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3319ede837
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Views: Column dictionaries now store and return pointers on column
pointers instead of column pointers.
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2017-02-22 13:49:50 +01:00 |
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431c1c8c6a
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Merge branch 'Eric_new_Python_API' of
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API
Conflicts:
python/obitools3/obidms/_obidms.pxd
python/obitools3/obidms/_obidms.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obiseq.pxd
python/obitools3/obidms/_obiseq.pyx
python/obitools3/obidms/_obitaxo.pxd
python/obitools3/obidms/_obitaxo.pyx
python/obitools3/obidms/_obiview.pxd
python/obitools3/obidms/_obiview.pyx
python/obitools3/obidms/_obiview_nuc_seq.pxd
python/obitools3/obidms/_obiview_nuc_seq.pyx
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
python/obitools3/obidms/capi/obialign.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obitaxonomy.pxd
python/obitools3/obidms/capi/obiview.pxd
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2017-02-20 14:55:36 +01:00 |
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e524041013
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Views: Files for unfinished views now have the extension
'.obiview_unfinished', renamed to '.obiview' when the view is finished.
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2017-02-07 17:16:09 +01:00 |
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a9102620f5
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Fixed missing email address
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2017-02-07 17:14:10 +01:00 |
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e50da64ea1
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The elements names when a column contains several elements per line are
now formatted with '\0' as separator and handled in a more optimized way
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2017-01-31 16:48:06 +01:00 |
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651c1d7845
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utilities: bsearch and qsort with additional user_data pointer argument
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2017-01-31 16:45:47 +01:00 |
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c0bcdce724
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Taxonomy: documentation for all the functions, and fixed bugs when
closing the taxonomy (overwriting of .pdx files, missing freeing, and
re-placed a misplaced condition)
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2017-01-18 18:22:49 +01:00 |
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c065c1914a
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Taxonomy: adding, writing and reading preferred names, changed some
function names, and fixed a bug with taxa indices not being properly
initialized
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2017-01-16 17:28:20 +01:00 |
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0385a92e02
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Taxonomy: Refactored the taxdump reading, and little fixes
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2017-01-11 16:36:08 +01:00 |
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41ad3deec0
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Taxonomy: informations about deleted taxids is now read from
delnodes.dmp file and added to *.adx file
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2017-01-09 17:28:49 +01:00 |
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d68374018b
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Taxonomy: functions to read the *.adx file (containing the deprecated
and current taxids and their corresponding indices in the taxa
structure) and to find the taxa using the merged index.
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2017-01-06 15:52:21 +01:00 |
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f396625f98
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Taxonomy: function to write *.adx files
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2017-01-05 15:37:13 +01:00 |
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897032387f
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Taxonomy: reading merged.dmp file in taxdump
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2017-01-05 14:28:36 +01:00 |
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daacd0df76
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Strong refactoring 1
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2016-12-26 13:35:31 +01:00 |
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8e92bf6dac
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LCS alignment: it is now checked that sequences are not longer than what
a 16 bits integer can code for (as the LCS and alignment lengths are
kept in 16 bits registers)
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2016-12-22 17:06:23 +01:00 |
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30e4359c85
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LCS alignment: documentation for all the lowest level functions
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2016-12-22 17:03:51 +01:00 |
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5c50e5b378
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Embryo of code for openMP parallelization of LCS alignment but
deactivated for now because can't make it compile with cython/clang
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2016-12-20 11:46:58 +01:00 |
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d99447c12b
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C function for LCS alignment of two columns, and optimized and fixed
line count bug in function to align one column
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2016-12-16 19:39:02 +01:00 |
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303bd6f445
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Added function to build kmer table for 2 columns, and fixed bug (with
line count) when building kmer table of one column
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2016-12-16 19:10:18 +01:00 |
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9b24818fe2
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Refactored alignment code for minimum redundancy between the function
that aligns 1 column and the function that aligns 2 columns
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2016-12-13 17:18:12 +01:00 |
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8afb1644e9
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Alignment: API rework. 'obi align' is now 'obi lcs', and the results are
now written to columns automatically created in the output view, all
optimally handled at the C level.
