obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
373 Commits 18 Branches 66 Tags
9ac522fde1c05bd73248078222457fe0e9d6b6a3
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Celine Mercier 9ac522fde1 Better obi test command 2016-09-21 17:06:35 +02:00
Celine Mercier 8f49553d5a First version of the obi test command, testing that the OBITools3 work 
correctly
 2016-09-15 12:26:07 +02:00
Celine Mercier 986f90c59e Fixed bug where column directories weren't closed correctly, leading to 
too many file descriptors open, and added error checking when closing
file descriptors
 2016-09-15 12:18:40 +02:00
Celine Mercier a240ec0169 Added error checking when closing file descriptors 2016-09-15 11:58:56 +02:00
Celine Mercier 0a3c23d9d0 Added a missing closedir 2016-09-15 11:58:34 +02:00
Celine Mercier 8724445fa1 Added error checking when closing files 2016-09-15 11:50:30 +02:00
Celine Mercier de189fd7e0 Fixed major bug when cloning an AVL where the bloom filter was not 
copied properly (because the sutructure copy via assignation does not
work for structures with a variable size)
 2016-09-15 11:47:02 +02:00
Celine Mercier 9a97f1f633 View predicates are now carried over when cloning a view 2016-09-06 16:22:24 +02:00
Celine Mercier 00014eb023 View files now have the *.obiview extension 2016-09-06 14:19:13 +02:00
Celine Mercier acc0da2d0b Readjusted some limits for file names and file numbers to be under OS 
limits
 2016-09-05 12:39:04 +02:00
Celine Mercier 668696fc5a Fixed major bug: when setting all the columns of a view to the same 
number of lines, columns are now cloned before being enlarged if needed
+ predicate functions now print error messages if the predicates are not
respected
 2016-09-05 12:37:36 +02:00
Celine Mercier ba84ef4847 Fixed typo 2016-09-05 12:31:06 +02:00
Celine Mercier c9dce03295 Fixed major bug when cloning an AVL group (last AVL of new group was not 
correctly enlarged before copying the data) + minor improvements
 2016-09-05 12:29:52 +02:00
Celine Mercier eb82d088cb Added some view class methods 2016-09-05 12:20:00 +02:00
Celine Mercier f46ea0b988 Finished fixing issues with DMS paths 2016-08-30 11:09:45 +02:00
Celine Mercier 5b2e370ffb Fixed a bug when using an absolute path for a DMS 2016-08-29 17:30:31 +02:00
Celine Mercier 8d360b0fac Minor improvements to obi export command 2016-08-19 17:49:22 +02:00
Celine Mercier b34769b27c Minor improvements to obi export command 2016-08-19 17:46:55 +02:00
Celine Mercier 2d0a714e37 Basic obi export command exporting from view to fasta or fastq format, 
for testing purposes
 2016-08-19 17:40:58 +02:00
Celine Mercier 7b780ffb28 View files now have a dynamic size to allow unlimited comments size 2016-08-18 17:57:03 +02:00
Celine Mercier e4129610cf Quality columns are now optional in NUC_SEQS views + minor fixes 2016-08-16 15:17:26 +02:00
Celine Mercier cf839522e7 Minor update and fix to obi grep command 2016-08-12 17:45:44 +02:00
Celine Mercier 10b22f79da The cython subclass is now correctly chosen when cloning a view 2016-08-12 17:39:19 +02:00
Celine Mercier ad8e10f2d1 Reworked a bit alignment API 2016-08-12 15:56:07 +02:00
Celine Mercier 92cad61417 Fixed bug when closing views with no associated predicate 2016-08-12 15:52:38 +02:00
Celine Mercier 64a745ce0b First very basic version of obi grep command 2016-08-11 17:32:08 +02:00
Celine Mercier 2d8ac2b035 Fixed bug when creating an OBI_IDX column 2016-08-11 17:30:32 +02:00
Celine Mercier 5b7917bb5a Fixed bug when writing predicates in view file 2016-08-11 17:30:09 +02:00
Celine Mercier d3c58780a0 Added __len__ function do OBIViews that returns the line count 2016-08-10 17:20:23 +02:00
Celine Mercier 029d395da1 Added __iter__ function to OBIView lines 2016-08-10 17:08:22 +02:00
Celine Mercier bea02cc7a5 Added (temporary?) check for the type of quality strings because the 
import now seems to return them with bytes type
 2016-08-10 16:25:45 +02:00
Celine Mercier 4ba01617af Fixed obscure compilation bug 2016-08-10 15:26:40 +02:00
Celine Mercier bec684d5e2 Fixed merge conflict 2016-08-10 15:05:37 +02:00
Celine Mercier 2aaa87edcc 1st version of obi align command and reworked functions that handle 
column alignment
 2016-08-10 14:51:02 +02:00
Celine Mercier 26b8e1f215 Modified C API to set and get in columns: added functions to set and get 
using column names instead of pointers, and changed function names
 2016-08-02 16:33:19 +02:00
Celine Mercier 312f50ff0f Major update: Column aliases. Columns are now identified in the context 
of a view by an alias that can be modified.
