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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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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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9c71b06117
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Removed deprecated TODOs
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2016-12-19 14:36:40 +01:00 |
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3bf5260174
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2016-12-19 10:31:18 +01:00 |
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857a5198e4
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Updated `obi lcs` for the LCS alignment of two columns
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2016-12-16 19:40:36 +01:00 |
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490f5fe6b9
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Updated deprecated code in cython API for columns (using line count of
view instead of column)
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2016-12-16 19:04:21 +01:00 |
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191c83aafc
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Added missing *.cfiles
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2016-12-15 15:28:34 +01:00 |
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fc805e5443
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Remove some warnings in the editor
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2016-12-13 08:29:22 +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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fa4e4ffaff
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Changed the cython API to create new views so as to have different
functions for the different cases
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2016-12-07 14:17:57 +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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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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98d0849653
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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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76a4c6b14e
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Fixed a bug when cloning a view and checking its type
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2016-11-23 11:28:17 +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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1c71c195fc
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Goes with a0ebc2d8
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2016-11-10 15:01:29 +01:00 |
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359578814b
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Added view type property to OBIView cython class and updated obi export
to use it
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2016-11-08 17:49:59 +01:00 |
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51b23915ca
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Added properties for Nuc_Seq cython classes (and updated commands using
them)
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2016-11-08 16:59:32 +01:00 |
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b5b889c4a2
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Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the
new properties of its parent class
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2016-11-08 11:26:37 +01:00 |
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36ac315125
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Fixed bugs with python view type when creating a new view, and a bug
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
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2016-11-08 11:23:54 +01:00 |
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8291693309
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obi grep: updated to work with the new line selection class and within
the local sequence environment, and progress bar functioning
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2016-11-08 11:19:12 +01:00 |
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4bc19c3e49
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obi export: view type is now checked and progress bar functioning
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2016-11-08 11:17:20 +01:00 |
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2d2fe5279d
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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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2504bf0fa9
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Added an iterator to the OBI_Taxonomy cython class
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2016-11-02 11:08:18 +01:00 |
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d8a257e711
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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
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2016-10-14 17:03:10 +02:00 |
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1b07109e51
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Removed deprecated code
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2016-10-10 17:01:51 +02:00 |
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60ab503a14
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Added properties in the OBI_Taxonomy class
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2016-10-10 17:01:17 +02:00 |
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2dcfdc59fc
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When a new view is created with a line selection, the view to clone is
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
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2016-10-06 17:55:18 +02:00 |
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399fc2c051
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Removed deprecated source files previously used for tests
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2016-09-30 17:49:37 +02:00 |
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9cd57deca9
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Added OBIView_line_selection class to make new line selections
associated with the view to clone, and improved and renamed method
closing a view
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2016-09-30 17:48:53 +02:00 |
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d88811ed7d
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Added a seed option to the obi test command for reproducible tests
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2016-09-29 17:34:48 +02:00 |
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8c402101e4
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Renamed private attributes as _* and removed some deprecated code
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2016-09-28 16:56:44 +02:00 |
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b717e8bb8b
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Added properties for the OBIView class and cleaned up deprecated code
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2016-09-28 14:26:23 +02:00 |
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03a2c8ef7c
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Finished restructuring the OBIDMS_column class properties
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2016-09-27 14:16:30 +02:00 |
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a7f891d1c9
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Added a lines_used property to the OBIDS_column class
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2016-09-26 18:04:28 +02:00 |
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bd50b3f972
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Added version property to OBIDMS_column class
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2016-09-26 17:45:10 +02:00 |
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81380363b7
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Added original_name property to OBIDMS_column class
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2016-09-26 17:31:32 +02:00 |
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a4b8349274
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Added data_type property to OBIDMS_column class
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2016-09-26 17:12:20 +02:00 |
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a474391b27
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Added nb_elements_per_line property to OBIDMS_column class
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2016-09-26 17:01:13 +02:00 |
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a0bc45cc92
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Added elements_names property to OBIDMS_column class
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2016-09-26 16:53:16 +02:00 |
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76f89717fe
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Added alias property to OBIDMS_column cython class
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2016-09-26 16:12:48 +02:00 |
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b408a4f6eb
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Changed file name limits to adapt to system limits + minor changes
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2016-09-22 18:05:07 +02:00 |
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b083745f56
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Deleted the "new line selection while editing a view" system
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2016-09-22 11:19:29 +02:00 |
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dd55aef3e5
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Added column class method to get the unique references (name and
version) of a column
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2016-09-21 17:08:44 +02:00 |
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9ac522fde1
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Better obi test command
|
2016-09-21 17:06:35 +02:00 |
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6adb9eb623
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Should solde issue #56
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2016-09-19 21:40:40 +02:00 |
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8f49553d5a
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First version of the obi test command, testing that the OBITools3 work
correctly
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2016-09-15 12:26:07 +02:00 |
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eb82d088cb
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Added some view class methods
|
2016-09-05 12:20:00 +02:00 |
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8d360b0fac
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Minor improvements to obi export command
|
2016-08-19 17:49:22 +02:00 |
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