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0ee728c4d0
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C: build_ref_db: now adds a comment with the threshold used to build the
DB
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2019-08-31 18:29:40 +02:00 |
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7423bacac0
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C: Json comments: added an obi_read_comment function to read one value
from comments
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2019-08-31 18:28:51 +02:00 |
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53dcbc8ea3
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Fixed log to be in str instead of bytes
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2019-08-29 18:26:51 +02:00 |
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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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e43e49d6f1
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C: optimized dir opening
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2019-08-29 16:35:10 +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
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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
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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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f5c472ffd1
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C: fixed a memory bug in the array indexer
|
2019-08-27 20:26:46 +02:00 |
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580db2f710
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minor comment
|
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
|
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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ae5f42c260
|
fixes #61 : now reading merged taxids information when building a
reference database
|
2019-08-19 12:30:56 +02:00 |
|
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af7cecf59f
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Fixed a bug where a directory was not closed properly resulting in errno
24 sometimes
|
2019-08-18 19:46:52 +02:00 |
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5f20be44b2
|
Minor fixes
|
2019-08-18 19:45:53 +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
|
2019-08-18 19:43:51 +02:00 |
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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 |
|
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9f38cd8cf6
|
updated a comment
|
2019-07-23 19:03:24 +02:00 |
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946f9723b8
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ecotag: fixed a bug where the wrong taxid for the best match was
retrieved
|
2019-07-23 19:02:17 +02:00 |
|
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9752ff8494
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embl parser: information display about progress when parsing multiple
files
|
2019-07-23 18:59:07 +02:00 |
|
|
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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 |
|
|
|
1759302829
|
C: ecotag: fixed 2 memory bugs
|
2019-07-06 16:31:19 +02:00 |
|
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86bfa96fbe
|
C: kmer similarity: small improvements
|
2019-07-06 16:30:32 +02:00 |
|
|
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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 |
|
|
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a83bf43ab9
|
obi stats: result display is now sorted
|
2019-07-06 16:27:51 +02:00 |
|
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3d9f0352ff
|
obiclean parallelized
|
2019-06-20 19:44:04 +02:00 |
|
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|
9b4c3537f9
|
multithreaded obiclean working but not cleaned
|
2019-06-19 17:29:58 +02:00 |
|
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fd0b7a9177
|
j loop with critical (untested)
|
2019-06-04 17:14:36 +02:00 |
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debf59b266
|
i loop parallelized: bad
|
2019-05-25 18:37:56 +02:00 |
|
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a04588da31
|
openmp on j loop (i loop probably better)
|
2019-05-24 16:51:04 +02:00 |
|
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ed5bb70c80
|
CMake: setting compiler higher to avoid conflicts, and linking libopenmp
|
2019-05-22 16:26:30 +02:00 |
|
|
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22a5ae72d1
|
obi clean: not using tsearch library anymore, a simple byte array
instead. A lot more time and memory efficient. Closes #67
|
2019-05-19 17:39:53 +02:00 |
|
|
|
dc88181eeb
|
Add a --cobitools3 options to setup.py
|
2019-04-12 14:55:05 +02:00 |
|
|
|
2f60e91d93
|
Comment the install of the packages
|
2019-04-12 13:03:53 +02:00 |
|
|
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7ba27b6a99
|
Ask for python 3.7
|
2019-04-01 09:08:27 +02:00 |
|
|
|
d3937e1051
|
Add the cmakefile to the manifest
|
2019-04-01 09:01:45 +02:00 |
|
|
|
35eeb07f08
|
Build the C src in build/cobject
|
2019-04-01 08:52:38 +02:00 |
|
|
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3afbbeb7e5
|
CMake: made required version 3.10 for ubuntu
|
2019-03-31 16:54:05 +02:00 |
|
|
|
d6056a8e50
|
dirty temporary fix for install
|
2019-03-31 16:19:05 +02:00 |
|
|
|
ac47bdce5d
|
history: fixed DMS history when multiple inputs
|
2019-03-31 15:44:20 +02:00 |
|
|
|
7f8d1e7196
|
C: obi lcs: cleaner progress print
|
2019-03-31 15:42:58 +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 |
|
|
|
26fb149efb
|
C: made build_ref_db cleaner
|
2019-03-31 15:40:13 +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 |
|
