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7a4cdc0cfe
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New command: obi sort
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2018-08-09 18:10:47 +02:00 |
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e8dc5eb123
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Commands: ngsfilter and alignpairedend can now be used in whichever
order
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2018-08-08 19:53:26 +02:00 |
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2ba6d16147
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New command: obi ecopcr
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2018-07-28 17:13:45 +02:00 |
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b98880b7fa
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Various non-important fixes and comments
|
2018-07-28 17:07:17 +02:00 |
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895d09b133
|
obi import: 'taxid' columns are imported as 'TAXID' to fit view
predicates, and fixed taxdump import and DMS closing
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2018-07-28 17:03:00 +02:00 |
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6911bf4d70
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obi clean: first version
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2018-05-18 14:26:54 +02:00 |
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b91b3176b0
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obi uniq: fixed a bug where merged values were wrongly reinitialized
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2018-05-17 14:58:15 +02:00 |
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31d8ba5085
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obi test: minor change
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2018-05-17 14:54:45 +02:00 |
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a166a169cf
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obi ngsfilter: fixed a bug with -u option
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2018-05-17 14:53:53 +02:00 |
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8a10072d99
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obi annotate: fixed a bug with --with-taxon-at-rank option and minor
improvements
|
2018-05-17 14:51:18 +02:00 |
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b380368264
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Obi count command
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2018-04-04 15:51:23 +02:00 |
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1f4e82e6f6
|
Fixed three bugs in obi uniq
|
2018-04-04 15:50:10 +02:00 |
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2684535e26
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New command: obi annotate
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2018-03-21 16:39:31 +01:00 |
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4a815785c4
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obi import: added basic taxdump import
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2018-03-21 16:35:44 +01:00 |
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75b54c83ca
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obi grep: fixed bug when reading URIs
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2018-03-21 16:34:57 +01:00 |
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53cb3354b8
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obi ls command
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2018-03-19 13:08:41 +01:00 |
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9fb63d4894
|
Minor fixes
|
2018-03-16 19:05:09 +01:00 |
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d4f7e02c85
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New obi grep working with URI API
|
2018-03-16 19:04:54 +01:00 |
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15e43bb9a1
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Cython API: obi import can now import ngsfilter files and tabular files
|
2018-03-12 18:10:43 +01:00 |
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8a0b95c1d6
|
New command: obi ngsfilter
|
2018-03-12 18:09:22 +01:00 |
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dd225a255f
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obi uniq: better error checking
|
2018-03-12 18:04:53 +01:00 |
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00993d4215
|
Cython API: fixed a bug where the quality format would not be read
properly from the configuration values
|
2018-02-12 14:42:30 +01:00 |
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370fb9272c
|
obi uniq: better typing
|
2018-02-12 14:38:07 +01:00 |
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c8097e14e1
|
obi import: removed old traces
|
2018-02-12 14:36:56 +01:00 |
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01ef85658c
|
New command: obi alignpairedend
|
2018-02-12 13:30:06 +01:00 |
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428c4eb5e6
|
obi import: fixed creation of quality columns (to discuss)
|
2017-12-19 11:07:00 +01:00 |
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e9e7fac999
|
New obi uniq: stores columns with too many elements per line as
character strings, and keeps a minimum of things in the memory
|
2017-12-13 22:49:08 +01:00 |
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38fef5b9d4
|
obi test: better taxonomy testing
|
2017-11-24 17:54:10 +01:00 |
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9a50803c00
|
Added tuple columns containing immutable indexed data arrays of any type
|
2017-11-15 13:48:59 +01:00 |
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43f65e7fd0
|
obi uniq: fixed bug where dictionary indexes were not read properly, and
added view rollback in case of an exception.
|
2017-10-26 19:00:05 +02:00 |
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1ae634d56b
|
Added atexit command to obi import, obi uniq and obi less
|
2017-10-16 11:09:55 +02:00 |
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5ddd1d9ae6
|
obi uniq: added taxonomy handling
|
2017-10-04 16:13:07 +02:00 |
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f2ece573ff
|
Removed deprecated command
|
2017-10-04 16:09:41 +02:00 |
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0ab081f79e
|
Updated obi test to work with changes in taxonomy API
|
2017-10-04 15:50:32 +02:00 |
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1cb05de7e3
|
Basic obi less
|
2017-10-04 15:46:26 +02:00 |
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532d8e9cd7
|
obi import: small efficiency improvement when dealing with NA values
|
2017-10-04 15:44:48 +02:00 |
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ae24a807da
|
obi uniq: added the option to merge ids, except it only works on small
sets until lists are implemented properly using obiblobs
|
2017-09-25 17:28:03 +02:00 |
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75c15594c4
|
obi uniq: added option to use categories additionally to the sequence to
determine uniqueness
|
2017-09-25 10:56:43 +02:00 |
|
|
|
73bca6288f
|
New obi uniq
|
2017-08-20 18:04:21 +02:00 |
|
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6a2759eee6
|
obi import with new input/ouput API
|
2017-08-20 17:58:36 +02:00 |
|
|
|
407f61a408
|
Add the possibility to create temporary objects like a temporary
directory and a temporary DMS
|
2017-07-28 16:33:19 +02:00 |
|
|
|
35b0c55a8c
|
Cython API: various improvements and checks
|
2017-07-28 13:15:13 +02:00 |
|
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|
b9c65a871f
|
Patch decoding of URL
|
2017-07-28 12:41:28 +02:00 |
|
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|
adf5cbef97
|
Added DMS method to create a DMS if it doesn't already exists, otherwise
opens it
|
2017-07-28 09:55:43 +02:00 |
|
|
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da48a9d1af
|
Patch group of option : types must be callable not a string
|
2017-07-28 09:36:18 +02:00 |
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|
9482c663c0
|
minor comments and changes
|
2017-07-27 19:46:34 +02:00 |
|
|
|
b2fc1f4611
|
obi uniq: first version
|
2017-07-27 19:40:19 +02:00 |
|
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|
99ceed5fff
|
Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon
|
2017-07-27 19:21:45 +02:00 |
|
|
|
fa8f826cdc
|
Cleanup the end of the file
|
2017-07-27 16:07:39 +02:00 |
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|
|
0f6ae7dfa6
|
Options stuff... ;-)
|
2017-07-25 13:07:03 +02:00 |
|
