e18b762d81
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
1fd3323372
Columns: elements names informations are now kept in a memory arena of
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adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
2017-12-13 22:46:50 +01:00
9a50803c00
Added tuple columns containing immutable indexed data arrays of any type
2017-11-15 13:48:59 +01:00
9482c663c0
minor comments and changes
2017-07-27 19:46:34 +02:00
f03928c679
Committing minor comments before merging branch with master
2017-07-06 10:56:39 +02:00
e524041013
Views: Files for unfinished views now have the extension
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'.obiview_unfinished', renamed to '.obiview' when the view is finished.
2017-02-07 17:16:09 +01:00
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
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
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
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
2aaa87edcc
1st version of obi align command and reworked functions that handle
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column alignment
2016-08-10 14:51:02 +02:00
ad2af0b512
Some comments updated
2016-06-16 11:26:54 +02:00
b3c47809da
First version of alignment functions (imported from suma* programs)
2016-05-11 16:36:23 +02:00
