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4e75514bad
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obi import: fixed entry count
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2019-08-29 18:26:09 +02:00 |
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1ed2d45ac4
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obi grep: made an error message clearer (error could be eventually be
handled by program, looking for str in bytes returned by a column)
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2019-08-29 17:17:52 +02:00 |
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187053026f
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Better detection of missing taxonomy
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2019-08-29 16:10:09 +02:00 |
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dcf8cf1d64
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Improved obi stats
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2019-08-29 15:18:26 +02:00 |
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3cfe3a9b00
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Improved progress display when importing files in a DMS
|
2019-08-29 10:12:06 +02:00 |
|
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728af51cb2
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Python: better display of tuple values in fasta format
|
2019-08-28 15:55:36 +02:00 |
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99a397b842
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obi uniq: various improvements and fixes #66
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2019-08-27 20:27:36 +02:00 |
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580db2f710
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minor comment
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2019-08-27 20:25:54 +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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3d1b2e8ed9
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Better handling of column lines with all values at NA
|
2019-08-27 20:20:26 +02:00 |
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66441e0aef
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Fixed a bug when sending a DMS path to a C function from Cython
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2019-08-18 19:43:51 +02:00 |
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13952358b3
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Fixed a bug where some commands wouldn't work if the input DMS was not
in the current directory
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2019-07-25 11:59:19 +02:00 |
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9752ff8494
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embl parser: information display about progress when parsing multiple
files
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2019-07-23 18:59:07 +02:00 |
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d99702f56f
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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 |
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f765c6f41e
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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 |
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a83bf43ab9
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obi stats: result display is now sorted
|
2019-07-06 16:27:51 +02:00 |
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3d9f0352ff
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obiclean parallelized
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2019-06-20 19:44:04 +02:00 |
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a04588da31
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openmp on j loop (i loop probably better)
|
2019-05-24 16:51:04 +02:00 |
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ac47bdce5d
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history: fixed DMS history when multiple inputs
|
2019-03-31 15:44:20 +02:00 |
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80068a3c19
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ngsfilter: fixed parsing error
|
2019-03-31 15:42:30 +02:00 |
|
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a3e6b7d913
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obi import: fixed import of View_NUC_SEQS to another DMS
|
2019-03-31 15:42:07 +02:00 |
|
|
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416c2d7ba0
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Cython: made fasta formatter cleaner
|
2019-03-31 15:41:32 +02:00 |
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2b8c066f8e
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Cython: added possibility to output in tabular format
|
2019-03-31 15:39:38 +02:00 |
|
|
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e39c1a7fbf
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Cython: added tab formatter and parser (for obi export)
|
2019-03-31 15:38:34 +02:00 |
|
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6841d879aa
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obi history: fixed a bug when displaying ascii history
|
2019-03-31 10:51:52 +02:00 |
|
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601a2cfd7d
|
obi uniq: various fixes...
|
2019-03-30 20:34:53 +01:00 |
|
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f16bbca8e2
|
obi grep: fixed a bug where -p option didn't work
|
2019-03-30 19:10:42 +01:00 |
|
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173483448a
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Merge commit '3d842ff7'
|
2019-03-30 15:29:52 +01:00 |
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ce686e9569
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obi import: progress bar fixed when using --only option
|
2019-03-30 15:16:57 +01:00 |
|
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c293cfabbb
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Python: embl parser: fixed a bug preventing taxids from being parsed
|
2019-03-30 15:15:49 +01:00 |
|
|
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3445579251
|
remove all the no more needed .cfiles
|
2019-03-29 16:56:58 +01:00 |
|
|
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5007b02cbc
|
cleaning stage 2
|
2019-03-29 16:46:17 +01:00 |
|
|
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cdd5975e8b
|
Cleaning first stage
|
2019-03-29 16:40:36 +01:00 |
|
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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 |
|
|
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6c52966033
|
Switch back to the original python source from the paster branch
|
2019-03-29 15:24:31 +01:00 |
|
|
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6b9da38087
|
patch some relative imports
|
2019-03-29 15:19:44 +01:00 |
|
|
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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 |
|
|
|
14eca43eac
|
Import taxo
|
2019-03-26 16:17:44 +01:00 |
|
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0b4ea49539
|
Convert relative import an delete cfiles
|
2019-03-26 16:14:03 +01:00 |
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cd88c37a7e
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Merge branch 'pip-standard' of git@git.metabarcoding.org:obitools/obitools3.git into pip-standard
|
2019-03-26 15:54:49 +01:00 |
|
|
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1095a617a3
|
Patch relative import to absolute
|
2019-03-26 15:54:33 +01:00 |
|
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5a05258fcb
|
fixed relative cython imports to be absolute
|
2019-03-26 15:52:59 +01:00 |
|
|
|
10ab557259
|
First version of the simplified setup.py script
|
2019-03-26 15:40:31 +01:00 |
|
|
|
8e70bf1ee1
|
obi import: fixed bug when rewriting a column (keeping wrong type in
import module)
|
2019-03-26 14:56:18 +01:00 |
|
|
|
d8a7bd42bd
|
Cython API, taxonomy: fixed parental tree iterator (skipped second to
last taxon, in OBI1 too)
|
2019-03-26 14:08:54 +01:00 |
|
|
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06178d9d61
|
Genbank file parser functions that should have been included in a
previous commit
|
2019-03-20 11:44:43 +01:00 |
|