 2016-08-01 18:25:30 +02:00
Celine Mercier 3843485a04 Deleted deprecated function declaration that would make compilation 
impossible and fixed error in documentation
 2016-07-22 16:21:02 +02:00
Celine Mercier 20425a5d2b Deleted deprecated structure declarations 2016-07-19 15:48:56 +02:00
Celine Mercier 56e4848ebd The predicates associated with a view are now described in its comments 
field
 2016-07-19 15:31:21 +02:00
Celine Mercier 8850e40b6e Minor changes for better presentation 2016-07-19 15:30:17 +02:00
Celine Mercier b89af38109 Goes with 38718320 2016-07-18 13:57:49 +02:00
Celine Mercier 38718320f9 First version for the association of one column to another. Closes #55 2016-07-15 15:38:49 +02:00
Celine Mercier 8ee85c3005 A first version of predicate functions that are checked when a new view 
is saved and closed
 2016-07-12 14:54:11 +02:00
Celine Mercier 0869b9ba3f Closes issue #47 by storing each view in a separate file named with the 
view's name and created upon view creation.
 2016-06-30 11:41:30 +02:00
Celine Mercier ad2af0b512 Some comments updated 2016-06-16 11:26:54 +02:00
Celine Mercier 38e603ed57 Deleted some redundant cython code 2016-06-10 10:34:47 +02:00
Celine Mercier f438c3d913 OBIQUAL columns can now handle multiple elements per line 2016-06-09 15:54:36 +02:00
Celine Mercier 2a1ea3ba3f Setting NA values is now handled properly for OBI_SEQ, OBI_STR and 
OBI_QUAL columns
 2016-06-09 14:22:36 +02:00
Celine Mercier fc3641d7ff Read-only AVLs are now hard-linked instead of copied when cloning an AVL 
group to make it writable. Also fixed several bugs when handling AVL
groups.
 2016-06-03 19:02:46 +02:00
Celine Mercier 799b942017 Deleted old debugging print 2016-06-03 18:57:32 +02:00
Celine Mercier 6e3f5b230e Fixed typo in doc 2016-06-03 18:56:45 +02:00
Celine Mercier 2f57f80c63 Fixed a bug where an unmapped variable would be read 2016-06-03 18:55:58 +02:00
Celine Mercier 2962c4d250 Goes with previous commit 2016-06-03 18:54:25 +02:00
Celine Mercier 69bf7ec2e7 NA value for OBI_STR and OBI_SEQ columns is now NULL 2016-06-03 18:53:22 +02:00
Celine Mercier e681ca646d Fixed a problem with some columns being shorter in views and triggering 
errors when trying to get values. Temporary fix that needs discussion
 2016-05-20 18:45:29 +02:00
Celine Mercier 3b59043ea8 Major update: New column type to store sequence qualities. Closes #41 2016-05-20 16:45:22 +02:00
Celine Mercier ffff91e76c Fixed variable name that had been accidentally changed for better 
clarity
 2016-05-18 13:27:41 +02:00
Celine Mercier 6a8df069ad Indexers are now cloned if needed to modify them after they've been 
closed. Obligatory indexers' names now follow the same pattern as other
indexers (columnname_version). Closes #46 and #49.
