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Major update: New column type to store sequence qualities. Closes #41

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Celine Mercier
2016-05-20 16:45:22 +02:00
parent ffff91e76c
commit 3b59043ea8
33 changed files with 962 additions and 267 deletions
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36
src/obidmscolumn_qual.h
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@ -6,7 +6,7 @@
* @file obidsmcolumn_qual.h
* @author Celine Mercier
* @date May 4th 2016
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to sequence quality arrays.
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to sequence qualities.
*/
@ -22,6 +22,12 @@
#include "obitypes.h"
#define QUALITY_ASCII_BASE (33) /**< The ASCII base of sequence quality.
* Used to convert sequence qualities from characters to integers
* and the other way around.
*/
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
@ -56,7 +62,8 @@ int obi_column_set_obiqual_char_with_elt_idx(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 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 integer format.
* @param value The value that should be set, in the integer array format.
* @param value_length The length of the integer array.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
@ -65,7 +72,7 @@ int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t lin
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, uint8_t* value);
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length);
/**
@ -79,7 +86,7 @@ int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line
* @param element_idx The index of the element that should be recovered in the line.
*
* @returns The recovered value, in the character string format.
* @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -96,14 +103,15 @@ char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t l
* @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 value_length A pointer on an integer to store the length of the integer array recovered.
*
* @returns The recovered value, in the integer format.
* @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
* @returns The recovered value, in the integer array format.
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length);
/**
@ -133,7 +141,7 @@ int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t li
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
*
* This function is for quality scores in the integer format.
* This function is for quality scores in the integer array format.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
@ -141,6 +149,7 @@ int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t li
* @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 integer format.
* @param value_length The length of the integer array.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
@ -149,7 +158,7 @@ int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t li
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, uint8_t* value);
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length);
/**
@ -163,7 +172,7 @@ int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t lin
* @param element_name The name of the element that should be recovered in the line.
*
* @returns The recovered value, in the character string format.
* @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
* @retval OBIQual_str_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -175,19 +184,20 @@ char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
*
* This function returns quality scores in the integer format.
* This function returns quality scores in the integer array format.
*
* @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 value_length A pointer on an integer to store the length of the integer array recovered.
*
* @returns The recovered value, in the integer format.
* @retval OBIQual_NA the NA value of the type if an error occurred and obi_errno is set.
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
utin8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length);
#endif /* OBIDMSCOLUMN_QUAL_H_ */