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201 Commits

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
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
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
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
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
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
3b59043ea8 Major update: New column type to store sequence qualities. Closes #41 2016-05-20 16:45:22 +02:00
Celine Mercier
b3c47809da First version of alignment functions (imported from suma* programs) 2016-05-11 16:36:23 +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
baba2d742e commenting _obidms.pyx 2016-04-29 16:07:03 +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
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
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
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
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