First version of quality handling (not working yet) and now it is

checked that a column is writable before enlarging it

src/obidmscolumn.c

@@ -587,7 +587,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	}
 
 	// Build the indexer name if needed
-	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
+	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
 	{
 		if (strcmp(indexer_name, "") == 0)
 		{
@@ -603,7 +603,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	}
 
 	returned_data_type = data_type;
-	if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
+	if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
 	// stored data is indices referring to data stored elsewhere
 		stored_data_type = OBI_IDX;
 	else
@@ -750,8 +750,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	if (comments != NULL)
 		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated obi_indexer is opened or created
+	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
-	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
+	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
 	{
 		new_column->indexer = obi_indexer(dms, final_indexer_name);
 		if (new_column->indexer == NULL)
@@ -900,8 +900,8 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 
 	column->writable = false;
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated indexer is opened
+	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is opened
-	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
+	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
 	{
 		column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
 		if (column->indexer == NULL)
@@ -1028,8 +1028,8 @@ int obi_close_column(OBIDMS_column_p column)
 		// Close column directory if it was the last column opened from that directory
 		close_dir = obi_dms_is_column_name_in_list(column->dms, (column->header)->name);
 
-		// If the data type is OBI_STR or OBI_SEQ, the associated indexer is closed
+		// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
-		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
+		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
 			if (obi_close_indexer(column->indexer) < 0)
 				ret_val = -1;
 
@@ -1155,6 +1155,14 @@ int obi_enlarge_column(OBIDMS_column_p column)
 	int 	column_file_descriptor;
 	char* 	column_file_name;
 
+	// Check if the column is read-only
+	if (!(column->writable))
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to enlarge a read-only column");
+    	return -1;
+	}
+
 	// Get the column file name
 	column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
 	if (column_file_name == NULL)
@@ -1274,6 +1282,12 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
 					}
 					break;
 
+	case OBI_QUAL:  for (i=start;i<end;i++)
+					{
+						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
+					}
+					break;
+
 	case OBI_STR:   for (i=start;i<end;i++)
 					{
 						*(((index_t*) (column->data)) + i) = OBIIdx_NA;

src/obidmscolumn_qual.c

@@ -0,0 +1,115 @@
+/****************************************************************************
+ * OBIDMS_column_qual functions                                             *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_qual.c
+ * @author Celine Mercier
+ * @date May 4th 2016
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to sequence quality arrays.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obidmscolumn_str.c"
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
+{	// TODO discuss
+	return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, 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)
+{
+	char* value_char;
+
+	// Transform the int array into a char array
+	// Length??
+	//value_char = ;
+
+	obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value_char)
+
+	return 0;
+}
+
+
+char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{	// TODO discuss
+	char* value;
+
+	value = obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+	if (strcmp(value, OBIStr_NA) == 0)
+		return OBIQual_char_NA;
+
+	return value;
+}
+
+
+uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)	// TODO const? (mapped)
+{
+	index_t idx;
+
+	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
+		return OBIQual_int_NA;
+
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+
+	// Check NA
+	if (idx == OBIIdx_NA)
+		return OBIQual_int_NA;
+
+	return obi_retrieve_quality_int(column->indexer, idx);
+}
+
+
+int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
+{
+	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);
+}
+
+
+int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, uint8_t* value)
+{
+	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_int_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
+char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	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);
+}
+
+
+uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)	// TODO const? (mapped)
+{
+	index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIQual_int_NA;
+
+	return obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx);
+}
+

src/obidmscolumn_qual.h

@@ -0,0 +1,194 @@
+/****************************************************************************
+ * OBIDMS_column_qual header file                                           *
+ ****************************************************************************/
+
+/**
+ * @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.
+ */
+
+
+#ifndef OBIDMSCOLUMN_QUAL_H_
+#define OBIDMSCOLUMN_QUAL_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+
+
+/**
+ * @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 qualities in the character string format.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @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 character string format.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @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);
+
+
+/**
+ * @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 qualities in the integer format.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @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.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @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);
+
+
+/**
+ * @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 character string format.
+ *
+ * @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.
+ *
+ * @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.
+ *
+ * @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);
+
+
+/**
+ * @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.
+ *
+ * @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.
+ *
+ * @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.
+ *
+ * @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);
+
+
+/**
+ * @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 character string format.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @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_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.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @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);
+
+
+/**
+ * @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.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @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_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.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @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);
+
+
+/**
+ * @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 character string 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.
+ *
+ * @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.
+ *
+ * @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);
+
+
+/**
+ * @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.
+ *
+ * @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.
+ *
+ * @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.
+ *
+ * @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);
+
+
+#endif /* OBIDMSCOLUMN_QUAL_H_ */
+

src/obidmscolumn_str.c

@@ -28,6 +28,17 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 {
 	index_t idx;
 
