58b42cd977
C: views: now correctly parses view names containing '.' when cleaning
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unfinished views. Closes #115
2021-09-08 10:52:42 +12:00
7f0f63cf26
C: now completely unmapping files before truncating them to a smaller
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size (#68 )
2021-03-11 15:12:40 +13:00
ad1fd3c341
Now handling dictionaries with one key
2021-03-10 16:50:30 +13:00
199f3772e8
Small fixes (potential compilation problems)
2020-10-30 10:41:58 +01:00
137c109f86
obi ls: now done in C (preparing things for R packages to read DMS) and
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switch to version 3.0.0b36
2020-09-29 17:51:39 +02:00
e28507639a
C and Cython: fixed and improved the associated columns system
2020-07-26 17:39:29 +02:00
aec5e69f2c
C, views: no more automatic COUNT column if MERGED_sample column exists
2020-05-07 17:08:07 +02:00
b6ab792ceb
C: made error message more detailed when checking that sequences and
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qualities match
2020-04-12 17:40:24 +02:00
1bfb96023c
obi import: rewriting a column now deletes the old one to save disk
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space
2020-02-01 15:31:14 +01:00
6282242a04
C: Views: fixed a bug when trying to add a comment after changing the
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file name of a finished view
2019-09-25 11:39:32 +02:00
44517db51f
Fixed gcc warnings
2019-09-25 11:38:00 +02:00
783a1343c4
DMS are now locked when used by a command. Added checks and changed
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cleaning mechanisms.
2019-09-20 20:37:19 +02:00
8f9f2a2d10
obi ls: various improvements
2019-09-10 14:41:43 +02:00
7c518300a0
C: Views: fixed a bug when creating automatic columns with unformatted
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comments
2019-03-30 20:33:14 +01:00
50e7cd61a6
added math.h import where needed
2019-03-13 11:17:25 +01:00
0a407436da
C Views: made an error message more specific
2018-12-09 19:14:05 +01:00
12087a6c3a
C, views: made 'view_exists' function public (now 'obi_view_exists')
2018-11-27 16:20:30 +01:00
31053591b5
Fixed 2 bugs when checking qualities matching sequences predicate: now
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closing and reopening indexers so that they are mapped properly, and
fixed memory leak when reading sequences
2018-11-19 11:05:53 +01:00
8a8e9e50b2
Fixed declaration going with previous commit
2018-10-31 18:01:04 +01:00
1b7bccb236
Small improvement when checking if a view exists
2018-10-31 17:51:10 +01:00
320561a582
Views: Added argument to not automatically create default columns in
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typed views, a function to delete a view and fixed view history bug
2018-10-31 14:38:05 +01:00
e18b762d81
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
0a0f0682a9
Better handling of errors and exceptions when new view name already
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exists
2018-10-17 19:47:40 +02:00
8ce6dd6d1a
Updated prototypes with no arguments with a void argument as suggested
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by compilation warnings
2018-10-17 12:00:40 +02:00
86bb582a17
Views: implemented handling of JSON formatted comments
2018-10-07 18:56:46 +02:00
3fcf29a76f
More explicit predicate error when checking that sequences and qualities
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match
2018-08-08 19:51:05 +02:00
4aef20add8
Fixed a bug where the line selection column of a view would not be
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flagged as finished
2018-05-17 15:17:19 +02:00
4c3478d8f8
Removed the predicate to check for a quality column (because for example
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with obi annotate, clone view so clone predicate, then modify seq, so
quality is deleted, and predicate becomes a problem)
2018-03-21 16:37:19 +01:00
b48330a5c9
Fixed a little bug when cleaning unfinished views
2018-02-12 14:44:56 +01:00
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
ea73047fc7
Added rewinddir before each readdir so that the directories are always
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read properly
2017-11-24 18:04:58 +01:00
3ba7ce1c91
View rollback: version files and column directories aren't deleted
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anymore to prevent indexer bug, and fixed a freeing bug
2017-11-15 17:27:26 +01:00
9a50803c00
Added tuple columns containing immutable indexed data arrays of any type
2017-11-15 13:48:59 +01:00
1684f96b79
Fixed a bug when flagging a read-only column as finished
2017-10-26 19:11:29 +02:00
dfd51939a0
Views are now rollbacked if an error occurs, and unfinished views and
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columns are deleted when an OBIDMS is opened.
2017-10-26 18:58:48 +02:00
7c57bd33e5
Added check to prevent views from having the name 'taxonomy' (used for
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URIs)
2017-09-15 14:54:55 +02:00
a3e81930c2
Views: finished handling and documenting the conditions for an existing
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column to be added to a view
2017-08-03 16:32:22 +02:00
15d383fa8b
Added possibility to specify the offset for encoding and decoding
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sequence quality character strings
2017-07-27 19:24:41 +02:00
59dd0a8a8c
Standardized and improved the API to create new columns, updated the doc
2017-07-18 17:34:32 +02:00
c88df2e12c
First version of automatic ID and COUNT columns, to discuss (for now,
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columns created when NUC_SEQ views are closed if the columns don't
already exist)
2017-07-17 17:31:09 +02:00
3e6aecc635
Added a C function to add a COUNT column to a view with all lines set to
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1
2017-07-11 16:44:23 +02:00
f03928c679
Committing minor comments before merging branch with master
2017-07-06 10:56:39 +02:00
71b1a43df8
Added functions to clone views with a simpler API
2017-04-21 11:58:15 +02:00
2f0c4b90d7
Fixed a problem where a view would have a wrong line count after adding
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a first column to it if there was already a Line selection associated
(happening when cloning), and fixed a bad error check.
2017-04-14 16:25:55 +02:00
ad8de80353
Views: better checks when adding an existing column to a view
2017-04-06 14:44:07 +02:00
778acc48cd
Added linked lists to handle lists of column pointers in views (not
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tested)
2017-03-06 16:06:17 +01:00
3319ede837
Views: Column dictionaries now store and return pointers on column
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pointers instead of column pointers.
2017-02-22 13:49:50 +01:00
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
e50da64ea1
The elements names when a column contains several elements per line are
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now formatted with '\0' as separator and handled in a more optimized way
2017-01-31 16:48:06 +01:00
936be64c34
Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
2016-12-05 11:18:29 +01:00
