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Author SHA1 Message Date
Celine Mercier 8e70bf1ee1 obi import: fixed bug when rewriting a column (keeping wrong type in 
import module)
 2019-03-26 14:56:18 +01:00
Celine Mercier d8a7bd42bd Cython API, taxonomy: fixed parental tree iterator (skipped second to 
last taxon, in OBI1 too)
 2019-03-26 14:08:54 +01:00
Celine Mercier 06178d9d61 Genbank file parser functions that should have been included in a 
previous commit
 2019-03-20 11:44:43 +01:00
Celine Mercier 3abe1b7ace obi_errno_to_exception function now properly reads obi_errno global 
variable directly
 2019-03-20 11:43:12 +01:00
Celine Mercier 802a3f5933 data import: entries now counted if there are multiple files 2019-03-18 18:16:39 +01:00
Celine Mercier 7e20870719 Added genbank parser 2019-03-15 16:06:27 +01:00
Celine Mercier e8090a44c9 Fixed the ultimate bug with embl (and genbank) parsers: raising any 
exception in a python generator makes it unable to resume. So now,
exceptions are not raised but printed, then functions return None and
that's handled at higher level.
 2019-03-15 16:06:06 +01:00
Celine Mercier 832f582802 Fixed no-skip-on-error option :p 2019-03-15 16:04:04 +01:00
Celine Mercier 58d0c850c2 Made skip on error option True by default...... 2019-03-15 15:50:40 +01:00
Celine Mercier 7737211ac2 Small fix in embl and genbank features parser 2019-03-15 15:50:11 +01:00
Celine Mercier c953f0cb00 Fixed embl import where sequences were not imported as Nuc_Seq objects 2019-03-15 11:41:07 +01:00
Celine Mercier bb045c3ae9 added TAXID_COLUMN to C API declarations for Cython 2019-03-15 11:40:06 +01:00
Celine Mercier 2a4f1b8feb obi import: now properly uses macros for column names 2019-03-15 11:39:21 +01:00
Celine Mercier 24a63f8732 URIs: URIs built with autocomplete now work too 2019-03-15 10:52:27 +01:00
Celine Mercier 478d19ab43 Cleaner stderr prints 2019-03-13 18:36:31 +01:00
Celine Mercier e3c565d6be Cleaner progress bar 2019-03-13 18:36:05 +01:00
Celine Mercier d88390c6d8 Cython API: when importing a file in a DMS, its length is computed 
beforehand for the progress bar
 2019-03-13 18:35:32 +01:00
Celine Mercier 50e7cd61a6 added math.h import where needed 2019-03-13 11:17:25 +01:00
Celine Mercier 49d5f6fb1e removed deprecated comment 2019-03-13 11:17:04 +01:00
Celine Mercier b45c2ee653 Cython API: cleaner column rewriting API 2019-03-13 11:13:55 +01:00
Celine Mercier 6afd1294a7 Cython API: Views: fixed a bug when rewriting a column with different 
attributes (last line is not written anymore)
 2019-03-12 16:40:30 +01:00
Celine Mercier 185a95e667 cleaner Makefile 2019-03-11 15:20:10 +01:00
Celine Mercier 8835a1a983 removed -R compilaiton flag that gcc doesn't like 2019-03-07 15:55:46 +01:00
Celine Mercier 1ee50b7222 Fixed a bug when creating a column and checking the comments string if 
it was NULL
 2019-03-07 15:09:59 +01:00
Celine Mercier 720bb65b24 Installation: basic Makefile that creates the shared obi3 library used 
by Cython
 2019-03-07 14:01:37 +01:00
Celine Mercier 2a1ab9db29 Cython API, Views: guessing an obitype from a python value is now done 
through the corresponding functions in utils
 2019-03-07 13:57:37 +01:00
Celine Mercier 4bc52c08c2 minor changes 2019-03-07 13:53:37 +01:00
Celine Mercier 306da846e3 obidistutils: link obi3 C shared library instead of compiling all C 
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
Celine Mercier af57e532da obidistutils: create doc/sphinx dir if needed 2019-03-07 13:47:23 +01:00
Celine Mercier de3d12af17 Renamed CAPI file 2019-02-19 14:50:30 +01:00
Celine Mercier 9ccddd5280 better cfiles 2019-02-19 14:11:29 +01:00
Celine Mercier e026e9ec83 Fixed the new alignpaired end to work after ngsfilter with the 9879847 
possible cases
 2019-02-17 18:32:35 +01:00
Celine Mercier 4ddd1a1c37 embl iterator: only option on embl directories now works as intended 2019-02-12 16:46:08 +01:00
Celine Mercier 3015310535 Fixed a bug in kmer similarity computation where the fact that sequences 
could be switched was not accounted for
 2019-02-10 21:02:24 +01:00
Celine Mercier 08bcbcd357 ngsfilter: reworked to use apat library 2019-02-06 18:13:54 +01:00
Celine Mercier 04a3682307 Cython API: added API to use apat (pattern search) C library 2019-02-06 18:12:49 +01:00