+//  TODO
+//	size_t i;
+//	uint8_t q;
+//	for (i=0;i<=strlen(value);i++)
+//	{
+//		if ()
+//		q = ((uint8_t) value[i]) - 33;
+//		fprintf(stderr, "\n%c == %u", value[i], q);
+//	}
+
+
 	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 

src/obitypes.c

@@ -40,6 +40,9 @@ size_t obi_sizeof(OBIType_t type)
 	case OBI_CHAR:  size = sizeof(obichar_t);
 					break;
 
+	case OBI_QUAL:	size = sizeof(index_t);
+					break;
+
 	case OBI_STR:	size = sizeof(index_t);
 					break;
 
@@ -96,6 +99,9 @@ char* name_data_type(int data_type)
 		case OBI_CHAR:  name = strdup("OBI_CHAR");
 						break;
 
+		case OBI_QUAL:  name = strdup("OBI_QUAL");
+						break;
+
 		case OBI_STR:   name = strdup("OBI_STR");
 						break;
 

src/obitypes.h

@@ -24,6 +24,8 @@
 #define OBIChar_NA (0)				/**< NA value for the type OBI_CHAR */ // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
 #define OBISeq_NA ("\0")			/**< NA value for the type OBI_SEQ */  // TODO discuss
 #define OBIStr_NA ("\0")			/**< NA value for the type OBI_STR */  // TODO discuss
+#define OBIQual_char_NA ("\0")		/**< NA value for the type OBI_QUAL if the quality is in character string format */  // TODO test and discuss
+#define OBIQual_int_NA ("\0")		/**< NA value for the type OBI_QUAL if the quality is in integer format */  // TODO test and discuss
 
 
 /**
@@ -45,6 +47,7 @@ typedef enum OBIType {
 	OBI_FLOAT,					/**< a floating value (C type : double) */
 	OBI_BOOL,					/**< a boolean true/false value, see obibool_t enum */
 	OBI_CHAR,					/**< a character (C type : char) */
+	OBI_QUAL,					/**< an index in a data structure (C type : int64_t) referring to a quality score array */
 	OBI_STR,				    /**< an index in a data structure (C type : int64_t) referring to a character string */
 	OBI_SEQ,					/**< an index in a data structure (C type : int64_t) referring to a DNA sequence */
 	OBI_IDX					    /**< an index referring to a line in another column (C type : int64_t) */

src/uint8_indexer.c

@@ -0,0 +1,102 @@
+/****************************************************************************
+ * Sequence quality scores indexing functions                               *
+ ****************************************************************************/
+
+/**
+ * @file quality_indexer.c
+ * @author Celine Mercier
+ * @date May 4th 2016
+ * @brief Functions handling the indexing and retrieval of sequence quality scores.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_uint8_to_blob(const char* quality)
+{
+	Obi_blob_p 		 value_b;
+	int32_t          length_encoded_seq;	// length of the encoded sequence in bytes
+	int32_t          seq_length;
+	byte_t*          encoded_seq;
+
+	seq_length = strlen(seq);
+
+	// Check if just ATGC and encode accordingly
+	if (only_ATGC(seq))
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 4.0);
+		// Encode
+		encoded_seq = encode_seq_on_2_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_2, length_encoded_seq, seq_length);
+	}
+	else
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 2.0);
+		// Encode
+		encoded_seq = encode_seq_on_4_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
+	}
+
+	free(encoded_seq);
+
+	return value_b;
+}
+
+
+char* obi_blob_to_quality_char(Obi_blob_p value_b)
+{
+	// Decode
+	if (value_b->element_size == 2)
+		return decode_seq_on_2_bits(value_b->value, value_b->length_decoded_value);
+	else
+		return decode_seq_on_4_bits(value_b->value, value_b->length_decoded_value);
+}
+
+
+index_t obi_index_quality_char(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_seq_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded sequence
+	return obi_blob_to_seq(value_b);
+}
+

src/uint8_indexer.h

@@ -0,0 +1,87 @@
+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef DNA_SEQ_INDEXER_H_
+#define DNA_SEQ_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a DNA sequence to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_seq_to_blob(const char* seq);
+
+
+/**
+ * @brief Converts a blob to a DNA sequence.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the blob.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_blob_to_seq(Obi_blob_p value_b);
+
+
+/**
+ * @brief Stores a DNA sequence in an indexer and returns the index.
+ *
+ * @param indexer The indexer structure.
+ * @param value The DNA sequence to index.
+ *
+ * @returns The index referring to the stored DNA sequence in the indexer.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value);
+
+
+/**
+ * @brief Retrieves a DNA sequence from an indexer.
+ *
+ * @warning The DNA sequence returned must be freed by the caller.
+ *
+ * @param indexer The indexer structure.
+ * @param idx The index referring to the DNA sequence to retrieve in the indexer.
+ *
+ * @returns A pointer on the DNA sequence.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* DNA_SEQ_INDEXER_H_ */
+