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Added possibility to specify the offset for encoding and decoding

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sequence quality character strings
This commit is contained in:
Celine Mercier
2017-07-27 19:24:41 +02:00
parent 99ceed5fff
commit 15d383fa8b
6 changed files with 95 additions and 61 deletions
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22
src/obidmscolumn_qual.c
View File

@ -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);
}

18
src/obidmscolumn_qual.h
View File

@ -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);
/**

32
src/obiview.c
View File

@ -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);
}

32
src/obiview.h
View File

@ -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);
/**