5c50e5b378
Embryo of code for openMP parallelization of LCS alignment but
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deactivated for now because can't make it compile with cython/clang
2016-12-20 11:46:58 +01:00
d99447c12b
C function for LCS alignment of two columns, and optimized and fixed
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line count bug in function to align one column
2016-12-16 19:39:02 +01:00
303bd6f445
Added function to build kmer table for 2 columns, and fixed bug (with
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line count) when building kmer table of one column
2016-12-16 19:10:18 +01:00
9b24818fe2
Refactored alignment code for minimum redundancy between the function
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that aligns 1 column and the function that aligns 2 columns
2016-12-13 17:18:12 +01:00
8afb1644e9
Alignment: API rework. 'obi align' is now 'obi lcs', and the results are
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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
936be64c34
Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
2016-12-05 11:18:29 +01:00
5e0c9f878b
Added the doc for the function building the element names, and a missing
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free
2016-12-05 10:46:21 +01:00
852e5488c8
The default element names for columns with multiple elements per line
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are now "O;1;2;...;n"
2016-12-02 17:54:51 +01:00
e60497651c
Updated the documentation for the functions to set and get in the
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context of a view
2016-11-30 12:22:47 +01:00
4ad8c16a73
Finished adding all the functions to directly set and get indices in
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columns containing indices referring to any type of data.
2016-11-30 11:08:11 +01:00
6f6099687d
Sequence alignment: if no sequence column is given and the view has the
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type NUC_SEQS_VIEW, the default sequence column is aligned
2016-11-29 16:52:41 +01:00
98d0849653
Sequence alignment: added the possibility to specify the index of the
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sequences to align in a column containing multiple sequences per line (C
level for now)
2016-11-29 16:15:02 +01:00
5fb025f310
When aligning, it is now quickly checked whether the sequences are
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identical using their indexes
2016-11-28 11:39:29 +01:00
8ce6f6c80b
Added an argument to specify whether the two sequences can be identical
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when applying filters before aligning
2016-11-28 11:38:02 +01:00
3e53f9418b
Added functions to recover the indexes themselves from any column
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referring to indexed values
2016-11-28 11:35:19 +01:00
d40d2d0c76
Fixed error in documentation
2016-11-28 10:55:23 +01:00
f897e87600
When closing a view, it is now automatically checked that all OBI_QUAL
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columns correspond to their associated OBI_SEQ column
2016-11-25 12:04:57 +01:00
70e056a2aa
It is now impossible to open or clone a view that is not finished (= has
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been closed at least once)
2016-11-24 11:19:07 +01:00
8abbfa203a
Good file for commit 6fa9a8bd: When a view is cloned, a comment is added
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to the new view specifying the name of the cloned view
2016-11-23 11:32:39 +01:00
6fa9a8bd76
When a view is cloned, a comment is added to the new view specifying the
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name of the cloned view
2016-11-23 11:29:21 +01:00
0ab9e6c05a
When adding an existing column to a view, it is checked that the
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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
70c49e214a
Added the kmer filter to LCS alignments, and now obiblobs containing
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encoded sequences are directly put in int16_t arrays for the alignment
2016-11-18 16:29:28 +01:00
08e67a090f
Changed the inline functions syntax, which should make it compatible
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with more compilers
2016-11-18 16:21:26 +01:00
621b4972db
Functions to get obiblobs through views
2016-11-18 15:59:50 +01:00
7d022c1a52
If the indexer name is NULL when creating a column, it now becomes the
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column name
2016-11-18 15:56:51 +01:00
1c71c195fc
Goes with a0ebc2d8
2016-11-10 15:01:29 +01:00
54cfeffd85
Goes with 8f724f4f, forgotten file
2016-11-10 14:48:31 +01:00
a0ebc2d871
Functions to directly retrieve Obiblobs from indexers
2016-11-10 14:45:28 +01:00
8f724f4f8e
Some code refactoring
2016-11-09 16:48:00 +01:00
2d2fe5279d
Added functions to add new taxa to a taxonomy with handling of
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associated *.ldx files
2016-11-03 17:59:21 +01:00
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
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
1a7b42018e
Added some error checking when opening or creating a view
2016-09-28 14:28:34 +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
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