Celine Mercier 6ca6d27ecb ecoPCR: fixed amplicon length computation bug 2019-02-06 18:11:20 +01:00
Celine Mercier 8f18907566 Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to 
be more explicit
 2019-02-06 18:09:11 +01:00
Celine Mercier 0b62619e4e Various commentaries and insignificant fixes 2019-01-21 17:32:44 +01:00
Celine Mercier c7f5b8d980 Alignpairedend: added alignment using shifting with best kmer similarity 
(low level layer in C and Cython API)
 2019-01-21 17:30:46 +01:00
Celine Mercier 59017c0d6b C: taxonomy: fixed a bug when checking for root node 2019-01-21 17:23:25 +01:00
Celine Mercier 9f6bba183f C: Added a function to get a nucleotide at a specific index in an 
encoded sequence
 2019-01-21 17:18:02 +01:00
Celine Mercier 2a6a112d29 obi import: fixed writing quality in views when appropriate (but still 
not a satisfying solution)
 2018-12-11 19:33:55 +01:00
Celine Mercier c437931a35 Cython: fixed history dot graph for all views, and fixed history 
recording for build_ref_db and ecotag
 2018-12-10 17:09:00 +01:00
Celine Mercier eb586b2f53 New command and C functions: obi ecotag 2018-12-09 19:19:32 +01:00
Celine Mercier 9556130b11 C obi_lcs: updated deprecated column names and associated comments 2018-12-09 19:17:13 +01:00
Celine Mercier 005aaeec06 C obi_lcs: fixed checking for identical sequences when aligning 2 
columns
 2018-12-09 19:16:44 +01:00
Celine Mercier 579f56bb54 obi align (pouic): fixed bug with the saved config when aligning 2 
different views
 2018-12-09 19:15:58 +01:00
Celine Mercier da445066f3 C alignment filter: added a check for sequences not being equal when the 
threshold requires that they are
 2018-12-09 19:14:51 +01:00
Celine Mercier 0a407436da C Views: made an error message more specific 2018-12-09 19:14:05 +01:00
Celine Mercier 54efff36c4 C build ref db: fixed 2 bugs when setting arrays: size of an element in 
in bits not bytes and using view API instead of column API
 2018-12-09 19:13:06 +01:00
Celine Mercier 6acb21712a Missing commit for build_ref_db: C API file for cython 2018-12-09 19:11:59 +01:00
Celine Mercier 12087a6c3a C, views: made 'view_exists' function public (now 'obi_view_exists') 2018-11-27 16:20:30 +01:00
Celine Mercier fbabbceb5a Fixed a bug in the array indexer where the value's length was no 
properly set to 0 if the value was NA (ignore previous commit with the
same message)
 2018-11-27 16:18:34 +01:00
Celine Mercier 6f27734d71 Cython: fxed a bug in INT tuple columns where values were converted to 
double instead of int
 2018-11-27 16:14:56 +01:00
Celine Mercier b3bfa9ca65 Fixed a bug in the array indexer where the value's length was not 
properly set to 0 if the value was NA
 2018-11-27 16:12:41 +01:00
Celine Mercier ece942e771 new command: build_ref_db to build a reference database with metadata 
for the taxonomic assignment of sequences
 2018-11-27 16:11:18 +01:00
Celine Mercier ef8dc85f3c C, taxonomy: new function to get the lowest common ancestor of two taxa 2018-11-27 16:00:29 +01:00
Celine Mercier f942dd856f C: new function to build a reference database with LCA and score 
metadata for the taxonomic assignment of sequences
 2018-11-27 15:56:50 +01:00
Celine Mercier 730ea99f85 minor fixes and comments 2018-11-19 11:23:54 +01:00
Celine Mercier 4d51f4f015 obi import: better checking of whether to import quality 2018-11-19 11:23:39 +01:00
Celine Mercier e9c1d5e48d AVLs: made maximum number of nodes per AVL 5 millions, as this combined 
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
Celine Mercier 7fc1b578cf AVLs: AVLs in a group are not unmapped and remapped constantly anymore 
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
Celine Mercier 31053591b5 Fixed 2 bugs when checking qualities matching sequences predicate: now 
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
Celine Mercier b0da36cb48 New command: obi align, except it's called obi pouic for now because of 
a Cython compilation bug
 2018-11-07 16:05:48 +01:00
Celine Mercier d1f1fd432e Minor fixes 2018-11-07 16:04:17 +01:00
Celine Mercier 75a28929a7 Renamed Cython alignment library in an attempt to limit some compilation 
bugs potentially involving name conflicts
