Skip to content

GitLab

O
OBITools3
Commit 15d383fa authored by Celine Mercier's avatar Celine Mercier
Browse files
Options

Added possibility to specify the offset for encoding and decoding 

sequence quality character strings
parent 99ceed5f
Hide whitespace changes
Inline Side-by-side
Showing with 95 additions and 61 deletions
python/obitools3/dms/column/typed_column/qual.pxd
View file @ 15d383fa
......@@ -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
python/obitools3/dms/column/typed_column/qual.pyx
View file @ 15d383fa
......@@ -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")
......
src/obidmscolumn_qual.c
View file @ 15d383fa
......@@ -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);
}
......
src/obidmscolumn_qual.h
View file @ 15d383fa
......@@ -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);
/**
......
src/obiview.c
View file @ 15d383fa
......@@ -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);
}
......
src/obiview.h
View file @ 15d383fa
......@@ -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);
/**
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment