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9701b1230ced21f078867481225bc6f6b83e25e8
Commit Graph

287 Commits

Author SHA1 Message Date
Celine Mercier
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
Celine Mercier
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
Celine Mercier
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
Celine Mercier
08e67a090f Changed the inline functions syntax, which should make it compatible 
with more compilers
 2016-11-18 16:21:26 +01:00
Celine Mercier
621b4972db Functions to get obiblobs through views 2016-11-18 15:59:50 +01:00
Celine Mercier
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
Celine Mercier
1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier
54cfeffd85 Goes with 8f724f4f, forgotten file 2016-11-10 14:48:31 +01:00
Celine Mercier
a0ebc2d871 Functions to directly retrieve Obiblobs from indexers 2016-11-10 14:45:28 +01:00
Celine Mercier
8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +01:00
Celine Mercier
2d2fe5279d Added functions to add new taxa to a taxonomy with handling of 
associated *.ldx files
 2016-11-03 17:59:21 +01:00
Celine Mercier
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
Celine Mercier
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
Celine Mercier
0dfd67ec89 The endianness of binary taxonomy files is now correctly checked 2016-10-10 17:04:29 +02:00
Celine Mercier
0faaac49cf The taxonomy directory of the DMS is now automatically created with the 
DMS
 2016-10-10 17:02:51 +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
1a7b42018e Added some error checking when opening or creating a view 2016-09-28 14:28:34 +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
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
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
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
92cad61417 Fixed bug when closing views with no associated predicate 2016-08-12 15:52:38 +02:00
Celine Mercier
2d8ac2b035 Fixed bug when creating an OBI_IDX column 2016-08-11 17:30:32 +02:00
Celine Mercier
5b7917bb5a Fixed bug when writing predicates in view file 2016-08-11 17:30:09 +02:00
Celine Mercier
2aaa87edcc 1st version of obi align command and reworked functions that handle 
column alignment
 2016-08-10 14:51:02 +02:00
Celine Mercier
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
 2016-08-02 16:33:19 +02:00
Celine Mercier
312f50ff0f Major update: Column aliases. Columns are now identified in the context 
of a view by an alias that can be modified.
 2016-08-01 18:25:30 +02:00
Celine Mercier
3843485a04 Deleted deprecated function declaration that would make compilation 
impossible and fixed error in documentation
 2016-07-22 16:21:02 +02:00
Celine Mercier
20425a5d2b Deleted deprecated structure declarations 2016-07-19 15:48:56 +02:00
Celine Mercier
56e4848ebd The predicates associated with a view are now described in its comments 
field
 2016-07-19 15:31:21 +02:00
Celine Mercier
38718320f9 First version for the association of one column to another. Closes #55 2016-07-15 15:38:49 +02:00
Celine Mercier
8ee85c3005 A first version of predicate functions that are checked when a new view 
is saved and closed
 2016-07-12 14:54:11 +02:00