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ef9d9674b0
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obi import: added SINTAX format import and switch to version 3.0.1b18
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2022-05-17 09:36:33 +12:00 |
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0a2b8adb50
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import: added import of UNITE fasta format
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2022-05-03 10:54:41 +12:00 |
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f6353fbf28
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obi export: added options to export to metabaR compatible format
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2021-11-11 15:24:12 +13:00 |
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99c1cd60d6
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export: now exports header for tabular files by default and added option
to only export specific columns
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2021-07-22 09:23:18 +12:00 |
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e2932b05f2
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Implements #108 export integer missing values as 0 for tables by default
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2021-07-21 14:41:54 +12:00 |
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3e45c34491
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import: now imports and adds taxids for SILVA and RDP files, added
import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option
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2021-06-01 09:21:07 +12:00 |
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6026129ca8
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Fixes 101
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2021-03-30 09:06:08 +13:00 |
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b9b4cec5b5
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import: now can import SILVA fasta files
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2020-10-30 10:43:04 +01:00 |
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9a9afde113
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Cython: progress bar: set default refresh rate to 5 seconds
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2020-07-24 15:29:12 +02:00 |
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822000cb70
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Fixes in documentation
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2020-01-18 17:26:18 +01:00 |
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53f18316b0
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ngsfilter: made more robust and practical to use with empty tags
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2019-11-29 15:21:08 +01:00 |
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d30f7e7317
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more cleaning
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2019-09-22 18:52:05 +02:00 |
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f0f7edf152
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Python API: small option improvements
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2019-09-21 12:08:36 +02:00 |
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9063e9159d
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Export options: output option is now only non-positional for obi export
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2019-09-17 13:19:17 +02:00 |
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f566618be6
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Added option for no progress bar and made output URI option non
positional (for stdout output)
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2019-09-17 12:29:33 +02:00 |
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dbe09f83a2
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Increased the threshold of elements per line in a column before they are
stored as a character string
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2019-08-27 20:25:14 +02:00 |
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2b8c066f8e
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Cython: added possibility to output in tabular format
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2019-03-31 15:39:38 +02:00 |
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3445579251
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remove all the no more needed .cfiles
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2019-03-29 16:56:58 +01:00 |
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832f582802
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Fixed no-skip-on-error option :p
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2019-03-15 16:04:04 +01:00 |
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58d0c850c2
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Made skip on error option True by default......
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2019-03-15 15:50:40 +01:00 |
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e3c565d6be
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Cleaner progress bar
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2019-03-13 18:36:05 +01:00 |
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29c56572cf
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Add cfiles everywhere ;-)
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2019-02-19 15:04:30 +01:00 |
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e18b762d81
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Weird buggy Eclipse commit with nothing changed
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2018-10-21 17:35:18 +02:00 |
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eb6d5581bd
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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
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2018-10-17 15:52:26 +02:00 |
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343dbc7e4d
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Cython: made the logger lighter (now prints just module name instead of
full module path)
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2018-10-17 15:49:55 +02:00 |
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6d018a2d28
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Cython: Added 'modulename' in the config informations
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2018-10-17 15:47:44 +02:00 |
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58589e04be
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Cython: rearranged input and output format options to have both and
updated commands accordingly
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2018-10-17 11:19:48 +02:00 |
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7f6d1597fc
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Taxonomy: added functions to check if a taxonomy already exists in a
DMS, and added taxdump import from a compressed file
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2018-07-28 16:48:11 +02:00 |
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15e43bb9a1
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Cython API: obi import can now import ngsfilter files and tabular files
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2018-03-12 18:10:43 +01:00 |
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b93b982a18
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Cython: added an option for input taxdump and and an option for the
maximum number of elements in columns with multiple elements per line
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2017-12-13 22:25:15 +01:00 |
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b4088a7928
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Cython API: Added basic taxonomy option
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2017-10-04 15:42:17 +02:00 |
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a776e46e6d
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Add the command name in the log
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2017-09-15 14:51:13 +02:00 |
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407f61a408
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Add the possibility to create temporary objects like a temporary
directory and a temporary DMS
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2017-07-28 16:33:19 +02:00 |
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b9c65a871f
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Patch decoding of URL
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2017-07-28 12:41:28 +02:00 |
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da48a9d1af
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Patch group of option : types must be callable not a string
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2017-07-28 09:36:18 +02:00 |
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dc91174a5e
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Complete the input option group functions
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2017-07-27 16:06:48 +02:00 |
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0f6ae7dfa6
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Options stuff... ;-)
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2017-07-25 13:07:03 +02:00 |
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b24be84b0a
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Add a first group of options
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2017-07-25 11:14:30 +02:00 |
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ac94b35336
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Removed unused import
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2017-07-05 11:52:31 +02:00 |
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6adb9eb623
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Should solde issue #56
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2016-09-19 21:40:40 +02:00 |
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4ba01617af
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Fixed obscure compilation bug
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2016-08-10 15:26:40 +02:00 |
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ccc877764e
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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
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2016-08-03 10:12:23 +02:00 |
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aff9831c13
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Substitute fprintf call by fputs call to conform with the new ubuntu
compilation rules
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2016-07-03 09:21:56 +02:00 |
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6fe4c6134a
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Allows for calling getConfiguration without parametter for geting the
default configuration
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2016-04-11 13:31:09 +02:00 |
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aacfefad26
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A set of utilitaty function for creating commands
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2016-03-28 15:03:26 +02:00 |
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