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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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32
src/obiview.h
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@ -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);
/**