7fc1b578cf
AVLs: AVLs in a group are not unmapped and remapped constantly anymore
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when adding new values, fixed a bug when calculating if an AVL data file
has reached the maximum size, fixed a casting bug, and added a boolean
so read-only AVLs files are not truncated
2018-11-19 11:19:07 +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
d1f1fd432e
Minor fixes
2018-11-07 16:04:17 +01:00
d076ea9900
Alignment: updated functions to align columns (LCS)
2018-11-07 16:00:58 +01:00
6b1c41f3fb
Changed an error message to be more specific
2018-11-07 13:37:25 +01:00
362df50fe9
Removed a deprecated element from the DMS structure
2018-11-07 13:36:08 +01:00
b1090574da
View import: associated column informations are now correctly updated
...
with the new versions
2018-11-07 13:35:11 +01:00
8a8e9e50b2
Fixed declaration going with previous commit
2018-10-31 18:01:04 +01:00
c7ff53b948
obi clean: temporary views are now deleted
2018-10-31 17:52:51 +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
92c0fbc9bf
Fixed a bug where an imported column was not flagged as finished,
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resulting in its deletion when reopening the DMS.
2018-10-29 17:39:30 +01:00
b11d52d630
Fixed a bug with the DMS counter being wrongly initialized to 0 instead
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of 1 (generating memory bugs when using the counter)
2018-10-29 16:12:37 +01:00
6305282305
obi clean: made more efficient with arrays (speed ~x15 compared with
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OBI1)
2018-10-21 17:59:02 +02:00
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
2c2df4e098
C: Added a trick to suppress compilation warnings about an unused
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function actually called in a macro
2018-10-17 13:13:23 +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
bc8c394061
Columns: implemented handling of JSON formatted comments
2018-10-07 18:54:51 +02:00
cef458f570
Obierrno: added errno for JSON related errors
2018-10-07 18:53:53 +02:00
2736a92699
DMS: implemented full information file with JSON formatted comments
2018-10-07 18:53:25 +02:00
79f4185757
C library to handle JSON formatted comments using the cJSON library
2018-10-07 18:51:27 +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
2ba6d16147
New command: obi ecopcr
2018-07-28 17:13:45 +02:00
a39f9697be
Views: added macro for taxid column name
2018-07-28 17:10:11 +02:00
b98880b7fa
Various non-important fixes and comments
2018-07-28 17:07:17 +02:00
7f6d1597fc
Taxonomy: added functions to check if a taxonomy already exists in a
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DMS, and added taxdump import from a compressed file
2018-07-28 16:48:11 +02:00
1de308a856
obi clean: option to only keep heads now works, fixed a bug where last
...
sequence was not properly labelled, and code is cleaned, fixed and error
checked
2018-05-31 15:11:41 +02:00
892ed83a33
Removed deprecated function declarations
2018-05-31 15:08:11 +02:00
6911bf4d70
obi clean: first version
2018-05-18 14:26:54 +02:00
f0c147c252
C API: Added a function to set an entire column to a specified (atomic)
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value.
2018-05-17 15:59:16 +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
156fb04e88
Implemented functions to build reverse complement sequences
2018-01-05 16:08:36 +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
0998268955
Fixed two little potential bugs when cleaning unfinished columns and
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deleted old trace
2017-11-24 18:03:59 +01:00
31726407a3
Taxonomy: fixed a bug where a pointer was not properly reallocated, and
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a bug where the merged list of taxids was not built correctly
2017-11-24 18:01:30 +01:00
9e3ac477eb
OBIDMS: Opened DMS now have a counter associated so that DMS are not
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actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
2017-11-24 17:58:47 +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
04e065094a
All DMS opened by a program are now listed and closed with atexit system
2017-10-16 10:35:07 +02:00
9fc6868341
Increased maximum length for elements names
2017-10-04 16:10:53 +02:00
535692b020
Taxonomy: new functions and improvements
2017-10-04 15:55:13 +02:00
5ed6835e0e
Fixed a bug where the new line count when truncating a column would not
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be computed correctly when dealing with high numbers (bad automatic type
for intermediate result)
2017-09-25 10:52:19 +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
