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
...
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
...
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
...
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
...
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
38029b1f77
Forgot a ;
2017-08-20 17:56:18 +02:00
c559ddf487
BUG FIX: creation of a new column would fail because of a case not
...
handled when a high number of elements per line would imply less than
one line per memory page
2017-08-20 17:30:23 +02:00
93cff94e7f
Fixed some compilation warnings
2017-08-20 17:25:58 +02:00
9744a48a67
BUG FIX: seemingly identical obiblobs would have different hash values
...
because of the padding added by the compiler. Fixed by using calloc
instead of malloc for obiblob memory allocation.
2017-08-20 17:25:15 +02:00
6afdc9fb5f
AVLs: Added an error check
2017-08-20 17:21:06 +02:00
6f202363f4
Fixed a typo in doc
2017-08-20 17:20:13 +02:00
4b86aa67a8
New C functions to import a column and a view from a DMS to another DMS
2017-08-03 16:33:12 +02:00
a3e81930c2
Views: finished handling and documenting the conditions for an existing
...
column to be added to a view
2017-08-03 16:32:22 +02:00
644b55b49f
Fixed doc typo
2017-08-03 16:29:25 +02:00
927c684fc2
Utils: new function to copy the content of a file into another file
2017-08-03 16:28:54 +02:00
344566d9e9
AVLs: made some functions public and changed some rights to be able to
...
import AVLs from a DMS to another
2017-08-03 16:27:43 +02:00
7c0d882bc9
Patch a bug when creating a DMS not in the current directory. Use the
...
basename function to locate the DMS name instead of the loop...
2017-07-28 15:56:21 +02:00
9482c663c0
minor comments and changes
2017-07-27 19:46:34 +02:00
c5f3fdc295
Increased maximum element names length in columns
2017-07-27 19:44:49 +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,
...
columns created when NUC_SEQ views are closed if the columns don't
already exist)
2017-07-17 17:31:09 +02:00
1e57bfacb4
Fixed some C documentation
2017-07-17 16:45:08 +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
