60ab503a14
Added properties in the OBI_Taxonomy class
Celine Mercier
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
Celine Mercier
2016-10-06 17:55:18 +02:00
399fc2c051
Removed deprecated source files previously used for tests
Celine Mercier
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
Celine Mercier
2016-09-30 17:48:53 +02:00
d88811ed7d
Added a seed option to the obi test command for reproducible tests
Celine Mercier
2016-09-29 17:34:48 +02:00
8c402101e4
Renamed private attributes as _* and removed some deprecated code
Celine Mercier
2016-09-28 16:56:44 +02:00
1a7b42018e
Added some error checking when opening or creating a view
Celine Mercier
2016-09-28 14:28:34 +02:00
b717e8bb8b
Added properties for the OBIView class and cleaned up deprecated code
Celine Mercier
2016-09-28 14:26:23 +02:00
03a2c8ef7c
Finished restructuring the OBIDMS_column class properties
Celine Mercier
2016-09-27 14:16:30 +02:00
a7f891d1c9
Added a lines_used property to the OBIDS_column class
Celine Mercier
2016-09-26 18:04:28 +02:00
bd50b3f972
Added version property to OBIDMS_column class
Celine Mercier
2016-09-26 17:45:10 +02:00
81380363b7
Added original_name property to OBIDMS_column class
Celine Mercier
2016-09-26 17:31:32 +02:00
a4b8349274
Added data_type property to OBIDMS_column class
Celine Mercier
2016-09-26 17:12:20 +02:00
a474391b27
Added nb_elements_per_line property to OBIDMS_column class
Celine Mercier
2016-09-26 17:01:13 +02:00
a0bc45cc92
Added elements_names property to OBIDMS_column class
Celine Mercier
2016-09-26 16:53:16 +02:00
76f89717fe
Added alias property to OBIDMS_column cython class
Celine Mercier
2016-09-26 16:12:48 +02:00
b408a4f6eb
Changed file name limits to adapt to system limits + minor changes
Celine Mercier
2016-09-22 18:05:07 +02:00
b083745f56
Deleted the "new line selection while editing a view" system
Celine Mercier
2016-09-22 11:19:29 +02:00
43f3c69a40
Fixed bug when cloning column with line selection
Celine Mercier
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
Celine Mercier
2016-09-21 17:42:17 +02:00
bb25723d99
Improved documentation of a function
Celine Mercier
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
Celine Mercier
2016-09-21 17:28:52 +02:00
802bae110b
Removed deprecated function
Celine Mercier
2016-09-21 17:09:59 +02:00
dd55aef3e5
Added column class method to get the unique references (name and version) of a column
Celine Mercier
2016-09-21 17:08:44 +02:00
9ac522fde1
Better obi test command
Celine Mercier
2016-09-21 17:06:35 +02:00
8f49553d5a
First version of the obi test command, testing that the OBITools3 work correctly
Celine Mercier
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
Celine Mercier
2016-09-15 12:18:40 +02:00
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)
Celine Mercier
2016-09-15 11:47:02 +02:00
9a97f1f633
View predicates are now carried over when cloning a view
Celine Mercier
2016-09-06 16:22:24 +02:00
00014eb023
View files now have the *.obiview extension
Celine Mercier
2016-09-06 14:19:13 +02:00
acc0da2d0b
Readjusted some limits for file names and file numbers to be under OS limits
Celine Mercier
2016-09-05 12:39:04 +02:00
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
Celine Mercier
2016-09-05 12:37:36 +02:00
c9dce03295
Fixed major bug when cloning an AVL group (last AVL of new group was not correctly enlarged before copying the data) + minor improvements
Celine Mercier
2016-09-05 12:29:52 +02:00
eb82d088cb
Added some view class methods
Celine Mercier
2016-09-05 12:20:00 +02:00
5b2e370ffb
Fixed a bug when using an absolute path for a DMS
Celine Mercier
2016-08-29 17:30:31 +02:00
8d360b0fac
Minor improvements to obi export command
Celine Mercier
2016-08-19 17:49:22 +02:00
b34769b27c
Minor improvements to obi export command
Celine Mercier
2016-08-19 17:46:55 +02:00
2d0a714e37
Basic obi export command exporting from view to fasta or fastq format, for testing purposes
Celine Mercier