 2018-11-07 16:03:32 +01:00
Celine Mercier d076ea9900 Alignment: updated functions to align columns (LCS) 2018-11-07 16:00:58 +01:00
Celine Mercier 6b1c41f3fb Changed an error message to be more specific 2018-11-07 13:37:25 +01:00
Celine Mercier 362df50fe9 Removed a deprecated element from the DMS structure 2018-11-07 13:36:08 +01:00
Celine Mercier b1090574da View import: associated column informations are now correctly updated 
with the new versions
 2018-11-07 13:35:11 +01:00
Celine Mercier 8faabd3ebf Cython, URI: Fixed a bug when using an output URI with just a view name 
to use the default DMS
 2018-11-02 19:04:27 +01:00
Celine Mercier 35f3e7c30b All commands now handle outputing to another DMS + small fixes 2018-11-02 19:03:09 +01:00
Celine Mercier 8a8e9e50b2 Fixed declaration going with previous commit 2018-10-31 18:01:04 +01:00
Celine Mercier c7ff53b948 obi clean: temporary views are now deleted 2018-10-31 17:52:51 +01:00
Celine Mercier 1b7bccb236 Small improvement when checking if a view exists 2018-10-31 17:51:10 +01:00
Celine Mercier d09aa43133 Cython API: added a function to get the full path to the DMS directory 2018-10-31 14:46:25 +01:00
Celine Mercier 123e5dc0ac Cython URI API: added an argument to only open the DMS and return the 
rest as a character string
 2018-10-31 14:45:17 +01:00
Celine Mercier 320561a582 Views: Added argument to not automatically create default columns in 
typed views, a function to delete a view and fixed view history bug
 2018-10-31 14:38:05 +01:00
Celine Mercier 92c0fbc9bf Fixed a bug where an imported column was not flagged as finished, 
resulting in its deletion when reopening the DMS.
 2018-10-29 17:39:30 +01:00
Celine Mercier b11d52d630 Fixed a bug with the DMS counter being wrongly initialized to 0 instead 
of 1 (generating memory bugs when using the counter)
 2018-10-29 16:12:37 +01:00
Celine Mercier 6305282305 obi clean: made more efficient with arrays (speed ~x15 compared with 
OBI1)
 2018-10-21 17:59:02 +02:00
Celine Mercier d53323e7f4 Fixed comments bug with obi head and obi tail 2018-10-21 17:39:17 +02:00
Celine Mercier e18b762d81 Weird buggy Eclipse commit with nothing changed 2018-10-21 17:35:18 +02:00
Celine Mercier 0a0f0682a9 Better handling of errors and exceptions when new view name already 
exists
 2018-10-17 19:47:40 +02:00
Celine Mercier 4802e32f72 Cython: Sequence objects: repr() method now returns a Fasta or Fastq 
formatted string
 2018-10-17 16:53:42 +02:00
Celine Mercier b027762059 Cython: export: fixed exception raising when no quality data when 
exporting to fastq
 2018-10-17 16:52:51 +02:00
Celine Mercier da0e3d4043 Cython: added full handling of NA strings when importing files 2018-10-17 16:41:15 +02:00
Celine Mercier da76f911db Cython: Views: improved repr() method 2018-10-17 15:54:03 +02:00
Celine Mercier 61ad2deeca obi uniq: Added line breaks when printing informations to cut progress 
bar properly
 2018-10-17 15:53:28 +02:00
Celine Mercier eb6d5581bd Cython: Progress bar: added a cut option to choose whether to do line 
breaks every tenth of the full bar, set to False by default for lighter
printing
 2018-10-17 15:52:26 +02:00
Celine Mercier 343dbc7e4d Cython: made the logger lighter (now prints just module name instead of 
full module path)
 2018-10-17 15:49:55 +02:00
Celine Mercier 6d018a2d28 Cython: Added 'modulename' in the config informations 2018-10-17 15:47:44 +02:00
Celine Mercier 2c2df4e098 C: Added a trick to suppress compilation warnings about an unused 
function actually called in a macro
 2018-10-17 13:13:23 +02:00
Celine Mercier 8ce6dd6d1a Updated prototypes with no arguments with a void argument as suggested 
by compilation warnings
 2018-10-17 12:00:40 +02:00
Celine Mercier df70086384 New command: obi export 2018-10-17 11:27:50 +02:00
Celine Mercier 32d8396ee2 Cython: Added fasta and fastq writers 2018-10-17 11:27:15 +02:00
Celine Mercier 6a8670d24a Cython: minor fixes 2018-10-17 11:26:13 +02:00
Celine Mercier ec73fa840a Cython: obi stats fixed to work with reworked options (forgotten in a 
previous commit)
 2018-10-17 11:25:53 +02:00
Celine Mercier 11032ec90b Cython: Sequence objects: Quality strings are now returned as bytes 
instead of str
 2018-10-17 11:24:44 +02:00