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Author SHA1 Message Date
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
Celine Mercier 5d08da46a2 Updated the documentation in obidmscolumn.h 2016-04-22 17:55:53 +02:00
Celine Mercier 66045acf1d Creating a column now uses the function to create the indexer name if 
one was not provided
 2016-04-22 17:47:00 +02:00
Celine Mercier 6977c4315c Improved function to build an indexer name 2016-04-22 17:38:23 +02:00
Celine Mercier 839b3000a8 Added a function to build indexer names 2016-04-22 17:08:23 +02:00
Celine Mercier ffa4557928 changed MAP_PRIVATE flags to MAP_SHARED when opening a column because it 
seems a lot more efficient
 2016-04-22 16:26:24 +02:00
Celine Mercier 003cd11362 Fixed initialization of NA values for OBI_STR and OBI_SEQ columns 2016-04-22 16:14:23 +02:00
Celine Mercier c87227b65a Uncommented an error message that doesn't need to be commented anymore 2016-04-22 16:11:56 +02:00
Celine Mercier c07e75f2ac Updated the documentation for OBI_STR columns 2016-04-22 15:59:32 +02:00