Commit b98880b7 by Celine Mercier

Various non-important fixes and comments

parent 895d09b1
build/lib.macosx-10.6-intel-3.4
......@@ -70,7 +70,6 @@ def run(config):
cdef Column def_col
cdef Column seq_col
cdef Column qual_col
cdef Column taxid_col
cdef Column old_column
cdef bint rewrite
cdef dict dcols
......
......@@ -26,12 +26,3 @@ def run(config):
print(repr(input[1]))
\ No newline at end of file
......@@ -37,7 +37,7 @@ def addOptions(parser):
group.add_argument('--merge-ids', '-e',
action="store_true", dest="uniq:mergeids",
default=False,
help="ONLY WORKING ON SMALL SETS FOR NOW Add the merged key with all ids of merged sequences.")
help="ONLY WORKING ON SMALL SETS FOR NOW Add the merged key with all ids of merged sequences.") # TODO ?
group.add_argument('--category-attribute', '-c',
action="append", dest="uniq:categories",
......
......@@ -601,7 +601,7 @@ cdef class Line_selection(list):
cpdef View materialize(self,
object view_name,
object comments=""):
object comments=b""):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
......
......@@ -307,7 +307,7 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
break;
default:
obi_set_errno(OBI_ENCODE_ERROR);
obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC), sequence: %s", seq);
return NULL;
}
}
......
......@@ -57,7 +57,6 @@
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int create_output_columns(Obiview_p o_view,
Obiview_p i_view,
OBIDMS_column_p sample_column,
int sample_count);
......@@ -85,7 +84,6 @@ static inline int idxcmp(const void* idx1, const void* idx2);
************************************************************************/
static int create_output_columns(Obiview_p o_view,
Obiview_p i_view,
OBIDMS_column_p sample_column,
int sample_count)
{
......@@ -279,7 +277,7 @@ int obi_clean(const char* dms_name,
sample_count = (sample_column->header)->nb_elements_per_line;
// Create the output columns
if (create_output_columns(o_view, i_view, sample_column, sample_count) < 0)
if (create_output_columns(o_view, sample_column, sample_count) < 0)
{
obidebug(1, "\nError creating the output columns");
return -1;
......
......@@ -67,7 +67,7 @@
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since April 2017
* @since April 2018
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_clean(const char* dms_name,
......
......@@ -33,7 +33,7 @@
#define MAX_NB_OF_AVLS_IN_GROUP (1000) /**< The maximum number of AVL trees in a group. // TODO discuss
*/
#define MAX_NODE_COUNT_PER_AVL (10000000) /**< The maximum number of nodes in an AVL tree.
* Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
* Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss. Try 30M?
*/
#define MAX_DATA_SIZE_PER_AVL (1073741824) /**< The maximum size of the data referred to by an AVL tree in a group.
* Only used to decide when to create a new AVL in a group.
......
......@@ -372,7 +372,6 @@ int obi_truncate_column(OBIDMS_column_p column);
int obi_enlarge_column(OBIDMS_column_p column);
/*
* @brief Sets the data in a column to the specified value.
*
......
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