Celine Mercier
1b07109e51
Removed deprecated code
2016-10-10 17:01:51 +02:00
Celine Mercier
60ab503a14
Added properties in the OBI_Taxonomy class
2016-10-10 17:01:17 +02:00
Celine Mercier
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
Celine Mercier
399fc2c051
Removed deprecated source files previously used for tests
2016-09-30 17:49:37 +02:00
Celine Mercier
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
Celine Mercier
d88811ed7d
Added a seed option to the obi test command for reproducible tests
2016-09-29 17:34:48 +02:00
Celine Mercier
8c402101e4
Renamed private attributes as _* and removed some deprecated code
2016-09-28 16:56:44 +02:00
Celine Mercier
1a7b42018e
Added some error checking when opening or creating a view
2016-09-28 14:28:34 +02:00
Celine Mercier
b717e8bb8b
Added properties for the OBIView class and cleaned up deprecated code
2016-09-28 14:26:23 +02:00
Celine Mercier
03a2c8ef7c
Finished restructuring the OBIDMS_column class properties
2016-09-27 14:16:30 +02:00
Celine Mercier
a7f891d1c9
Added a lines_used property to the OBIDS_column class
2016-09-26 18:04:28 +02:00
Celine Mercier
bd50b3f972
Added version property to OBIDMS_column class
2016-09-26 17:45:10 +02:00
Celine Mercier
81380363b7
Added original_name property to OBIDMS_column class
2016-09-26 17:31:32 +02:00
Celine Mercier
a4b8349274
Added data_type property to OBIDMS_column class
2016-09-26 17:12:20 +02:00
Celine Mercier
a474391b27
Added nb_elements_per_line property to OBIDMS_column class
2016-09-26 17:01:13 +02:00
Celine Mercier
a0bc45cc92
Added elements_names property to OBIDMS_column class
2016-09-26 16:53:16 +02:00
Celine Mercier
76f89717fe
Added alias property to OBIDMS_column cython class
2016-09-26 16:12:48 +02:00
Celine Mercier
b408a4f6eb
Changed file name limits to adapt to system limits + minor changes
2016-09-22 18:05:07 +02:00
Celine Mercier
b083745f56
Deleted the "new line selection while editing a view" system
2016-09-22 11:19:29 +02:00
Celine Mercier
43f3c69a40
Fixed bug when cloning column with line selection
2016-09-21 17:50:21 +02:00
Celine Mercier
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
Celine Mercier
bb25723d99
Improved documentation of a function
2016-09-21 17:30:39 +02:00
Celine Mercier
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
Celine Mercier
802bae110b
Removed deprecated function
2016-09-21 17:09:59 +02:00
Celine Mercier
dd55aef3e5
Added column class method to get the unique references (name and
...
version) of a column
2016-09-21 17:08:44 +02:00
Celine Mercier
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
Celine Mercier
8f49553d5a
First version of the obi test command, testing that the OBITools3 work
...
correctly
2016-09-15 12:26:07 +02:00
Celine Mercier
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
Celine Mercier
a240ec0169
Added error checking when closing file descriptors
2016-09-15 11:58:56 +02:00
Celine Mercier
0a3c23d9d0
Added a missing closedir
2016-09-15 11:58:34 +02:00
Celine Mercier
8724445fa1
Added error checking when closing files
2016-09-15 11:50:30 +02:00
Celine Mercier
de189fd7e0
Fixed major bug when cloning an AVL where the bloom filter was not
...
copied properly (because the sutructure copy via assignation does not
work for structures with a variable size)
2016-09-15 11:47:02 +02:00
Celine Mercier
9a97f1f633
View predicates are now carried over when cloning a view
2016-09-06 16:22:24 +02:00
Celine Mercier
00014eb023
View files now have the *.obiview extension
2016-09-06 14:19:13 +02:00
Celine Mercier
acc0da2d0b
Readjusted some limits for file names and file numbers to be under OS
...
limits
2016-09-05 12:39:04 +02:00
Celine Mercier
668696fc5a
Fixed major bug: when setting all the columns of a view to the same
...
number of lines, columns are now cloned before being enlarged if needed
+ predicate functions now print error messages if the predicates are not
respected
2016-09-05 12:37:36 +02:00
Celine Mercier
ba84ef4847
Fixed typo
2016-09-05 12:31:06 +02:00
Celine Mercier
c9dce03295
Fixed major bug when cloning an AVL group (last AVL of new group was not
...
correctly enlarged before copying the data) + minor improvements
2016-09-05 12:29:52 +02:00
Celine Mercier
eb82d088cb
Added some view class methods
2016-09-05 12:20:00 +02:00
Celine Mercier
f46ea0b988
Finished fixing issues with DMS paths
2016-08-30 11:09:45 +02:00
Celine Mercier
5b2e370ffb
Fixed a bug when using an absolute path for a DMS
2016-08-29 17:30:31 +02:00
Celine Mercier
8d360b0fac
Minor improvements to obi export command
2016-08-19 17:49:22 +02:00
Celine Mercier
b34769b27c
Minor improvements to obi export command
2016-08-19 17:46:55 +02:00
Celine Mercier
2d0a714e37
Basic obi export command exporting from view to fasta or fastq format,
...
for testing purposes
2016-08-19 17:40:58 +02:00
Celine Mercier
7b780ffb28
View files now have a dynamic size to allow unlimited comments size
2016-08-18 17:57:03 +02:00
Celine Mercier
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
2016-08-16 15:17:26 +02:00
Celine Mercier
cf839522e7
Minor update and fix to obi grep command
2016-08-12 17:45:44 +02:00
Celine Mercier
10b22f79da
The cython subclass is now correctly chosen when cloning a view
2016-08-12 17:39:19 +02:00
Celine Mercier
ad8e10f2d1
Reworked a bit alignment API
2016-08-12 15:56:07 +02:00
