|
|
6b1c41f3fb
|
Changed an error message to be more specific
|
2018-11-07 13:37:25 +01:00 |
|
|
|
362df50fe9
|
Removed a deprecated element from the DMS structure
|
2018-11-07 13:36:08 +01:00 |
|
|
|
b1090574da
|
View import: associated column informations are now correctly updated
with the new versions
|
2018-11-07 13:35:11 +01:00 |
|
|
|
8faabd3ebf
|
Cython, URI: Fixed a bug when using an output URI with just a view name
to use the default DMS
|
2018-11-02 19:04:27 +01:00 |
|
|
|
35f3e7c30b
|
All commands now handle outputing to another DMS + small fixes
|
2018-11-02 19:03:09 +01:00 |
|
|
|
8a8e9e50b2
|
Fixed declaration going with previous commit
|
2018-10-31 18:01:04 +01:00 |
|
|
|
c7ff53b948
|
obi clean: temporary views are now deleted
|
2018-10-31 17:52:51 +01:00 |
|
|
|
1b7bccb236
|
Small improvement when checking if a view exists
|
2018-10-31 17:51:10 +01:00 |
|
|
|
d09aa43133
|
Cython API: added a function to get the full path to the DMS directory
|
2018-10-31 14:46:25 +01:00 |
|
|
|
123e5dc0ac
|
Cython URI API: added an argument to only open the DMS and return the
rest as a character string
|
2018-10-31 14:45:17 +01:00 |
|
|
|
320561a582
|
Views: Added argument to not automatically create default columns in
typed views, a function to delete a view and fixed view history bug
|
2018-10-31 14:38:05 +01:00 |
|
|
|
92c0fbc9bf
|
Fixed a bug where an imported column was not flagged as finished,
resulting in its deletion when reopening the DMS.
|
2018-10-29 17:39:30 +01:00 |
|
|
|
b11d52d630
|
Fixed a bug with the DMS counter being wrongly initialized to 0 instead
of 1 (generating memory bugs when using the counter)
|
2018-10-29 16:12:37 +01:00 |
|
|
|
6305282305
|
obi clean: made more efficient with arrays (speed ~x15 compared with
OBI1)
|
2018-10-21 17:59:02 +02:00 |
|
|
|
d53323e7f4
|
Fixed comments bug with obi head and obi tail
|
2018-10-21 17:39:17 +02:00 |
|
|
|
e18b762d81
|
Weird buggy Eclipse commit with nothing changed
|
2018-10-21 17:35:18 +02:00 |
|
|
|
0a0f0682a9
|
Better handling of errors and exceptions when new view name already
exists
|
2018-10-17 19:47:40 +02:00 |
|
|
|
4802e32f72
|
Cython: Sequence objects: repr() method now returns a Fasta or Fastq
formatted string
|
2018-10-17 16:53:42 +02:00 |
|
|
|
b027762059
|
Cython: export: fixed exception raising when no quality data when
exporting to fastq
|
2018-10-17 16:52:51 +02:00 |
|
|
|
da0e3d4043
|
Cython: added full handling of NA strings when importing files
|
2018-10-17 16:41:15 +02:00 |
|
|
|
da76f911db
|
Cython: Views: improved repr() method
|
2018-10-17 15:54:03 +02:00 |
|
|
|
61ad2deeca
|
obi uniq: Added line breaks when printing informations to cut progress
bar properly
|
2018-10-17 15:53:28 +02:00 |
|
|
|
eb6d5581bd
|
Cython: Progress bar: added a cut option to choose whether to do line
breaks every tenth of the full bar, set to False by default for lighter
printing
|
2018-10-17 15:52:26 +02:00 |
|
|
|
343dbc7e4d
|
Cython: made the logger lighter (now prints just module name instead of
full module path)
|
2018-10-17 15:49:55 +02:00 |
|
|
|
6d018a2d28
|
Cython: Added 'modulename' in the config informations
|
2018-10-17 15:47:44 +02:00 |
|
|
|
2c2df4e098
|
C: Added a trick to suppress compilation warnings about an unused
function actually called in a macro
|
2018-10-17 13:13:23 +02:00 |
|
|
|
8ce6dd6d1a
|
Updated prototypes with no arguments with a void argument as suggested
by compilation warnings
|
2018-10-17 12:00:40 +02:00 |
|
|
|
df70086384
|
New command: obi export
|
2018-10-17 11:27:50 +02:00 |
|
|
|
32d8396ee2
|
Cython: Added fasta and fastq writers
|
2018-10-17 11:27:15 +02:00 |
|
|
|
6a8670d24a
|
Cython: minor fixes
|
2018-10-17 11:26:13 +02:00 |
|
|
|
ec73fa840a
|
Cython: obi stats fixed to work with reworked options (forgotten in a
previous commit)
|
2018-10-17 11:25:53 +02:00 |
|
|
|
11032ec90b
|
Cython: Sequence objects: Quality strings are now returned as bytes
instead of str
|
2018-10-17 11:24:44 +02:00 |
|
|
|
8a9ba8b0a8
|
Cython: Added Column line methods to get a Column line as a str or
bytes, and elements (keys, values) with None values are not returned
anymore
|
2018-10-17 11:23:07 +02:00 |
|
|
|
135d3b6e67
|
Cython: updated the URI decoding to handle outputs other than DMS
|
2018-10-17 11:21:29 +02:00 |
|
|
|
58589e04be
|
Cython: rearranged input and output format options to have both and
updated commands accordingly
|
2018-10-17 11:19:48 +02:00 |
|
|
|
e6bbe13d81
|
Cython: fasta and fastq parsers now return bytes and take NA string
argument
|
2018-10-17 11:16:20 +02:00 |
|
|
|
61b00d6013
|
Cython: fastq formatter
|
2018-10-09 16:41:14 +02:00 |
|
|
|
8029493c10
|
Cython: fasta and fastq header formatter
|
2018-10-09 16:41:00 +02:00 |
|
|
|
aa5ee53478
|
Cython: fasta writer
|
2018-10-09 16:40:30 +02:00 |
|
|
|
e31c8ea57a
|
New command: obi history to print DMS or view history in bash, dot or
ascii formats
|
2018-10-07 19:11:36 +02:00 |
|
|
|
9e700ddc21
|
obi test: updated to test comments
|
2018-10-07 19:10:46 +02:00 |
|
|
|
e9a41c5b97
|
Commands: updated for JSON formatted comments with history
|
2018-10-07 19:10:34 +02:00 |
|
|
|
35cf2962cc
|
Cython: DMS: JSON formatted comments and history handling
|
2018-10-07 19:06:59 +02:00 |
|
|
|
74be3c39f0
|
Cython: Views: JSON formatted comments and history handling
|
2018-10-07 19:06:23 +02:00 |
|
|
|
c6ee0bade9
|
Cython: Columns: goes with handling of JSON formatted comments
|
2018-10-07 19:04:50 +02:00 |
|
|
|
ffd5bc76bf
|
Cython utils: functions convert to bytes or str and to remove all empty
objects from a complex object
|
2018-10-07 19:03:38 +02:00 |
|
|
|
704d9b0474
|
Cython: Columns: added support for JSON formatted comments
|
2018-10-07 18:59:43 +02:00 |
|
|
|
86bb582a17
|
Views: implemented handling of JSON formatted comments
|
2018-10-07 18:56:46 +02:00 |
|
|
|
bc8c394061
|
Columns: implemented handling of JSON formatted comments
|
2018-10-07 18:54:51 +02:00 |
|
|
|
cef458f570
|
Obierrno: added errno for JSON related errors
|
2018-10-07 18:53:53 +02:00 |
|