2016-08-19 17:40:58 +02:00
7b780ffb28
View files now have a dynamic size to allow unlimited comments size
Celine Mercier
2016-08-18 17:57:03 +02:00
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
Celine Mercier
2016-08-16 15:17:26 +02:00
cf839522e7
Minor update and fix to obi grep command
Celine Mercier
2016-08-12 17:45:44 +02:00
10b22f79da
The cython subclass is now correctly chosen when cloning a view
Celine Mercier
2016-08-12 17:39:19 +02:00
ad8e10f2d1
Reworked a bit alignment API
Celine Mercier
2016-08-12 15:56:07 +02:00
92cad61417
Fixed bug when closing views with no associated predicate
Celine Mercier
2016-08-12 15:52:38 +02:00
64a745ce0b
First very basic version of obi grep command
Celine Mercier
2016-08-11 17:32:08 +02:00
2d8ac2b035
Fixed bug when creating an OBI_IDX column
Celine Mercier
2016-08-11 17:30:32 +02:00
5b7917bb5a
Fixed bug when writing predicates in view file
Celine Mercier
2016-08-11 17:30:09 +02:00
d3c58780a0
Added __len__ function do OBIViews that returns the line count
Celine Mercier
2016-08-10 17:20:23 +02:00
029d395da1
Added __iter__ function to OBIView lines
Celine Mercier
2016-08-10 17:08:22 +02:00
bea02cc7a5
Added (temporary?) check for the type of quality strings because the import now seems to return them with bytes type
Celine Mercier
2016-08-10 16:25:45 +02:00
ccc877764e
Patch a bug in the printing of the progress bar leading to a bus error when compiled with some C compilers and Cython >= 0.24
Eric Coissac2016-08-03 10:12:23 +02:00
8f0462c407
Merge branch 'master' into Eric_version_for_sequence
Eric Coissac2016-08-03 10:09:20 +02:00
26b8e1f215
Modified C API to set and get in columns: added functions to set and get using column names instead of pointers, and changed function names
Celine Mercier
2016-08-02 16:33:19 +02:00
312f50ff0f
Major update: Column aliases. Columns are now identified in the context of a view by an alias that can be modified.
Celine Mercier
2016-08-01 18:25:30 +02:00
3843485a04
Deleted deprecated function declaration that would make compilation impossible and fixed error in documentation
Celine Mercier
2016-07-22 16:21:02 +02:00
6af62d8124
Change a fprintf without argument to a fputs to comply with the new default parameter on ubuntu
Eric Coissac2016-07-03 08:25:06 +02:00
0869b9ba3f
Closes issue #47 by storing each view in a separate file named with the view's name and created upon view creation.
Celine Mercier
2016-06-30 11:41:30 +02:00
ad2af0b512
Some comments updated
Celine Mercier
2016-06-16 11:26:54 +02:00
f438c3d913
OBIQUAL columns can now handle multiple elements per line
Celine Mercier
2016-06-09 15:54:36 +02:00
2a1ea3ba3f
Setting NA values is now handled properly for OBI_SEQ, OBI_STR and OBI_QUAL columns
Celine Mercier
2016-06-09 14:22:36 +02:00
fc3641d7ff
Read-only AVLs are now hard-linked instead of copied when cloning an AVL group to make it writable. Also fixed several bugs when handling AVL groups.
Celine Mercier
2016-06-03 19:02:46 +02:00
799b942017
Deleted old debugging print
Celine Mercier
2016-06-03 18:57:32 +02:00
6e3f5b230e
Fixed typo in doc
Celine Mercier
2016-06-03 18:56:45 +02:00
2f57f80c63
Fixed a bug where an unmapped variable would be read
Celine Mercier
2016-06-03 18:55:58 +02:00
2962c4d250
Goes with previous commit
Celine Mercier
2016-06-03 18:54:25 +02:00
69bf7ec2e7
NA value for OBI_STR and OBI_SEQ columns is now NULL
Celine Mercier
2016-06-03 18:53:22 +02:00
bac7ce7184
Start of the implementation of the export methods
Eric Coissac2016-06-02 19:10:33 +02:00
f186395661
Trap potential exception generated by char* to bytes casts
Eric Coissac2016-05-29 21:18:20 +02:00
85395dfc1a
value returned for sequence is now bytes and no more str
Eric Coissac2016-05-29 13:53:32 +02:00
f830389974
Add some comment on the location of the align method.
Eric Coissac2016-05-29 12:58:31 +02:00
2e35229357
Add conversion checking on the value of a seq column
Eric Coissac2016-05-29 12:54:13 +02:00
Celine Mercier
Eric Coissac