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4a1d3167a7
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Last change on my branch
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2017-01-02 16:46:52 +01:00 |
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153c22257f
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Last change on my branch
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2017-01-02 16:46:17 +01:00 |
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2139bfc748
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refactoring...
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2017-01-02 13:05:22 +01:00 |
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65f3b16e6d
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Refactoring ...
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2016-12-29 18:22:05 +01:00 |
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0526386337
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first working DMS class
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2016-12-27 06:17:45 +01:00 |
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62caf1346e
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temporary remove some files
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2016-12-26 15:03:24 +01:00 |
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3ac6e85fb3
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Big refactoring 4
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2016-12-26 14:58:03 +01:00 |
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5156f6bb9e
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Big refactoring 3
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2016-12-26 14:18:01 +01:00 |
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e6db2086d5
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Big refactoring 2
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2016-12-26 13:56:31 +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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3cedd00d7f
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Add register function for column type
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2016-12-20 11:13:57 +01:00 |
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82fbe43980
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transfert method to obiviews
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2016-12-20 08:18:47 +01:00 |
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d1a972dfcb
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patch import
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2016-12-20 08:15:42 +01:00 |
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f43dc3e3ab
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separate the obicolumn classes in new files
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2016-12-20 08:15:08 +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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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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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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04d39c62ab
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Try for a new API
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2016-12-14 08:44:44 +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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06cb7a9a58
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Some change in the way to manage access to special items of the
dictionary like sequence or quality
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2016-12-13 12:49:34 +01:00 |
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fc55fc117d
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Some cosmetic on the code
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2016-12-13 12:48:13 +01:00 |
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4ef5cb0d87
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Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and
_obiview_nuc_seq.pyx to avoid circular inclusion
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2016-12-13 12:46:49 +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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8d7ef7d3d1
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patch the distutils to add the C source directory in the include path.
This should solve most of the compilation problems related to .h files
located in this directory
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2016-12-13 08:02:09 +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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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
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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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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
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2016-11-28 11:38:02 +01:00 |
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3e53f9418b
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Added functions to recover the indexes themselves from any column
referring to indexed values
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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
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2016-11-23 11:32:39 +01:00 |
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6fa9a8bd76
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When a view is cloned, a comment is added to the new view specifying the
name of the cloned view
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2016-11-23 11:29:21 +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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0ab9e6c05a
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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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