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2016-12-12 11:58:59 +01:00 |
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936be64c34
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Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
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2016-12-05 11:18:29 +01:00 |
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5e0c9f878b
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Added the doc for the function building the element names, and a missing
free
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2016-12-05 10:46:21 +01:00 |
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852e5488c8
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The default element names for columns with multiple elements per line
are now "O;1;2;...;n"
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2016-12-02 17:54:51 +01:00 |
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e60497651c
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Updated the documentation for the functions to set and get in the
context of a view
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2016-11-30 12:22:47 +01:00 |
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4ad8c16a73
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Finished adding all the functions to directly set and get indices in
columns containing indices referring to any type of data.
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2016-11-30 11:08:11 +01:00 |
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6f6099687d
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Sequence alignment: if no sequence column is given and the view has the
type NUC_SEQS_VIEW, the default sequence column is aligned
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2016-11-29 16:52:41 +01:00 |
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98d0849653
|
Sequence alignment: added the possibility to specify the index of the
sequences to align in a column containing multiple sequences per line (C
level for now)
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2016-11-29 16:15:02 +01:00 |
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5fb025f310
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When aligning, it is now quickly checked whether the sequences are
identical using their indexes
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2016-11-28 11:39:29 +01:00 |
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8ce6f6c80b
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Added an argument to specify whether the two sequences can be identical
when applying filters before aligning
|
2016-11-28 11:38:02 +01:00 |
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3e53f9418b
|
Added functions to recover the indexes themselves from any column
referring to indexed values
|
2016-11-28 11:35:19 +01:00 |
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d40d2d0c76
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Fixed error in documentation
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2016-11-28 10:55:23 +01:00 |
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f897e87600
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When closing a view, it is now automatically checked that all OBI_QUAL
columns correspond to their associated OBI_SEQ column
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2016-11-25 12:04:57 +01:00 |
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70e056a2aa
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It is now impossible to open or clone a view that is not finished (= has
been closed at least once)
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2016-11-24 11:19:07 +01:00 |
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8abbfa203a
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Good file for commit 6fa9a8bd: When a view is cloned, a comment is added
to the new view specifying the name of the cloned view
|
2016-11-23 11:32:39 +01:00 |
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6fa9a8bd76
|
When a view is cloned, a comment is added to the new view specifying the
name of the cloned view
|
2016-11-23 11:29:21 +01:00 |
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0ab9e6c05a
|
When adding an existing column to a view, it is checked that the
column's line count is at least the view's line count. This can't be
more stringent for reasons that need to be rediscussed
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2016-11-23 11:04:53 +01:00 |
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70c49e214a
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Added the kmer filter to LCS alignments, and now obiblobs containing
encoded sequences are directly put in int16_t arrays for the alignment
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2016-11-18 16:29:28 +01:00 |
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08e67a090f
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Changed the inline functions syntax, which should make it compatible
with more compilers
|
2016-11-18 16:21:26 +01:00 |
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621b4972db
|
Functions to get obiblobs through views
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2016-11-18 15:59:50 +01:00 |
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7d022c1a52
|
If the indexer name is NULL when creating a column, it now becomes the
column name
|
2016-11-18 15:56:51 +01:00 |
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1c71c195fc
|
Goes with a0ebc2d8
|
2016-11-10 15:01:29 +01:00 |
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54cfeffd85
|
Goes with 8f724f4f, forgotten file
|
2016-11-10 14:48:31 +01:00 |
|
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|
a0ebc2d871
|
Functions to directly retrieve Obiblobs from indexers
|
2016-11-10 14:45:28 +01:00 |
|
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8f724f4f8e
|
Some code refactoring
|
2016-11-09 16:48:00 +01:00 |
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2d2fe5279d
|
Added functions to add new taxa to a taxonomy with handling of
associated *.ldx files
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2016-11-03 17:59:21 +01:00 |
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d8a257e711
|
Taxonomy handling functions in C. Features: read taxdump, read binary
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
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2016-10-27 18:56:11 +02:00 |
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b63d0fb9fb
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Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a
taxonomy C structure
|
2016-10-14 17:03:10 +02:00 |
|
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0dfd67ec89
|
The endianness of binary taxonomy files is now correctly checked
|
2016-10-10 17:04:29 +02:00 |
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0faaac49cf
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The taxonomy directory of the DMS is now automatically created with the
DMS
|
2016-10-10 17:02:51 +02:00 |
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