From b98880b7fa909138929b86ef6cfe41abc690a078 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Sat, 28 Jul 2018 17:07:17 +0200 Subject: [PATCH] Various non-important fixes and comments --- doc/sphinx/build_dir.txt | 1 - python/obitools3/commands/import.pyx | 1 - python/obitools3/commands/ls.pyx | 9 --------- python/obitools3/commands/uniq.pyx | 2 +- python/obitools3/dms/view/view.pyx | 2 +- src/encode.c | 2 +- src/obi_clean.c | 4 +--- src/obi_clean.h | 2 +- src/obiavl.h | 2 +- src/obidmscolumn.h | 1 - 10 files changed, 6 insertions(+), 20 deletions(-) delete mode 100644 doc/sphinx/build_dir.txt diff --git a/doc/sphinx/build_dir.txt b/doc/sphinx/build_dir.txt deleted file mode 100644 index 6d44141..0000000 --- a/doc/sphinx/build_dir.txt +++ /dev/null @@ -1 +0,0 @@ -build/lib.macosx-10.6-intel-3.4 diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index 7e786ae..19953b6 100644 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -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 diff --git a/python/obitools3/commands/ls.pyx b/python/obitools3/commands/ls.pyx index 1c210c6..90b6dd8 100644 --- a/python/obitools3/commands/ls.pyx +++ b/python/obitools3/commands/ls.pyx @@ -26,12 +26,3 @@ def run(config): print(repr(input[1])) - - - - - - - - - \ No newline at end of file diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx index 232628a..379394f 100644 --- a/python/obitools3/commands/uniq.pyx +++ b/python/obitools3/commands/uniq.pyx @@ -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", diff --git a/python/obitools3/dms/view/view.pyx b/python/obitools3/dms/view/view.pyx index a9e1466..32fae7b 100644 --- a/python/obitools3/dms/view/view.pyx +++ b/python/obitools3/dms/view/view.pyx @@ -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 diff --git a/src/encode.c b/src/encode.c index e9f4f29..b1be7cd 100644 --- a/src/encode.c +++ b/src/encode.c @@ -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; } } diff --git a/src/obi_clean.c b/src/obi_clean.c index c814ac0..08e491f 100644 --- a/src/obi_clean.c +++ b/src/obi_clean.c @@ -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; diff --git a/src/obi_clean.h b/src/obi_clean.h index 029ef0c..4be87e0 100644 --- a/src/obi_clean.h +++ b/src/obi_clean.h @@ -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, diff --git a/src/obiavl.h b/src/obiavl.h index 93fed50..e898b51 100644 --- a/src/obiavl.h +++ b/src/obiavl.h @@ -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. diff --git a/src/obidmscolumn.h b/src/obidmscolumn.h index 790421d..9ff83a7 100644 --- a/src/obidmscolumn.h +++ b/src/obidmscolumn.h @@ -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. *