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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
|
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)
|
2016-11-29 16:15:02 +01:00 |
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5fb025f310
|
When aligning, it is now quickly checked whether the sequences are
identical using their indexes
|
2016-11-28 11:39:29 +01:00 |
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8ce6f6c80b
|
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
|
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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76a4c6b14e
|
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
|
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
|
2016-11-23 11:04:53 +01:00 |
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70c49e214a
|
Added the kmer filter to LCS alignments, and now obiblobs containing
encoded sequences are directly put in int16_t arrays for the alignment
|
2016-11-18 16:29:28 +01:00 |
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08e67a090f
|
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
|
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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|
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8f724f4f8e
|
Some code refactoring
|
2016-11-09 16:48:00 +01:00 |
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359578814b
|
Added view type property to OBIView cython class and updated obi export
to use it
|
2016-11-08 17:49:59 +01:00 |
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51b23915ca
|
Added properties for Nuc_Seq cython classes (and updated commands using
them)
|
2016-11-08 16:59:32 +01:00 |
|
|
|
b5b889c4a2
|
Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the
new properties of its parent class
|
2016-11-08 11:26:37 +01:00 |
|
|
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36ac315125
|
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
|
2016-11-08 11:23:54 +01:00 |
|
|
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8291693309
|
obi grep: updated to work with the new line selection class and within
the local sequence environment, and progress bar functioning
|
2016-11-08 11:19:12 +01:00 |
|
|
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4bc19c3e49
|
obi export: view type is now checked and progress bar functioning
|
2016-11-08 11:17:20 +01:00 |
|
|
|
2d2fe5279d
|
Added functions to add new taxa to a taxonomy with handling of
associated *.ldx files
|
2016-11-03 17:59:21 +01:00 |
|
|
|
2504bf0fa9
|
Added an iterator to the OBI_Taxonomy cython class
|
2016-11-02 11:08:18 +01:00 |
|
|
|
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.
|
2016-10-27 18:56:11 +02:00 |
|
|
|
b63d0fb9fb
|
Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a
taxonomy C structure
|
2016-10-14 17:03:10 +02:00 |
|
|
|
0dfd67ec89
|
The endianness of binary taxonomy files is now correctly checked
|
2016-10-10 17:04:29 +02:00 |
|
|
|
0faaac49cf
|
The taxonomy directory of the DMS is now automatically created with the
DMS
|
2016-10-10 17:02:51 +02:00 |
|
|
|
1b07109e51
|
Removed deprecated code
|
2016-10-10 17:01:51 +02:00 |
|
|
|
60ab503a14
|
Added properties in the OBI_Taxonomy class
|
2016-10-10 17:01:17 +02:00 |
|
|
|
2dcfdc59fc
|
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
|
2016-10-06 17:55:18 +02:00 |
|
|
|
399fc2c051
|
Removed deprecated source files previously used for tests
|
2016-09-30 17:49:37 +02:00 |
|
|
|
9cd57deca9
|
Added OBIView_line_selection class to make new line selections
associated with the view to clone, and improved and renamed method
closing a view
|
2016-09-30 17:48:53 +02:00 |
|
|
|
d88811ed7d
|
Added a seed option to the obi test command for reproducible tests
|
2016-09-29 17:34:48 +02:00 |
|
|
|
8c402101e4
|
Renamed private attributes as _* and removed some deprecated code
|
2016-09-28 16:56:44 +02:00 |
|
|
|
1a7b42018e
|
Added some error checking when opening or creating a view
|
2016-09-28 14:28:34 +02:00 |
|
|
|
b717e8bb8b
|
Added properties for the OBIView class and cleaned up deprecated code
|
2016-09-28 14:26:23 +02:00 |
|
|
|
03a2c8ef7c
|
Finished restructuring the OBIDMS_column class properties
|
2016-09-27 14:16:30 +02:00 |
|
|
|
a7f891d1c9
|
Added a lines_used property to the OBIDS_column class
|
2016-09-26 18:04:28 +02:00 |
|
|
|
bd50b3f972
|
Added version property to OBIDMS_column class
|
2016-09-26 17:45:10 +02:00 |
|
|
|
81380363b7
|
Added original_name property to OBIDMS_column class
|
2016-09-26 17:31:32 +02:00 |
|
|
|
a4b8349274
|
Added data_type property to OBIDMS_column class
|
2016-09-26 17:12:20 +02:00 |
|
|
|
a474391b27
|
Added nb_elements_per_line property to OBIDMS_column class
|
2016-09-26 17:01:13 +02:00 |
|
|
|
a0bc45cc92
|
Added elements_names property to OBIDMS_column class
|
2016-09-26 16:53:16 +02:00 |
|
|
|
76f89717fe
|
Added alias property to OBIDMS_column cython class
|
2016-09-26 16:12:48 +02:00 |
|
|
|
b408a4f6eb
|
Changed file name limits to adapt to system limits + minor changes
|
2016-09-22 18:05:07 +02:00 |
|
