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Author SHA1 Message Date
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
coissac 400a3f9f3d Merge branch 'Eric_version_for_sequence' 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-04 09:42:42 +02:00
coissac d1d26b9028 Simplify the code 2016-08-04 08:00:54 +02:00
coissac 465ea81c77 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-08-03 10:13:47 +02:00
coissac 1e6d6e32e0 Switch to Cython version >= 0.24 2016-08-03 10:13:10 +02:00
coissac ccc877764e Patch a bug in the printing of the progress bar leading to a bus error 
when compiled with some C compilers and Cython >= 0.24
 2016-08-03 10:12:23 +02:00
coissac 8f0462c407 Merge branch 'master' into Eric_version_for_sequence 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-03 10:09:20 +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
coissac 000b9999ad Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-07-03 09:22:22 +02:00
coissac aff9831c13 Substitute fprintf call by fputs call to conform with the new ubuntu 
compilation rules
 2016-07-03 09:21:56 +02:00
coissac 448fa8d325 first trial for a fasta formater 2016-07-03 09:18:52 +02:00
coissac 6af62d8124 Change a fprintf without argument to a fputs to comply with the new 
default parameter on ubuntu
 2016-07-03 08:25:06 +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