Celine Mercier
76f89717fe
Added alias property to OBIDMS_column cython class
2016-09-26 16:12:48 +02:00
Celine Mercier
b408a4f6eb
Changed file name limits to adapt to system limits + minor changes
2016-09-22 18:05:07 +02:00
Celine Mercier
b083745f56
Deleted the "new line selection while editing a view" system
2016-09-22 11:19:29 +02:00
Celine Mercier
43f3c69a40
Fixed bug when cloning column with line selection
2016-09-21 17:50:21 +02:00
Celine Mercier
e79507b629
Fixed bugs in the process ensuring that all the columns of a view have
...
the same line count, fixed a bug when trying to set a value in a view
when a line selection exists, fixed a bug when adding a new column to a
view where line counts would be wrong
2016-09-21 17:42:17 +02:00
Celine Mercier
bb25723d99
Improved documentation of a function
2016-09-21 17:30:39 +02:00
Celine Mercier
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
Celine Mercier
802bae110b
Removed deprecated function
2016-09-21 17:09:59 +02:00
Celine Mercier
dd55aef3e5
Added column class method to get the unique references (name and
...
version) of a column
2016-09-21 17:08:44 +02:00
Celine Mercier
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
Celine Mercier
8f49553d5a
First version of the obi test command, testing that the OBITools3 work
...
correctly
2016-09-15 12:26:07 +02:00
Celine Mercier
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
Celine Mercier
a240ec0169
Added error checking when closing file descriptors
2016-09-15 11:58:56 +02:00
Celine Mercier
0a3c23d9d0
Added a missing closedir
2016-09-15 11:58:34 +02:00
Celine Mercier
8724445fa1
Added error checking when closing files
2016-09-15 11:50:30 +02:00
Celine Mercier
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
Celine Mercier
9a97f1f633
View predicates are now carried over when cloning a view
2016-09-06 16:22:24 +02:00
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
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
