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5c50e5b378a3240ce8ea07ef1fa2d4fce80eea79
Commit Graph

256 Commits

Author SHA1 Message Date
Celine Mercier
5c50e5b378 Embryo of code for openMP parallelization of LCS alignment but 
deactivated for now because can't make it compile with cython/clang
 2016-12-20 11:46:58 +01:00
Celine Mercier
d99447c12b C function for LCS alignment of two columns, and optimized and fixed 
line count bug in function to align one column
 2016-12-16 19:39:02 +01:00
Celine Mercier
303bd6f445 Added function to build kmer table for 2 columns, and fixed bug (with 
line count) when building kmer table of one column
 2016-12-16 19:10:18 +01:00
Celine Mercier
9b24818fe2 Refactored alignment code for minimum redundancy between the function 
that aligns 1 column and the function that aligns 2 columns
 2016-12-13 17:18:12 +01:00
Celine Mercier
8afb1644e9 Alignment: API rework. 'obi align' is now 'obi lcs', and the results are 
now written to columns automatically created in the output view, all
optimally handled at the C level.
 2016-12-12 11:58:59 +01:00
Celine Mercier
936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00
Celine Mercier
5e0c9f878b Added the doc for the function building the element names, and a missing 
free
 2016-12-05 10:46:21 +01:00
Celine Mercier
852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier
e60497651c Updated the documentation for the functions to set and get in the 
context of a view
 2016-11-30 12:22:47 +01:00
Celine Mercier
4ad8c16a73 Finished adding all the functions to directly set and get indices in 
columns containing indices referring to any type of data.
 2016-11-30 11:08:11 +01:00
Celine Mercier
6f6099687d Sequence alignment: if no sequence column is given and the view has the 
type NUC_SEQS_VIEW, the default sequence column is aligned
 2016-11-29 16:52:41 +01:00
Celine Mercier
98d0849653 Sequence alignment: added the possibility to specify the index of the 
sequences to align in a column containing multiple sequences per line (C
level for now)
 2016-11-29 16:15:02 +01:00
Celine Mercier
5fb025f310 When aligning, it is now quickly checked whether the sequences are 
identical using their indexes
 2016-11-28 11:39:29 +01:00
Celine Mercier
8ce6f6c80b Added an argument to specify whether the two sequences can be identical 
when applying filters before aligning
 2016-11-28 11:38:02 +01:00
Celine Mercier
3e53f9418b Added functions to recover the indexes themselves from any column 
referring to indexed values
 2016-11-28 11:35:19 +01:00
Celine Mercier
d40d2d0c76 Fixed error in documentation 2016-11-28 10:55:23 +01:00
Celine Mercier
f897e87600 When closing a view, it is now automatically checked that all OBI_QUAL 
columns correspond to their associated OBI_SEQ column
 2016-11-25 12:04:57 +01:00
Celine Mercier
70e056a2aa It is now impossible to open or clone a view that is not finished (= has 
been closed at least once)
 2016-11-24 11:19:07 +01:00
Celine Mercier
8abbfa203a Good file for commit 6fa9a8bd: When a view is cloned, a comment is added 
to the new view specifying the name of the cloned view
 2016-11-23 11:32:39 +01:00
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