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Various non-important fixes and comments

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This commit is contained in:
Celine Mercier
2018-07-28 17:07:17 +02:00
parent 895d09b133
commit b98880b7fa
10 changed files with 6 additions and 20 deletions
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1
doc/sphinx/build_dir.txt
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@ -1 +0,0 @@
build/lib.macosx-10.6-intel-3.4

1
python/obitools3/commands/import.pyx
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@ -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

9
python/obitools3/commands/ls.pyx
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@ -26,12 +26,3 @@ def run(config):
print(repr(input[1]))

2
python/obitools3/commands/uniq.pyx
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@ -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",

2
python/obitools3/dms/view/view.pyx
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@ -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

2
src/encode.c
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@ -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;
}
}

4
src/obi_clean.c
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@ -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;

2
src/obi_clean.h
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@ -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,

2
src/obiavl.h
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@ -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.

1
src/obidmscolumn.h
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@ -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.
*