2a4f1b8feb
obi import: now properly uses macros for column names
2019-03-15 11:39:21 +01:00
d88390c6d8
Cython API: when importing a file in a DMS, its length is computed
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beforehand for the progress bar
2019-03-13 18:35:32 +01:00
b45c2ee653
Cython API: cleaner column rewriting API
2019-03-13 11:13:55 +01:00
2a6a112d29
obi import: fixed writing quality in views when appropriate (but still
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not a satisfying solution)
2018-12-11 19:33:55 +01:00
4d51f4f015
obi import: better checking of whether to import quality
2018-11-19 11:23:39 +01:00
e18b762d81
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
da0e3d4043
Cython: added full handling of NA strings when importing files
2018-10-17 16:41:15 +02:00
58589e04be
Cython: rearranged input and output format options to have both and
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updated commands accordingly
2018-10-17 11:19:48 +02:00
e9a41c5b97
Commands: updated for JSON formatted comments with history
2018-10-07 19:10:34 +02:00
b98880b7fa
Various non-important fixes and comments
2018-07-28 17:07:17 +02:00
895d09b133
obi import: 'taxid' columns are imported as 'TAXID' to fit view
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predicates, and fixed taxdump import and DMS closing
2018-07-28 17:03:00 +02:00
4a815785c4
obi import: added basic taxdump import
2018-03-21 16:35:44 +01:00
15e43bb9a1
Cython API: obi import can now import ngsfilter files and tabular files
2018-03-12 18:10:43 +01:00
c8097e14e1
obi import: removed old traces
2018-02-12 14:36:56 +01:00
428c4eb5e6
obi import: fixed creation of quality columns (to discuss)
2017-12-19 11:07:00 +01:00
1ae634d56b
Added atexit command to obi import, obi uniq and obi less
2017-10-16 11:09:55 +02:00
532d8e9cd7
obi import: small efficiency improvement when dealing with NA values
2017-10-04 15:44:48 +02:00
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
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directory and a temporary DMS
2017-07-28 16:33:19 +02:00
b9c65a871f
Patch decoding of URL
2017-07-28 12:41:28 +02:00
adf5cbef97
Added DMS method to create a DMS if it doesn't already exists, otherwise
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opens it
2017-07-28 09:55:43 +02:00
9482c663c0
minor comments and changes
2017-07-27 19:46:34 +02:00
ced9a268a1
obi import: added an option to specify the NA value in the input file
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(default is 'NA', same as in R's read.table function)
2017-07-11 12:10:33 +02:00
b6b95f26b6
obi import: Skipping sequences is now done through the iterators so that
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sequences are not uselessly parsed
2017-07-10 17:02:30 +02:00
740d021276
obi import: fixed bugs when rewriting a column: a bug with new elements
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names ignoring previous elements names found, a bug with the global
obi_errno being reset too late, and a bug with the column dictionary
used by obi import not being updated after rewriting a column
2017-07-07 15:33:43 +02:00
101f764cce
New obi import with rewriting of columns when column type or line
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elements (keys) change
2017-07-05 17:15:23 +02:00
b998373be5
Cython API: updated the test command for the new API and deactivated the
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other commands for now
2017-04-14 16:21:33 +02:00
381194194c
Cython API: compiling but not working
2017-03-06 16:07:02 +01:00
f23315e26f
New Cython API: compile but doesn't work
2017-02-17 15:14:06 +01:00
51b23915ca
Added properties for Nuc_Seq cython classes (and updated commands using
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them)
2016-11-08 16:59:32 +01:00
9cd57deca9
Added OBIView_line_selection class to make new line selections
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associated with the view to clone, and improved and renamed method
closing a view
2016-09-30 17:48:53 +02:00
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
2016-08-16 15:17:26 +02:00
3b59043ea8
Major update: New column type to store sequence qualities. Closes #41
2016-05-20 16:45:22 +02:00
d159b921eb
Fixed obi import trying to print all lines at the end (source of
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segfault?)
2016-04-27 13:14:19 +02:00
a6c8d35491
import command a bit modified for tests
2016-04-26 14:29:54 +02:00
7a88ca619a
First obi import (doesn't import tags yet because NA values aren't
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handled)
2016-04-15 17:00:08 +02:00
