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Author SHA1 Message Date
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
Eric Coissac
400a3f9f3d Merge branch 'Eric_version_for_sequence' 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-04 09:42:42 +02:00
Eric Coissac
d1d26b9028 Simplify the code 2016-08-04 08:00:54 +02:00
Eric Coissac
465ea81c77 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-08-03 10:13:47 +02:00
Eric Coissac
1e6d6e32e0 Switch to Cython version >= 0.24 2016-08-03 10:13:10 +02:00
Eric 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
Eric 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
Eric Coissac
000b9999ad Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-07-03 09:22:22 +02:00
Eric Coissac
aff9831c13 Substitute fprintf call by fputs call to conform with the new ubuntu 
compilation rules
 2016-07-03 09:21:56 +02:00
Eric Coissac
448fa8d325 first trial for a fasta formater 2016-07-03 09:18:52 +02:00
Eric 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
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
Eric Coissac
bac7ce7184 Start of the implementation of the export methods 2016-06-02 19:10:33 +02:00
Eric Coissac
f186395661 Trap potential exception generated by char* to bytes casts 2016-05-29 21:18:20 +02:00
Eric Coissac
85395dfc1a value returned for sequence is now bytes and no more str 2016-05-29 13:53:32 +02:00
Eric Coissac
f830389974 Add some comment on the location of the align method. 2016-05-29 12:58:31 +02:00
Eric Coissac
2e35229357 Add conversion checking on the value of a seq column 2016-05-29 12:54:13 +02:00
Eric Coissac
a8ed57dc6e few small changes 2016-05-21 12:29:55 +02:00
Eric Coissac
c3274d419c remove an extra debug log 2016-05-21 12:29:08 +02:00
Eric Coissac
cca0dbb46b Close issue #54 by adding a read1 method to the MagicKeyFile class 2016-05-21 12:24:48 +02:00
Eric Coissac
5a78157112 increase parsing speed of the header 2016-05-21 10:29:11 +02:00
Eric Coissac
0b9a41d952 Patch a bug about the reading of the last sequence 2016-05-21 10:28:03 +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