52b3a9fc39
C: taxonomy: fixed a segfault on linux when trying to fclose an unopened
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file
2019-03-30 15:19:12 +01:00
0847d618d6
fixed typo
2019-03-30 15:14:30 +01:00
9fcebd7643
C: build_reference_db: made some errors more explicit
2019-03-30 15:11:49 +01:00
0c466046f4
Merge branch 'pip-standard-orig-python' into 'master'
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The new install version based on classical setup.py
See merge request obitools/obitools3!1
2019-03-29 16:25:01 +01:00
bf62960ee8
Add some .ignore files
2019-03-29 15:52:54 +01:00
52b8008bdc
Add the location of install
2019-03-29 15:21:30 +01:00
ee9947217c
alignpairedend: fixed the worst memory leak and the handling of the case
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where 0 common kmers are found
2019-03-29 11:16:25 +01:00
10ab557259
First version of the simplified setup.py script
2019-03-26 15:40:31 +01:00
50e7cd61a6
added math.h import where needed
2019-03-13 11:17:25 +01:00
1ee50b7222
Fixed a bug when creating a column and checking the comments string if
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it was NULL
2019-03-07 15:09:59 +01:00
e026e9ec83
Fixed the new alignpaired end to work after ngsfilter with the 9879847
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possible cases
2019-02-17 18:32:35 +01:00
3015310535
Fixed a bug in kmer similarity computation where the fact that sequences
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could be switched was not accounted for
2019-02-10 21:02:24 +01:00
6ca6d27ecb
ecoPCR: fixed amplicon length computation bug
2019-02-06 18:11:20 +01:00
0b62619e4e
Various commentaries and insignificant fixes
2019-01-21 17:32:44 +01:00
c7f5b8d980
Alignpairedend: added alignment using shifting with best kmer similarity
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(low level layer in C and Cython API)
2019-01-21 17:30:46 +01:00
59017c0d6b
C: taxonomy: fixed a bug when checking for root node
2019-01-21 17:23:25 +01:00
9f6bba183f
C: Added a function to get a nucleotide at a specific index in an
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encoded sequence
2019-01-21 17:18:02 +01:00
eb586b2f53
New command and C functions: obi ecotag
2018-12-09 19:19:32 +01:00
9556130b11
C obi_lcs: updated deprecated column names and associated comments
2018-12-09 19:17:13 +01:00
005aaeec06
C obi_lcs: fixed checking for identical sequences when aligning 2
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columns
2018-12-09 19:16:44 +01:00
da445066f3
C alignment filter: added a check for sequences not being equal when the
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threshold requires that they are
2018-12-09 19:14:51 +01:00
0a407436da
C Views: made an error message more specific
2018-12-09 19:14:05 +01:00
54efff36c4
C build ref db: fixed 2 bugs when setting arrays: size of an element in
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in bits not bytes and using view API instead of column API
2018-12-09 19:13:06 +01:00
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
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
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
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
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
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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
