value, int offset);
 
 
 /**
@@ -1301,6 +1303,8 @@ int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colu
  * @param line_nb The number of the line where the value should be set.
  * @param element_idx The index of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -1309,7 +1313,7 @@ int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colu
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value);
+int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value, int offset);
 
 
 /**
@@ -1375,6 +1379,8 @@ int obi_set_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const cha
  * @param column_p A pointer as returned by obi_create_column().
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_idx The index of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -1382,7 +1388,7 @@ int obi_set_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const cha
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx);
+char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, int offset);
 
 
 /**
@@ -1396,6 +1402,8 @@ char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_co
  * @param column_name The alias of the column in the view.
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_idx The index of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -1403,7 +1411,7 @@ char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_co
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
+char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, int offset);
 
 
 /**
@@ -1464,6 +1472,8 @@ const uint8_t* obi_get_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view
  * @param line_nb The number of the line where the value should be set.
  * @param element_name The name of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -1472,7 +1482,7 @@ const uint8_t* obi_get_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, const char* value);
+int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, const char* value, int offset);
 
 
 /**
@@ -1489,6 +1499,8 @@ int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_col
  * @param line_nb The number of the line where the value should be set.
  * @param element_name The name of the element that should be set in the line.
  * @param value The value that should be set, in the character string format.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns An integer value indicating the success of the operation.
  * @retval 0 on success.
@@ -1497,7 +1509,7 @@ int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_col
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value);
+int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value, int offset);
 
 
 /**
@@ -1563,6 +1575,8 @@ int obi_set_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const ch
  * @param column_p A pointer as returned by obi_create_column() or obi_clone_column().
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_name The name of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -1570,7 +1584,7 @@ int obi_set_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const ch
  * @since May 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name);
+char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, int offset);
 
 
 /**
@@ -1584,6 +1598,8 @@ char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_c
  * @param column_name The alias of the column in the view.
  * @param line_nb The number of the line where the value should be recovered.
  * @param element_name The name of the element that should be recovered in the line.
+ * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers
+ *				 and the other way around.
  *
  * @returns The recovered value, in the character string format.
  * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
@@ -1591,7 +1607,7 @@ char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_c
  * @since August 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
+char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, int offset);
 
 
 /**