a0da984003
Fixed bug where columns would not get truncated to the right size, and
...
fixed bug where column directories would be open and not closed in some
instances
2016-09-21 17:28:52 +02:00
802bae110b
Removed deprecated function
2016-09-21 17:09:59 +02:00
dd55aef3e5
Added column class method to get the unique references (name and
...
version) of a column
2016-09-21 17:08:44 +02:00
9ac522fde1
Better obi test command
2016-09-21 17:06:35 +02:00
6adb9eb623
Should solde issue #56
2016-09-19 21:40:40 +02:00
8f49553d5a
First version of the obi test command, testing that the OBITools3 work
...
correctly
2016-09-15 12:26:07 +02:00
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
a240ec0169
Added error checking when closing file descriptors
2016-09-15 11:58:56 +02:00
0a3c23d9d0
Added a missing closedir
2016-09-15 11:58:34 +02:00
8724445fa1
Added error checking when closing files
2016-09-15 11:50:30 +02:00
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
9a97f1f633
View predicates are now carried over when cloning a view
2016-09-06 16:22:24 +02:00
00014eb023
View files now have the *.obiview extension
2016-09-06 14:19:13 +02:00
acc0da2d0b
Readjusted some limits for file names and file numbers to be under OS
...
limits
2016-09-05 12:39:04 +02:00
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
ba84ef4847
Fixed typo
2016-09-05 12:31:06 +02:00
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
eb82d088cb
Added some view class methods
2016-09-05 12:20:00 +02:00
f46ea0b988
Finished fixing issues with DMS paths
2016-08-30 11:09:45 +02:00
5b2e370ffb
Fixed a bug when using an absolute path for a DMS
2016-08-29 17:30:31 +02:00
8d360b0fac
Minor improvements to obi export command
2016-08-19 17:49:22 +02:00
b34769b27c
Minor improvements to obi export command
2016-08-19 17:46:55 +02:00
2d0a714e37
Basic obi export command exporting from view to fasta or fastq format,
...
for testing purposes
2016-08-19 17:40:58 +02:00
7b780ffb28
View files now have a dynamic size to allow unlimited comments size
2016-08-18 17:57:03 +02:00
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
2016-08-16 15:17:26 +02:00
cf839522e7
Minor update and fix to obi grep command
2016-08-12 17:45:44 +02:00
10b22f79da
The cython subclass is now correctly chosen when cloning a view
2016-08-12 17:39:19 +02:00
ad8e10f2d1
Reworked a bit alignment API
2016-08-12 15:56:07 +02:00
92cad61417
Fixed bug when closing views with no associated predicate
2016-08-12 15:52:38 +02:00
64a745ce0b
First very basic version of obi grep command
2016-08-11 17:32:08 +02:00
2d8ac2b035
Fixed bug when creating an OBI_IDX column
2016-08-11 17:30:32 +02:00
5b7917bb5a
Fixed bug when writing predicates in view file
2016-08-11 17:30:09 +02:00
d3c58780a0
Added __len__ function do OBIViews that returns the line count
2016-08-10 17:20:23 +02:00
029d395da1
Added __iter__ function to OBIView lines
2016-08-10 17:08:22 +02:00
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
4ba01617af
Fixed obscure compilation bug
2016-08-10 15:26:40 +02:00
bec684d5e2
Fixed merge conflict
2016-08-10 15:05:37 +02:00
2aaa87edcc
1st version of obi align command and reworked functions that handle
...
column alignment
2016-08-10 14:51:02 +02:00
400a3f9f3d
Merge branch 'Eric_version_for_sequence'
...
Conflicts:
python/obitools3/obidms/_obidmscolumn_seq.pyx
2016-08-04 09:42:42 +02:00
d1d26b9028
Simplify the code
2016-08-04 08:00:54 +02:00
465ea81c77
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
2016-08-03 10:13:47 +02:00
1e6d6e32e0
Switch to Cython version >= 0.24
2016-08-03 10:13:10 +02:00
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
8f0462c407
Merge branch 'master' into Eric_version_for_sequence
...
Conflicts:
python/obitools3/obidms/_obidmscolumn_seq.pyx
2016-08-03 10:09:20 +02:00
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
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
3843485a04
Deleted deprecated function declaration that would make compilation
...
impossible and fixed error in documentation
2016-07-22 16:21:02 +02:00
20425a5d2b
Deleted deprecated structure declarations
2016-07-19 15:48:56 +02:00
56e4848ebd
The predicates associated with a view are now described in its comments
...
field
2016-07-19 15:31:21 +02:00
8850e40b6e
Minor changes for better presentation
2016-07-19 15:30:17 +02:00
