b45c2ee653
Cython API: cleaner column rewriting API
2019-03-13 11:13:55 +01:00
6afd1294a7
Cython API: Views: fixed a bug when rewriting a column with different
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attributes (last line is not written anymore)
2019-03-12 16:40:30 +01:00
a9ba7744cf
obidistutils: added fPIC flag needed for linux compilation and set
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minimum python version to 3.7
2019-03-12 14:20:59 +01:00
185a95e667
cleaner Makefile
2019-03-11 15:20:10 +01:00
8835a1a983
removed -R compilaiton flag that gcc doesn't like
2019-03-07 15:55:46 +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
720bb65b24
Installation: basic Makefile that creates the shared obi3 library used
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by Cython
2019-03-07 14:01:37 +01:00
2a1ab9db29
Cython API, Views: guessing an obitype from a python value is now done
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through the corresponding functions in utils
2019-03-07 13:57:37 +01:00
4bc52c08c2
minor changes
2019-03-07 13:53:37 +01:00
306da846e3
obidistutils: link obi3 C shared library instead of compiling all C
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files with all modules (creating issues with global/static variables).
EXCEPT RUNTIME LINKING DOESN'T WORK YET
2019-03-07 13:50:29 +01:00
af57e532da
obidistutils: create doc/sphinx dir if needed
2019-03-07 13:47:23 +01:00
52de6f2717
Update distutils for openmp and new version of pip
2019-02-19 17:30:53 +01:00
29c56572cf
Add cfiles everywhere ;-)
2019-02-19 15:04:30 +01:00
de3d12af17
Renamed CAPI file
2019-02-19 14:50:30 +01:00
9ccddd5280
better cfiles
2019-02-19 14:11:29 +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
4ddd1a1c37
embl iterator: only option on embl directories now works as intended
2019-02-12 16:46:08 +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
08bcbcd357
ngsfilter: reworked to use apat library
2019-02-06 18:13:54 +01:00
04a3682307
Cython API: added API to use apat (pattern search) C library
2019-02-06 18:12:49 +01:00
6ca6d27ecb
ecoPCR: fixed amplicon length computation bug
2019-02-06 18:11:20 +01:00
8f18907566
Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to
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be more explicit
2019-02-06 18:09:11 +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
2a6a112d29
obi import: fixed writing quality in views when appropriate (but still
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not a satisfying solution)
2018-12-11 19:33:55 +01:00
c437931a35
Cython: fixed history dot graph for all views, and fixed history
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recording for build_ref_db and ecotag
2018-12-10 17:09:00 +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
579f56bb54
obi align (pouic): fixed bug with the saved config when aligning 2
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different views
2018-12-09 19:15:58 +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
6acb21712a
Missing commit for build_ref_db: C API file for cython
2018-12-09 19:11:59 +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
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
