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55d4f98d60
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obi annotate: fixed annotation at ranks
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2020-04-29 14:24:40 +02:00 |
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0bec2631e8
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ecotag: fixed a bug where all the full DMS path weren't properly sent to
the C layer
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2020-04-29 10:35:55 +02:00 |
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60bfd3ae8d
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obi annotate: now defaults to setting str if expression is not valid
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2020-04-24 11:35:20 +02:00 |
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da8de52ba4
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export: fixed progress bar bug
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2020-04-17 15:09:10 +02:00 |
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4d0299904e
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all commands (almost): cleaner DMS closing at the end
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2020-04-12 17:31:58 +02:00 |
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eef5156d95
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obi stats: fixed error when printing bool keys
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2020-04-12 17:12:04 +02:00 |
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b9f68c76c8
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ecopcr: added warnings and check of primer length (related to #75)
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2020-04-05 18:40:56 +02:00 |
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0b98371688
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ngsfilter: added warning about primer length in -h (#75)
|
2020-04-05 18:39:20 +02:00 |
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f0d152fcbd
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ngsfilter: now checking primer length (fixes #75)
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2020-04-05 18:29:10 +02:00 |
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8019dee68e
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ecotag: now closing all DMS properly
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2020-04-05 13:20:49 +02:00 |
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219c0d6fdc
|
obi cat: Fixed the handling when concatenating views with dictionaries
having different key sets
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2020-02-12 14:21:39 +01:00 |
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bb72682f7d
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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 |
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c67d668989
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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 |
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b4b2e62195
|
Cleaner handling of reverse quality columns
|
2020-01-18 19:28:12 +01:00 |
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a524f8829e
|
New command: obi cat to concatenate views (not optimized yet)
|
2020-01-18 17:28:31 +01:00 |
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822000cb70
|
Fixes in documentation
|
2020-01-18 17:26:18 +01:00 |
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6c018b403c
|
ecopcr: fixed and improved the options to keep nuclotides around the
amplicon
|
2019-12-26 20:45:54 +01:00 |
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fc3ac03630
|
clean_dms: now works with extension
|
2019-12-12 17:02:50 +01:00 |
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d75e54a078
|
uniq: added forced deletion of reverse sequence quality
|
2019-12-12 17:02:36 +01:00 |
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|
6bfd7441f3
|
ngsfilter: fixed sequence cutting when dealing with unaligned sequences.
Could use optimization
|
2019-12-12 17:01:31 +01:00 |
|
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81a179239c
|
ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for
unaligned sequences
|
2019-12-10 18:13:27 +01:00 |
|
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35ce37c0f7
|
ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and
made error annotations more explicit
|
2019-12-10 13:43:32 +01:00 |
|
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53f18316b0
|
ngsfilter: made more robust and practical to use with empty tags
|
2019-11-29 15:21:08 +01:00 |
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fa9555deb9
|
obi stats: fixed bug with None values
|
2019-09-22 20:21:53 +02:00 |
|
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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 |
|
|
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336100f716
|
obi less: now actually behaves like less
|
2019-09-21 18:29:12 +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 |
|
|
|
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 |
|
|
|
a0c8deb806
|
obi export: made output to stdout and pipe in less possible
|
2019-09-17 12:31:03 +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 |
|
|
|
8f9f2a2d10
|
obi ls: various improvements
|
2019-09-10 14:41:43 +02:00 |
|
|
|
5e3c41b058
|
C: Fixed opened DIR leak
|
2019-09-04 16:48:13 +02:00 |
|
|
|
f296517716
|
Various display improvements
|
2019-09-03 21:46:39 +02:00 |
|
|
|
1ed2d45ac4
|
obi grep: made an error message clearer (error could be eventually be
handled by program, looking for str in bytes returned by a column)
|
2019-08-29 17:17:52 +02:00 |
|
|
|
187053026f
|
Better detection of missing taxonomy
|
2019-08-29 16:10:09 +02:00 |
|
|
|
dcf8cf1d64
|
Improved obi stats
|
2019-08-29 15:18:26 +02:00 |
|
|
|
3cfe3a9b00
|
Improved progress display when importing files in a DMS
|
2019-08-29 10:12:06 +02:00 |
|
|
|
99a397b842
|
obi uniq: various improvements and fixes #66
|
2019-08-27 20:27:36 +02:00 |
|
|
|
66441e0aef
|
Fixed a bug when sending a DMS path to a C function from Cython
|
2019-08-18 19:43:51 +02:00 |
|
|
|
13952358b3
|
Fixed a bug where some commands wouldn't work if the input DMS was not
in the current directory
|
2019-07-25 11:59:19 +02:00 |
|
|
|
d99702f56f
|
ngsfilter and alignpairedend: paired-end reads are now correctly
reversed and labeled to be aligned correctly by alignpairedend
|
2019-07-23 18:56:51 +02:00 |
|
|
|
a83bf43ab9
|
obi stats: result display is now sorted
|
2019-07-06 16:27:51 +02:00 |
|
