d8a257e711
Taxonomy handling functions in C. Features: read taxdump, read binary
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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
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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
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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
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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
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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
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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
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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
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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
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correctly
2016-09-15 12:26:07 +02:00
986f90c59e
Fixed bug where column directories weren't closed correctly, leading to
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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
0a3c23d9d0
Added a missing closedir
2016-09-15 11:58:34 +02:00
8724445fa1
Added error checking when closing files
2016-09-15 11:50:30 +02:00
de189fd7e0
Fixed major bug when cloning an AVL where the bloom filter was not
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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
9a97f1f633
View predicates are now carried over when cloning a view
2016-09-06 16:22:24 +02:00
00014eb023
View files now have the *.obiview extension
2016-09-06 14:19:13 +02:00
acc0da2d0b
Readjusted some limits for file names and file numbers to be under OS
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limits
2016-09-05 12:39:04 +02:00
668696fc5a
Fixed major bug: when setting all the columns of a view to the same
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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
ba84ef4847
Fixed typo
2016-09-05 12:31:06 +02:00
c9dce03295
Fixed major bug when cloning an AVL group (last AVL of new group was not
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correctly enlarged before copying the data) + minor improvements
2016-09-05 12:29:52 +02:00
eb82d088cb
Added some view class methods
2016-09-05 12:20:00 +02:00
f46ea0b988
Finished fixing issues with DMS paths
2016-08-30 11:09:45 +02:00
5b2e370ffb
Fixed a bug when using an absolute path for a DMS
2016-08-29 17:30:31 +02:00
8d360b0fac
Minor improvements to obi export command
2016-08-19 17:49:22 +02:00
b34769b27c
Minor improvements to obi export command
2016-08-19 17:46:55 +02:00
2d0a714e37
Basic obi export command exporting from view to fasta or fastq format,
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for testing purposes
2016-08-19 17:40:58 +02:00
7b780ffb28
View files now have a dynamic size to allow unlimited comments size
2016-08-18 17:57:03 +02:00
