12087a6c3a
C, views: made 'view_exists' function public (now 'obi_view_exists')
2018-11-27 16:20:30 +01:00
fbabbceb5a
Fixed a bug in the array indexer where the value's length was no
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properly set to 0 if the value was NA (ignore previous commit with the
same message)
2018-11-27 16:18:34 +01:00
6f27734d71
Cython: fxed a bug in INT tuple columns where values were converted to
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double instead of int
2018-11-27 16:14:56 +01:00
b3bfa9ca65
Fixed a bug in the array indexer where the value's length was not
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properly set to 0 if the value was NA
2018-11-27 16:12:41 +01:00
ece942e771
new command: build_ref_db to build a reference database with metadata
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for the taxonomic assignment of sequences
2018-11-27 16:11:18 +01:00
ef8dc85f3c
C, taxonomy: new function to get the lowest common ancestor of two taxa
2018-11-27 16:00:29 +01:00
f942dd856f
C: new function to build a reference database with LCA and score
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metadata for the taxonomic assignment of sequences
2018-11-27 15:56:50 +01:00
730ea99f85
minor fixes and comments
2018-11-19 11:23:54 +01:00
4d51f4f015
obi import: better checking of whether to import quality
2018-11-19 11:23:39 +01:00
e9c1d5e48d
AVLs: made maximum number of nodes per AVL 5 millions, as this combined
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with keeping all AVLs mapped seems the most efficient. Now 1 million
sequences more or less constantly takes 1 minute.
2018-11-19 11:22:26 +01:00
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
b0da36cb48
New command: obi align, except it's called obi pouic for now because of
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a Cython compilation bug
2018-11-07 16:05:48 +01:00
d1f1fd432e
Minor fixes
2018-11-07 16:04:17 +01:00
75a28929a7
Renamed Cython alignment library in an attempt to limit some compilation
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bugs potentially involving name conflicts
2018-11-07 16:03:32 +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
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with the new versions
2018-11-07 13:35:11 +01:00
8faabd3ebf
Cython, URI: Fixed a bug when using an output URI with just a view name
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to use the default DMS
2018-11-02 19:04:27 +01:00
35f3e7c30b
All commands now handle outputing to another DMS + small fixes
2018-11-02 19:03:09 +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
d09aa43133
Cython API: added a function to get the full path to the DMS directory
2018-10-31 14:46:25 +01:00
123e5dc0ac
Cython URI API: added an argument to only open the DMS and return the
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rest as a character string
2018-10-31 14:45:17 +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
d53323e7f4
Fixed comments bug with obi head and obi tail
2018-10-21 17:39:17 +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
4802e32f72
Cython: Sequence objects: repr() method now returns a Fasta or Fastq
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formatted string
2018-10-17 16:53:42 +02:00
b027762059
Cython: export: fixed exception raising when no quality data when
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exporting to fastq
2018-10-17 16:52:51 +02:00
da0e3d4043
Cython: added full handling of NA strings when importing files
2018-10-17 16:41:15 +02:00
da76f911db
Cython: Views: improved repr() method
2018-10-17 15:54:03 +02:00
61ad2deeca
obi uniq: Added line breaks when printing informations to cut progress
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bar properly
2018-10-17 15:53:28 +02:00
eb6d5581bd
Cython: Progress bar: added a cut option to choose whether to do line
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breaks every tenth of the full bar, set to False by default for lighter
printing
2018-10-17 15:52:26 +02:00
343dbc7e4d
Cython: made the logger lighter (now prints just module name instead of
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full module path)
2018-10-17 15:49:55 +02:00
6d018a2d28
Cython: Added 'modulename' in the config informations
2018-10-17 15:47:44 +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
df70086384
New command: obi export
2018-10-17 11:27:50 +02:00
32d8396ee2
Cython: Added fasta and fastq writers
2018-10-17 11:27:15 +02:00
6a8670d24a
Cython: minor fixes
2018-10-17 11:26:13 +02:00
ec73fa840a
Cython: obi stats fixed to work with reworked options (forgotten in a
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previous commit)
2018-10-17 11:25:53 +02:00
11032ec90b
Cython: Sequence objects: Quality strings are now returned as bytes
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instead of str
2018-10-17 11:24:44 +02:00
8a9ba8b0a8
Cython: Added Column line methods to get a Column line as a str or
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bytes, and elements (keys, values) with None values are not returned
anymore
2018-10-17 11:23:07 +02:00
135d3b6e67
Cython: updated the URI decoding to handle outputs other than DMS
2018-10-17 11:21:29 +02:00