 2016-05-18 13:23:48 +02:00
Celine Mercier 8ae7644945 First version of quality handling (not working yet) and now it is 
checked that a column is writable before enlarging it
 2016-05-11 16:38:14 +02:00
Celine Mercier b3c47809da First version of alignment functions (imported from suma* programs) 2016-05-11 16:36:23 +02:00
Celine Mercier 3567681339 Now when a column is added to a view, if there is a line selection, all 
columns in the view are cloned first
 2016-05-11 16:34:20 +02:00
Celine Mercier 757ef8509a Deleting CeCILL license duplicates 2016-05-09 11:17:45 +02:00
Celine Mercier f961621f5d Minor improvements in _obidms Cython layer 2016-05-04 13:43:26 +02:00
Celine Mercier bc12360490 Reworked and commented a bit the cython layer for dms, columns and views 2016-05-02 15:16:06 +02:00
Celine Mercier 872071b104 Removed a list of column pointers kept in the OBIView class that was not 
really needed
 2016-05-02 14:23:42 +02:00
Celine Mercier 32cc8968e8 Adding CeCILL license 2016-05-02 11:51:59 +02:00
Celine Mercier d6481f0db8 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-04-29 17:46:59 +02:00
Celine Mercier a32920e401 Relative paths when creating or opening a DMS now work 2016-04-29 17:46:36 +02:00
Celine Mercier 31cf27d676 Added indexer function that returns the name of the indexer 2016-04-29 16:18:56 +02:00
Celine Mercier baba2d742e commenting _obidms.pyx 2016-04-29 16:07:03 +02:00
Celine Mercier 5bd12079ae Added comments about listing columns and indexers in obidms functions 2016-04-29 16:06:01 +02:00
Celine Mercier 072ee5ac03 Re-re-fixed line breaks in README file 2016-04-29 15:44:40 +02:00
Celine Mercier 9fe21316ff Refixed line breaks in README file 2016-04-29 15:39:46 +02:00
Celine Mercier 3dc3aaa46b Fixed line breaks in README file 2016-04-29 15:36:58 +02:00
Celine Mercier b371030edd Adding README file 2016-04-29 15:35:08 +02:00
Celine Mercier b3976fa461 Merge branch 'luke_tests' 2016-04-28 11:17:24 +02:00
Celine Mercier 6ea2cfb9ca Merging luke_tests branch without the commit turning inline functions in macros 2016-04-28 11:17:18 +02:00
Celine Mercier 0eca86107e Pseudo obihead for tests 2016-04-27 14:27:28 +02:00
Celine Mercier 0de953a3ef pseudo obigrep for tests 2016-04-27 14:19:55 +02:00
Celine Mercier f3b20b809d Fixed bug with indexer names being defined and generating seg fault if 
creating a column not using indexers
 2016-04-27 14:01:36 +02:00
Celine Mercier d159b921eb Fixed obi import trying to print all lines at the end (source of 
segfault?)
 2016-04-27 13:14:19 +02:00
Celine Mercier 4e4cf46b16 Added all C files as source files for all cython files to stop having 
that kind of problem with linux systems
 2016-04-27 10:44:24 +02:00
Celine Mercier 6b61533650 Added more C source files for _obiseq 2016-04-27 10:41:00 +02:00
Celine Mercier 419885485b Added files in _obitaxo C sources for cython 2016-04-27 10:30:16 +02:00
Celine Mercier 0c8504b6db Commented #ifdef directive for detect_bucket_size function because it 
causes errors
 2016-04-27 10:24:40 +02:00
Celine Mercier 2d8c06f7b7 Fixed variable initialization for error detection 2016-04-26 14:38:46 +02:00
Celine Mercier a6c8d35491 import command a bit modified for tests 2016-04-26 14:29:54 +02:00
Celine Mercier 366264828e Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem 2016-04-26 14:29:17 +02:00
Celine Mercier d3a6ff6043 Removed deprecated code 2016-04-26 14:27:16 +02:00
Celine Mercier 5ca84b91dc Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-04-25 18:35:57 +02:00
Celine Mercier 87935c6678 Fixed all compilation problems with new function names, locations etc 2016-04-25 18:35:02 +02:00
Celine Mercier 92980508c0 Made the function to clone a column in the context of a view private 2016-04-25 18:15:25 +02:00
Celine Mercier 65880db422 Made function to update the line count of a view private 2016-04-25 18:11:37 +02:00
Celine Mercier 767d9c7804 Reordered view functions for better coherence 2016-04-25 18:07:58 +02:00
Celine Mercier 2566377e2a Updated the documentation for utils functions 2016-04-25 18:02:58 +02:00
Celine Mercier 1fbbdd43f9 Updated obiversion_t declaration 2016-04-25 17:58:37 +02:00
Celine Mercier 8cdfbb379e Documentation for views and reworked the code a little 2016-04-25 17:58:12 +02:00
Celine Mercier 0a55e26520 Reworked obiview code and added more comments 2016-04-25 11:37:53 +02:00
Celine Mercier 68a8509c12 Updated documentation in obitypes.h 2016-04-25 10:33:01 +02:00
Celine Mercier 5f98d2ed5c Fixed the calculation of the size of data for OBI_STR and OBI_SEQ 
columns
 2016-04-25 10:26:51 +02:00