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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
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@ -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);
}