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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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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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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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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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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
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2016-11-18 16:21:26 +01:00 |
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621b4972db
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Functions to get obiblobs through views
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2016-11-18 15:59:50 +01:00 |
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7d022c1a52
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If the indexer name is NULL when creating a column, it now becomes the
column name
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2016-11-18 15:56:51 +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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54cfeffd85
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Goes with 8f724f4f, forgotten file
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2016-11-10 14:48:31 +01:00 |
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a0ebc2d871
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Functions to directly retrieve Obiblobs from indexers
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2016-11-10 14:45:28 +01:00 |
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8f724f4f8e
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Some code refactoring
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2016-11-09 16:48:00 +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
|
2016-10-14 17:03:10 +02:00 |
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0dfd67ec89
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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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