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Author SHA1 Message Date
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
Celine Mercier 8a9ba8b0a8 Cython: Added Column line methods to get a Column line as a str or 
bytes, and elements (keys, values) with None values are not returned
anymore
 2018-10-17 11:23:07 +02:00
Celine Mercier 135d3b6e67 Cython: updated the URI decoding to handle outputs other than DMS 2018-10-17 11:21:29 +02:00
Celine Mercier 58589e04be Cython: rearranged input and output format options to have both and 
updated commands accordingly
 2018-10-17 11:19:48 +02:00
Celine Mercier e6bbe13d81 Cython: fasta and fastq parsers now return bytes and take NA string 
argument
 2018-10-17 11:16:20 +02:00
Celine Mercier 61b00d6013 Cython: fastq formatter 2018-10-09 16:41:14 +02:00
Celine Mercier 8029493c10 Cython: fasta and fastq header formatter 2018-10-09 16:41:00 +02:00
Celine Mercier aa5ee53478 Cython: fasta writer 2018-10-09 16:40:30 +02:00
Celine Mercier e31c8ea57a New command: obi history to print DMS or view history in bash, dot or 
ascii formats
 2018-10-07 19:11:36 +02:00
Celine Mercier 9e700ddc21 obi test: updated to test comments 2018-10-07 19:10:46 +02:00
Celine Mercier e9a41c5b97 Commands: updated for JSON formatted comments with history 2018-10-07 19:10:34 +02:00
Celine Mercier 35cf2962cc Cython: DMS: JSON formatted comments and history handling 2018-10-07 19:06:59 +02:00
Celine Mercier 74be3c39f0 Cython: Views: JSON formatted comments and history handling 2018-10-07 19:06:23 +02:00
Celine Mercier c6ee0bade9 Cython: Columns: goes with handling of JSON formatted comments 2018-10-07 19:04:50 +02:00
Celine Mercier ffd5bc76bf Cython utils: functions convert to bytes or str and to remove all empty 
objects from a complex object
 2018-10-07 19:03:38 +02:00
Celine Mercier 704d9b0474 Cython: Columns: added support for JSON formatted comments 2018-10-07 18:59:43 +02:00
Celine Mercier 86bb582a17 Views: implemented handling of JSON formatted comments 2018-10-07 18:56:46 +02:00
Celine Mercier bc8c394061 Columns: implemented handling of JSON formatted comments 2018-10-07 18:54:51 +02:00
Celine Mercier cef458f570 Obierrno: added errno for JSON related errors 2018-10-07 18:53:53 +02:00
Celine Mercier 2736a92699 DMS: implemented full information file with JSON formatted comments 2018-10-07 18:53:25 +02:00
Celine Mercier 79f4185757 C library to handle JSON formatted comments using the cJSON library 2018-10-07 18:51:27 +02:00
Celine Mercier 1b6b6d825a obi grep: added all the missing filtering options 2018-08-14 17:11:41 +02:00
Celine Mercier 3847850a9d Taxonomy Cython API: added is_ancestor() function 2018-08-14 17:09:40 +02:00
Celine Mercier b57e938cc4 New command: obi stats 2018-08-13 15:08:10 +02:00
Celine Mercier 2dc7fcceac Minor fixes 2018-08-10 10:39:46 +02:00
Celine Mercier e096b929dc New command: obi tail 2018-08-10 10:39:26 +02:00
Celine Mercier 2c634dae7c New command: obi head 2018-08-10 10:29:37 +02:00
Celine Mercier 7a4cdc0cfe New command: obi sort 2018-08-09 18:10:47 +02:00
Celine Mercier e8dc5eb123 Commands: ngsfilter and alignpairedend can now be used in whichever 
order
 2018-08-08 19:53:26 +02:00
Celine Mercier 3fcf29a76f More explicit predicate error when checking that sequences and qualities 
match
 2018-08-08 19:51:05 +02:00
Celine Mercier 080a97cccf Cython API: more explicit "Can't guess type" exception 2018-08-08 19:50:26 +02:00
Celine Mercier 9c9aec2556 Cython API: the associated sequence column for a quality column can now 
be specified at the Python level
 2018-08-08 19:49:56 +02:00
Celine Mercier 303648bd47 Cython: embl file parser 2018-07-28 17:14:10 +02:00
Celine Mercier 2ba6d16147 New command: obi ecopcr 2018-07-28 17:13:45 +02:00
Celine Mercier 275d85dc5d Cython: fixed a bug when reading an uncompressed file in binary mode 
where the first 4 characters would not be read
 2018-07-28 17:11:51 +02:00
Celine Mercier a39f9697be Views: added macro for taxid column name 2018-07-28 17:10:11 +02:00
Celine Mercier b98880b7fa Various non-important fixes and comments 2018-07-28 17:07:17 +02:00
Celine Mercier 895d09b133 obi import: 'taxid' columns are imported as 'TAXID' to fit view 
predicates, and fixed taxdump import and DMS closing
 2018-07-28 17:03:00 +02:00
Celine Mercier c02c15b93f Cython API: URI decoding now returns the character string with the 
object path if it could not be opened
 2018-07-28 17:00:42 +02:00