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a0c8deb806
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obi export: made output to stdout and pipe in less possible
|
2019-09-17 12:31:03 +02:00 |
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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 |
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88451116e8
|
URIs: added stdout output (empty URI)
|
2019-09-17 12:28:10 +02:00 |
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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 |
|
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f8d1fa678a
|
obi stats: improved display with str instead of bytes
|
2019-09-10 16:20:36 +02:00 |
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8f9f2a2d10
|
obi ls: various improvements
|
2019-09-10 14:41:43 +02:00 |
|
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5e3c41b058
|
C: Fixed opened DIR leak
|
2019-09-04 16:48:13 +02:00 |
|
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f296517716
|
Various display improvements
|
2019-09-03 21:46:39 +02:00 |
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53dcbc8ea3
|
Fixed log to be in str instead of bytes
|
2019-08-29 18:26:51 +02:00 |
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4e75514bad
|
obi import: fixed entry count
|
2019-08-29 18:26:09 +02:00 |
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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 |
|
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187053026f
|
Better detection of missing taxonomy
|
2019-08-29 16:10:09 +02:00 |
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dcf8cf1d64
|
Improved obi stats
|
2019-08-29 15:18:26 +02:00 |
|
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3cfe3a9b00
|
Improved progress display when importing files in a DMS
|
2019-08-29 10:12:06 +02:00 |
|
|
|
728af51cb2
|
Python: better display of tuple values in fasta format
|
2019-08-28 15:55:36 +02:00 |
|
|
|
99a397b842
|
obi uniq: various improvements and fixes #66
|
2019-08-27 20:27:36 +02:00 |
|
|
|
580db2f710
|
minor comment
|
2019-08-27 20:25:54 +02:00 |
|
|
|
dbe09f83a2
|
Increased the threshold of elements per line in a column before they are
stored as a character string
|
2019-08-27 20:25:14 +02:00 |
|
|
|
3d1b2e8ed9
|
Better handling of column lines with all values at NA
|
2019-08-27 20:20:26 +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 |
|
|
|
9752ff8494
|
embl parser: information display about progress when parsing multiple
files
|
2019-07-23 18:59:07 +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 |
|
|
|
f765c6f41e
|
obi alignpairedend: fixed a bug where first seq was kept in result view
instead of consensus seq
|
2019-07-06 16:29:32 +02:00 |
|
|
|
a83bf43ab9
|
obi stats: result display is now sorted
|
2019-07-06 16:27:51 +02:00 |
|
|
|
3d9f0352ff
|
obiclean parallelized
|
2019-06-20 19:44:04 +02:00 |
|
|
|
a04588da31
|
openmp on j loop (i loop probably better)
|
2019-05-24 16:51:04 +02:00 |
|
|
|
ac47bdce5d
|
history: fixed DMS history when multiple inputs
|
2019-03-31 15:44:20 +02:00 |
|
|
|
80068a3c19
|
ngsfilter: fixed parsing error
|
2019-03-31 15:42:30 +02:00 |
|
|
|
a3e6b7d913
|
obi import: fixed import of View_NUC_SEQS to another DMS
|
2019-03-31 15:42:07 +02:00 |
|
|
|
416c2d7ba0
|
Cython: made fasta formatter cleaner
|
2019-03-31 15:41:32 +02:00 |
|
|
|
2b8c066f8e
|
Cython: added possibility to output in tabular format
|
2019-03-31 15:39:38 +02:00 |
|
|
|
e39c1a7fbf
|
Cython: added tab formatter and parser (for obi export)
|
2019-03-31 15:38:34 +02:00 |
|
|
|
6841d879aa
|
obi history: fixed a bug when displaying ascii history
|
2019-03-31 10:51:52 +02:00 |
|
|
|
601a2cfd7d
|
obi uniq: various fixes...
|
2019-03-30 20:34:53 +01:00 |
|
|
|
f16bbca8e2
|
obi grep: fixed a bug where -p option didn't work
|
2019-03-30 19:10:42 +01:00 |
|
|
|
173483448a
|
Merge commit '3d842ff7'
|
2019-03-30 15:29:52 +01:00 |
|
|
|
ce686e9569
|
obi import: progress bar fixed when using --only option
|
2019-03-30 15:16:57 +01:00 |
|
|
|
c293cfabbb
|
Python: embl parser: fixed a bug preventing taxids from being parsed
|
2019-03-30 15:15:49 +01:00 |
|
|
|
3445579251
|
remove all the no more needed .cfiles
|
2019-03-29 16:56:58 +01:00 |
|
|
|
5007b02cbc
|
cleaning stage 2
|
2019-03-29 16:46:17 +01:00 |
|
|
|
cdd5975e8b
|
Cleaning first stage
|
2019-03-29 16:40:36 +01:00 |
|
|
|
0c466046f4
|
Merge branch 'pip-standard-orig-python' into 'master'
The new install version based on classical setup.py
See merge request obitools/obitools3!1
|
2019-03-29 16:25:01 +01:00 |
|
|
|
bf62960ee8
|
Add some .ignore files
|
2019-03-29 15:52:54 +01:00 |
|
|
|
9c41b1e9da
|
Move and rename the obi.py script
|
2019-03-29 15:45:38 +01:00 |
|
|
|
6c52966033
|
Switch back to the original python source from the paster branch
|
2019-03-29 15:24:31 +01:00 |
|
|
|
6b9da38087
|
patch some relative imports
|
2019-03-29 15:19:44 +01:00 |
|
|
|
ee9947217c
|
alignpairedend: fixed the worst memory leak and the handling of the case
where 0 common kmers are found
|
2019-03-29 11:16:25 +01:00 |
|
|
|
ceaafca427
|
ngsfilter: fixed a bug (maybe 2) in the algo for the choice of the
reverse primer when running on unaligned sequences
|
2019-03-29 10:56:17 +01:00 |
|
|
|
7c2787b6b3
|
trying to fix cython difficulties
|
2019-03-26 16:19:55 +01:00 |
|
