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
08e67a090f
Changed the inline functions syntax, which should make it compatible
...
with more compilers
2016-11-18 16:21:26 +01:00
621b4972db
Functions to get obiblobs through views
2016-11-18 15:59:50 +01:00
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
1c71c195fc
Goes with a0ebc2d8
2016-11-10 15:01:29 +01:00
54cfeffd85
Goes with 8f724f4f, forgotten file
2016-11-10 14:48:31 +01:00
a0ebc2d871
Functions to directly retrieve Obiblobs from indexers
2016-11-10 14:45:28 +01:00
8f724f4f8e
Some code refactoring
2016-11-09 16:48:00 +01:00
359578814b
Added view type property to OBIView cython class and updated obi export
...
to use it
2016-11-08 17:49:59 +01:00
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
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
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
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
b083745f56
Deleted the "new line selection while editing a view" system
2016-09-22 11:19:29 +02:00
43f3c69a40
Fixed bug when cloning column with line selection
2016-09-21 17:50:21 +02:00
e79507b629
Fixed bugs in the process ensuring that all the columns of a view have
...
the same line count, fixed a bug when trying to set a value in a view
when a line selection exists, fixed a bug when adding a new column to a
view where line counts would be wrong
2016-09-21 17:42:17 +02:00
bb25723d99
Improved documentation of a function
2016-09-21 17:30:39 +02:00
a0da984003
Fixed bug where columns would not get truncated to the right size, and
...
fixed bug where column directories would be open and not closed in some
instances
2016-09-21 17:28:52 +02:00
802bae110b
Removed deprecated function
2016-09-21 17:09:59 +02:00
dd55aef3e5
Added column class method to get the unique references (name and
...
version) of a column
2016-09-21 17:08:44 +02:00
9ac522fde1
Better obi test command
2016-09-21 17:06:35 +02:00
6adb9eb623
Should solde issue #56
2016-09-19 21:40:40 +02:00
8f49553d5a
First version of the obi test command, testing that the OBITools3 work
...
correctly
2016-09-15 12:26:07 +02:00
986f90c59e
Fixed bug where column directories weren't closed correctly, leading to
...
too many file descriptors open, and added error checking when closing
file descriptors
2016-09-15 12:18:40 +02:00
a240ec0169
Added error checking when closing file descriptors
2016-09-15 11:58:56 +02:00
