obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Quality columns are now optional in NUC_SEQS views + minor fixes

Browse Source
This commit is contained in:
Celine Mercier
2016-08-16 15:17:26 +02:00
parent cf839522e7
commit e4129610cf
8 changed files with 54 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files

35
src/obiview.c
View File

@ -1134,7 +1134,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
}
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments, bool quality_column)
{
Obiview_p view;
OBIDMS_column_p associated_nuc_column;
@ -1176,30 +1176,41 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
return NULL;
}
// Adding quality column
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
if (obi_view_add_column(view, QUALITY_COLUMN, -1, QUALITY_COLUMN, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0) // TODO discuss automatic association
if (quality_column)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
if (obi_view_add_column(view, QUALITY_COLUMN, -1, QUALITY_COLUMN, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0) // TODO discuss automatic association
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
}
}
// Add predicate functions of the view type
view->nb_predicates = 5; // TODO macro?
// TODO macros?
if (quality_column)
view->nb_predicates = 5;
else
view->nb_predicates = 3;
view->predicate_functions = malloc((view->nb_predicates) * sizeof(char* (*) (bool)));
(view->predicate_functions)[0] = view_has_nuc_sequence_column;
(view->predicate_functions)[1] = view_has_quality_column;
(view->predicate_functions)[2] = view_has_id_column;
(view->predicate_functions)[3] = view_has_definition_column;
(view->predicate_functions)[4] = view_check_quality_matches_seq_column;
(view->predicate_functions)[1] = view_has_id_column;
(view->predicate_functions)[2] = view_has_definition_column;
if (quality_column)
{
(view->predicate_functions)[3] = view_has_quality_column;
(view->predicate_functions)[4] = view_check_quality_matches_seq_column;
}
return view;
}
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments)
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments, bool quality_column)
{
Obiview_p view;
Obiview_p view_to_clone;
@ -1207,7 +1218,7 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
view_to_clone = obi_open_view(dms, view_to_clone_name);
if (view_to_clone == NULL)
return NULL;
view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments);
view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection, comments, quality_column);
obi_close_view(view_to_clone);

8
src/obiview.h
View File

@ -183,6 +183,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
* - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored
* - ID_COLUMN where sequence identifiers are stored
* - DEFINITION_COLUMN where sequence definitions are stored
* And, if quality_column is True:
* - QUALITY_COLUMN where sequence qualities are stored
*
* @param dms A pointer on the OBIDMS.
@ -191,6 +192,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
* @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone
* if there is one. NULL if there is no line selection or no view to clone.
* @param comments Eventually, comments to associate with the view. NULL if not.
* @param quality_column Whether or not a sequence quality column is associated with the view.
*
* @returns A pointer to the newly created view structure.
* @retval NULL if an error occurred.
@ -198,7 +200,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments);
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments, bool quality_column);
/**
@ -215,6 +217,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
* - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored
* - ID_COLUMN where sequence identifiers are stored
* - DEFINITION_COLUMN where sequence definitions are stored
* And, if quality_column is True:
* - QUALITY_COLUMN where sequence qualities are stored
*
* @param dms A pointer on the OBIDMS.
@ -223,6 +226,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
* @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone
* if there is one. NULL if there is no line selection or no view to clone.
* @param comments Eventually, comments to associate with the view. NULL if not.
* @param quality_column Whether or not a sequence quality column is associated with the view.
*
* @returns A pointer to the newly created view structure.
* @retval NULL if an error occurred.
@ -230,7 +234,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments, bool quality_column);
/**