|
|
219c0d6fdc
|
obi cat: Fixed the handling when concatenating views with dictionaries
having different key sets
|
2020-02-12 14:21:39 +01:00 |
|
|
|
dc9f897917
|
switch to version 3.0.0-beta10
|
2020-02-02 21:15:27 +01:00 |
|
|
|
bb72682f7d
|
obi import: new option --preread to do a first readthrough of the
dataset if it contains huge dictionaries for a much faster import.
|
2020-02-02 21:12:34 +01:00 |
|
|
|
52920c3c71
|
URI decoding: dirty temp fix for bug where default dms makes a mess when
should guess file
|
2020-02-02 21:11:05 +01:00 |
|
|
|
18c22cecf9
|
switch to version 3.0.0-beta9
|
2020-02-01 15:48:55 +01:00 |
|
|
|
1bfb96023c
|
obi import: rewriting a column now deletes the old one to save disk
space
|
2020-02-01 15:31:14 +01:00 |
|
|
|
c67d668989
|
obi import: fixed a bug when the first entry would contain a dictionary
with one key. Switch to beta8
|
2020-01-29 20:23:39 +01:00 |
|
|
|
db0ac37d41
|
switch to version 3.0.0-beta7
|
2020-01-29 16:18:53 +01:00 |
|
|
|
53212168a2
|
History: added 'obi' in bash history for practical reasons
|
2020-01-23 16:51:49 +01:00 |
|
|
|
b4b2e62195
|
Cleaner handling of reverse quality columns
|
2020-01-18 19:28:12 +01:00 |
|
|
|
ced82c4242
|
Switching to version 3.0-beta6
|
2020-01-18 17:29:23 +01:00 |
|
|
|
a524f8829e
|
New command: obi cat to concatenate views (not optimized yet)
|
2020-01-18 17:28:31 +01:00 |
|
|
|
822000cb70
|
Fixes in documentation
|
2020-01-18 17:26:18 +01:00 |
|
|
|
b1f3e082f9
|
ngsfilter: fixed a bug when there is only one tag introduced in latest
edit
|
2020-01-06 13:53:38 +01:00 |
|
|
|
6c018b403c
|
ecopcr: fixed and improved the options to keep nuclotides around the
amplicon
|
2019-12-26 20:45:54 +01:00 |
|
|
|
694d1934a8
|
Tagging version beta3
|
2019-12-12 17:03:13 +01:00 |
|
|
|
fc3ac03630
|
clean_dms: now works with extension
|
2019-12-12 17:02:50 +01:00 |
|
|
|
d75e54a078
|
uniq: added forced deletion of reverse sequence quality
|
2019-12-12 17:02:36 +01:00 |
|
|
|
6bfd7441f3
|
ngsfilter: fixed sequence cutting when dealing with unaligned sequences.
Could use optimization
|
2019-12-12 17:01:31 +01:00 |
|
|
|
81a179239c
|
ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for
unaligned sequences
|
2019-12-10 18:13:27 +01:00 |
|
|
|
35ce37c0f7
|
ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and
made error annotations more explicit
|
2019-12-10 13:43:32 +01:00 |
|
|
|
53f18316b0
|
ngsfilter: made more robust and practical to use with empty tags
|
2019-11-29 15:21:08 +01:00 |
|
|
|
8bc249b2f4
|
Version 3.0.0-beta1
|
2019-09-27 14:52:05 +02:00 |
|
|
|
e308c2e822
|
versioning 1.0.beta
|
2019-09-26 21:05:05 +02:00 |
|
|
|
be85c55c9e
|
Python: URIs: fixed bug on linux systems
|
2019-09-25 14:41:52 +02:00 |
|
|
|
44517db51f
|
Fixed gcc warnings
|
2019-09-25 11:38:00 +02:00 |
|
|
|
28b7fce59a
|
Cython API: simpler column repr display
|
2019-09-22 20:23:31 +02:00 |
|
|
|
fa9555deb9
|
obi stats: fixed bug with None values
|
2019-09-22 20:21:53 +02:00 |
|
|
|
d30f7e7317
|
more cleaning
|
2019-09-22 18:52:05 +02:00 |
|
|
|
71276537a6
|
obi import: fixed bug when importing a taxdump
|
2019-09-22 16:45:30 +02:00 |
|
|
|
ba9ba7aa60
|
obi grep: now able to convert str to bytes in predicate expressions
|
2019-09-22 16:44:45 +02:00 |
|
|
|
336100f716
|
obi less: now actually behaves like less
|
2019-09-21 18:29:12 +02:00 |
|
|
|
d83398c0e0
|
Cython: View: lines from simple View instances are now displayed in tab
instead of dict format
|
2019-09-21 18:28:56 +02:00 |
|
|
|
974d25b815
|
Cython: Fixed bug in tab formatter with header option always being set
to true
|
2019-09-21 18:27:47 +02:00 |
|
|
|
ec0737a600
|
Added signal catching and handling in C and Cython
|
2019-09-21 16:47:22 +02:00 |
|
|
|
06f9d6da60
|
obi import: importing a view to a DMS now uses the C API (more efficient
and imports all metadata)
|
2019-09-21 12:49:29 +02:00 |
|
|
|
f0f7edf152
|
Python API: small option improvements
|
2019-09-21 12:08:36 +02:00 |
|
|
|
9e72c8d16a
|
obi ls: improved taxonomy list
|
2019-09-20 20:46:33 +02:00 |
|
|
|
7c3fa14789
|
obi import: fixed bug when reading output URI
|
2019-09-20 20:43:48 +02:00 |
|
|
|
ec874c095b
|
new command: clean_dms to clean and unlock a DMS after a bad exit.
|
2019-09-20 20:38:25 +02:00 |
|
|
|
783a1343c4
|
DMS are now locked when used by a command. Added checks and changed
cleaning mechanisms.
|
2019-09-20 20:37:19 +02:00 |
|
|
|
eb6c59dc1e
|
obi import: proper check for taxonomy name already existing in DMS when
importing a taxdump
|
2019-09-17 13:41:49 +02:00 |
|
|
|
ad46056179
|
obi export: if export format is not specified, it is guessed from the
view type
|
2019-09-17 13:22:41 +02:00 |
|
|
|
9063e9159d
|
Export options: output option is now only non-positional for obi export
|
2019-09-17 13:19:17 +02:00 |
|
|
|
0159385943
|
URI decoding: fixed bug with dms-only URI
|
2019-09-17 12:50:37 +02:00 |
|
|
|
a0c8deb806
|
obi export: made output to stdout and pipe in less possible
|
2019-09-17 12:31:03 +02:00 |
|
|
|
f566618be6
|
Added option for no progress bar and made output URI option non
positional (for stdout output)
|
2019-09-17 12:29:33 +02:00 |
|
|
|
88451116e8
|
URIs: added stdout output (empty URI)
|
2019-09-17 12:28:10 +02:00 |
|
|
|
eb913b2742
|
ecotag: trying to use a threshold lower than the ref db threshold now
returns an error instead of a warning
|
2019-09-15 19:27:47 +02:00 |
|
|
|
f8d1fa678a
|
obi stats: improved display with str instead of bytes
|
2019-09-10 16:20:36 +02:00 |
|
